Conditions: Gonococcal Infection
Keywords: Ciprofloxacin-susceptibility Efficacy Gyrase A Assay Neisseria gonorrhoeae
Allocation: NA | Intervention model: SINGLE_GROUP
Enrollment: 211
Healthy volunteers: no

Brief summary:
This study is a multi-center, single-arm, open-label clinical study to assess the efficacy of one dose of ciprofloxacin given orally in subjects infected with untreated gyrase A (gyrA) serine 91 genotype Neisseria gonorrhoeae (N. gonorrhoeae) as determined by a real-time Polymerase Chain Reaction (PCR) assay. The study will enroll approximately 381 subjects to obtain an eligibility target of 257 subjects, per protocol, age 18 and older regardless of gender identification who are seeking care in Sexually Transmitted Disease (STD) clinics of up to eight of the participating sites in the United States. Subjects who have untreated gyrA serine 91 genotype N. gonorrhoeae of the rectum, or male or female urogenital tract identified by a positive culture or Nucleic Acid Amplification Test (NAAT) conducted at a prior visit will be offered enrollment in the study. They will receive one dose of directly observed ciprofloxacin 500 milligrams. Subjects not consenting to participate in the study will receive treatment per local standard of care. The duration of the study for each subject will be approximately 11 through 14 days. The primary objective of this study is to determine the efficacy of ciprofloxacin for treatment of uncomplicated N. gonorrhoeae infections with gyrA serine 91 genotype.

Detailed description:
This study is a multi-center, single-arm, open-label clinical study to assess the efficacy of one dose of ciprofloxacin given orally in subjects infected with untreated gyrase A (gyrA) serine 91 genotype Neisseria gonorrhoeae (N. gonorrhoeae) as determined by a real-time Polymerase Chain Reaction (PCR) assay. The study will enroll approximately 381 subjects to obtain an eligibility target of 257 subjects, per protocol, age 18 and older regardless of gender identification who are seeking care in Sexually Transmitted Disease (STD) clinics of up to eight of the participating sites in the United States. Subjects who have untreated gyrA serine 91 genotype N. gonorrhoeae of the rectum, or male or female urogenital tract identified by a positive culture or Nucleic Acid Amplification Test (NAAT) conducted at a prior visit will be offered enrollment in the study. They will receive one dose of directly observed ciprofloxacin 500 milligrams. Subjects not consenting to participate in the study will receive treatment per local standard of care. The duration of the study for each subject will be approximately 11 through 14 days. The primary objective of this study is to determine the efficacy of ciprofloxacin for treatment of uncomplicated N. gonorrhoeae infections with gyrA serine 91 genotype. The secondary objectives of the study are to 1) investigate the efficacy of ciprofloxacin for treatment of uncomplicated serine 91 gyrA N. gonorrhoeae infection by anatomic site and 2) to determine the sensitivity of the gyrA assay for detection of ciprofloxacin-susceptible N. gonorrhoeae infections.

Arms:
arm 1: One dose of directly-observed ciprofloxacin 500 mg administered orally. N=381

Interventions: intervention 1: Ciprofloxacin
Intervention descriptions: intervention 1: Directly observed treatment with a single dose of ciprofloxacin 500 mg orally with or without food.

Protocol document:
Prot_000.pdf: 
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Clinical Validation of a Molecular Test for Ciprofloxacin-
Susceptibility in Neisseria gonorrhoeae 
 
DMID Protocol Number: 15-0090 
 
DMID Funding Mechanism:  
Contract Number: HHSN272201300014I 
Task Order Number: HHSN27200006  
 
 
Sponsor:   
Division of Microbiology and Infectious Diseases 
National Institute of Allergy and Infectious Diseases 
National Institutes of Health 
 
 
Principal Investigator: Jeffrey D. Klausner, MD, MPH 
 
 
 
DMID Clinical Project Manager: Peter Wolff, MHA 
 
 
Version Number: 7.0 
 
Date: 17 December 2018  
 


 
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STATEMENT OF COMPLIANCE 
The study will be carried out in accordance with Good Clinical Practice (GCP) as required by the 
following: 
• 
United States (US) Code of Federal Regulations (CFR) applicable to clinical studies 
(45 CFR Part 46; 21 CFR Part 50, 21 CFR Part 56, and 21 CFR Part 812) 
• 
International Conference on Harmonisation: Good Clinical Practice (ICH) E6; 62 Federal 
Register 25691 (1997); and future revisions 
• 
NIH Clinical Terms of Award 
The study is a nonsignificant risk device study and must comply with the abbreviated 
Investigational Device Exemption (IDE) requirements under 21 CFR §812.2 (b). 
All key personnel (all individuals responsible for the design and conduct of this study) have 
completed Human Subjects Protections Training. 


 
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SIGNATURE PAGE 
The signature below constitutes the approval of this protocol and the attachments, and provides 
the necessary assurances that this trial will be conducted according to all stipulations of the 
protocol, including all statements regarding confidentiality, and according to local legal and 
regulatory requirements and applicable US federal regulations and ICH guidelines. 
 
Site Investigator: 
 
Signed: 
 
Date: 
 
 
Name 
Title 
 
 
 


 
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TABLE OF CONTENTS 
Page 
Statement of Compliance .............................................................................................................. 2 
Signature Page ............................................................................................................................. 3 
List of Abbreviations ...................................................................................................................... 7 
Protocol Summary ........................................................................................................................ 8 
1 
Key Roles ........................................................................................................................... 10 
2 
Background Information and Scientific Rationale .............................................................. 11 
2.1 
Background Information ......................................................................................... 11 
2.2 
Rationale ................................................................................................................ 11 
2.3 
Potential Risks and Benefits ................................................................................... 12 
2.3.1 
Potential Risks ............................................................................................ 12 
2.3.2 
Known Potential Benefits ............................................................................ 13 
3 
Objectives .......................................................................................................................... 15 
3.1 
Study Objectives .................................................................................................... 15 
3.1.1 
Primary Objective ....................................................................................... 15 
3.1.2 
Secondary Objectives ................................................................................. 15 
3.1.3 
Exploratory Objectives ................................................................................ 15 
3.2 
Study Outcome Measures ...................................................................................... 15 
3.2.1 
Primary Outcome Measure ......................................................................... 15 
3.2.2 
Secondary Outcome Measures .................................................................. 15 
3.2.3 
Exploratory Outcome Measures ................................................................. 15 
4 
Study Design ...................................................................................................................... 17 
5 
Study Enrollment and Withdrawal ...................................................................................... 18 
5.1 
Subject Inclusion Criteria ........................................................................................ 18 
5.2 
Subject Exclusion Criteria ...................................................................................... 19 
5.3 
Subject Withdrawal ................................................................................................. 19 
5.3.1 
Reasons for Withdrawal ............................................................................. 19 
5.3.2 
Handling of Withdrawals ............................................................................. 20 
6 
GYRASE A ASSAY/study treatment .................................................................................. 21 
6.1 
Gyrase A Assay Description ................................................................................... 21 
6.2 
Ciprofloxacin Description ........................................................................................ 21 
6.2.1 
Ciprofloxacin Formulation ........................................................................... 21 


 
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6.2.2 
Ciprofloxacin Acquisition ............................................................................ 22 
6.2.3 
Storage and Stability .................................................................................. 22 
6.2.4 
Dosage Preparation and Administration ..................................................... 22 
6.2.5 
Accountability Procedures .......................................................................... 22 
6.2.6 
Assessment of Subject Compliance ........................................................... 22 
6.2.7 
Concomitant Medications ........................................................................... 22 
7 
Study Schedule .................................................................................................................. 24 
7.1 
Visit 1, Day 1 (Screening/Enrollment) .................................................................... 24 
7.2 
Visit 2, Day 5-10  (Test of Cure Visit) ..................................................................... 25 
7.3 
Visit 3, Day 11 to 14 (Test of Cure Results) ........................................................... 26 
7.4 
Unscheduled/Early Termination Visit ..................................................................... 26 
8 
Study Procedures/Evaluations ........................................................................................... 27 
8.1 
Clinical Evaluations ................................................................................................ 27 
8.2 
Laboratory Evaluations ........................................................................................... 28 
8.2.1 
Clinical Laboratory Evaluations .................................................................. 28 
8.2.2 
Special Assays or Procedures for Enrolled Subjects.................................. 28 
8.2.3 
Specimen Preparation, Handling, and Shipping ......................................... 29 
9 
Assessment of Safety ........................................................................................................ 31 
10 
Clinical Monitoring .............................................................................................................. 32 
10.1 
Site Monitoring Plan ............................................................................................... 32 
11 
Statistical Considerations ................................................................................................... 33 
11.1 
Study Hypotheses .................................................................................................. 33 
11.2 
Sample Size Considerations .................................................................................. 33 
11.3 
Planned Analyses ................................................................................................... 35 
11.3.1 Planned Futility Review .............................................................................. 35 
11.4 
Final Analysis Plan ................................................................................................. 35 
11.4.1 Analysis Populations .................................................................................. 35 
11.4.2 Baseline Characteristics ............................................................................. 36 
11.4.3 Efficacy and Other Analysis Plan ............................................................... 36 
12 
Source Documents and Access to Source Data/Documents ............................................. 39 
13 
Quality Control and Quality Assurance .............................................................................. 40 
14 
Ethics/Protection of Human Subjects ................................................................................. 41 
14.1 
Ethical Standard ..................................................................................................... 41 
14.2 
Institutional Review Board ...................................................................................... 41 


 
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14.3 
Informed Consent Process ..................................................................................... 41 
14.4 
Exclusion of Women, Minorities, and Children (Special Populations) .................... 42 
14.5 
Subject Confidentiality ............................................................................................ 42 
14.6 
Study Discontinuation ............................................................................................. 43 
14.7 
Future Use of Stored Specimens ........................................................................... 43 
15 
Data Handling and Record Keeping .................................................................................. 44 
15.1 
Data Management Responsibilities ........................................................................ 44 
15.2 
Data Capture Methods ........................................................................................... 44 
15.3 
Types of Data ......................................................................................................... 44 
15.4 
Timing/Reports ....................................................................................................... 45 
15.5 
Study Records Retention ....................................................................................... 45 
15.6 
Protocol Deviations ................................................................................................ 45 
16 
Publication Policy ............................................................................................................... 46 
17 
Literature References ........................................................................................................ 47 
Appendix A: Schedule of Events ................................................................................................. 49 
 
 


 
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LIST OF ABBREVIATIONS 
BV 
Bacterial Vaginosis 
CDC 
Centers for Disease Control and Prevention 
CFR 
Code of Federal Regulations 
CRF 
Case Report Form 
DHHS 
Department of Health and Human Services 
DMID 
Division of Microbiology and Infectious Diseases, NIAID, NIH,  
 
DHHS 
DNA 
Deoxyribonucleic Acid 
eCRF 
Electronic Case Report Form 
gyrA 
Gyrase A Genotype 
ICH 
International Council for Harmonisation 
ICMJE 
International Committee of Medical Journal Editors 
IEC 
Independent or Institutional Ethics Committee 
IRB 
Institutional Review Board 
ITT 
Intent-to-Treat 
MIC 
Minimum Inhibitory Concentration 
micro-ITT 
Microbiological Intent-to-Treat 
NAAT 
Nucleic Acid Amplification Test 
NIAID 
National Institute of Allergy and Infectious Diseases, NIH, DHHS 
NIH 
National Institutes of Health 
OHRP 
Office for Human Research Protections 
PCR 
Polymerase Chain Reaction 
PP 
Per-Protocol 
QA 
Quality Assurance 
QC 
Quality Control 
SDCC 
Statistical Data and Coordinating Center 
SOP 
Standard Operating Procedure 
STD 
Sexually Transmitted Disease 
 
 
 
 


 
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PROTOCOL SUMMARY 
Title: 
Clinical Validation of a Molecular Test for Ciprofloxacin-
Susceptibility in Neisseria gonorrhoeae 
 
Population: 
Approximately 381 subjects will be enrolled to identify 
approximately 257 per protocol eligible subjects diagnosed with 
untreated serine 91 gyrase A genotype Neisseria gonorrhoeae 
of the rectum, or male or female urogenital tract   
 
Number of Sites: 
Up to eight sites in the United States 
 
Study Duration: 
Approximately 30 months after enrollment of the first subject  
 
Subject Participation Duration: 
11-14 days per subject 
 
Description of Agent or Intervention: 
Directly observed treatment with a single dose of ciprofloxacin 
500 mg orally for Neisseria gonorrhoeae infections deemed 
serine 91 gyrase A genotype by real-time polymerase chain 
reaction with fluorescent hybridization probe detection of 
sequence  
 
Objectives: 
Primary: 
To determine the efficacy of ciprofloxacin for treatment of 
uncomplicated Neisseria gonorrhoeae infections with gyrA 
serine 91 genotype 
 
Secondary: 
To investigate efficacy of ciprofloxacin for treatment of 
uncomplicated serine 91 gyrase A genotype Neisseria 
gonorrhoeae infection by anatomic site  
To determine the sensitivity of the gyrase A assay for detection 
of ciprofloxacin-susceptible Neisseria gonorrhoeae infections 
 
Description of Study Design: 
See Schematic  
 
Estimated Time to Complete 
Enrollment: 
Approximately 24 months 


 
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Schematic  
 
                      
 
Prior to enrollment, screen subjects for eligibility  
(N. gonorrhoeae positive and untreated and gyrA serine 91 positive) 
 
 Visit 1, Day 1 (Enrollment) 
Obtain Informed Consent 
Collect specimen for N. gonorrhoeae culture, N. gonorrhoeae NAAT, and gyrA serine 91 
genotype from all suspected N. gonorrhoeae positive anatomic sites (throat, rectum, or male 
or female urogenital tract)  
Administer directly observed single dose of ciprofloxacin 500 mg PO 
Collect specimens for N. gonorrhoeae culture, N. gonorrhoeae NAAT, and gyrA serine 91 
genotype from all anatomic sites swabbed at Visit 1, Day 
Test results provided by phone 
 
N. gonorrhoeae negative 
or  
treated or  
gyrA serine 91  negative 
N. gonorrhoeae 
positive and  
untreated and  
gyrA serine 91 positive 
 Visit 2, Day 5-10 (Test of Cure) 
 Visit 3, Day 11-14 (Test of Cure Results) 
Test of Cure Negative 
Culture-/NAAT- 
 
Test of Cure Positive 
Culture-/NAAT+ 
Culture+/NAAT+ 
Culture+/NAAT- 
 
Off Study 
 
Off Study 
Refer for standard of care 
treatment for N. 
gonorrhoeae 
 
 


 
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1 
KEY ROLES 
Principal Investigator 
Jeffrey D. Klausner, MD, MPH 
Principal Investigator, STAR STI CTG 
Professor of Medicine and Public Health 
Division of Infectious Diseases  
David Geffen School of Medicine and Jonathan 
and Karin Fielding School of Public Health 
University of California, Los Angeles 
Los Angeles, CA 90095-1772 
Phone: XXXXXXXXXX 
Email: XXXXXXXXXX 
Co-Investigator 
Sheldon Morris, MD, MPH 
Antiviral Research Center  
University of California, San Diego  
220 Dickinson Street, Suite A 
San Diego, CA 92103 
Phone: XXXXXXXXXX 
Email: XXXXXXXXXX 
 
Contact information for site investigators and key staff at DMID, the coordinating center, and the 
SDCC is located in the Manual of Procedures. 


 
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2 
BACKGROUND INFORMATION AND SCIENTIFIC RATIONALE 
2.1 
Background Information 
Gonorrhea is the second most commonly reported notifiable disease in the United States 
with more than 330,000 cases reported in 2012, a rate of 107.5 per 100,000 population 
[1]. Over the past 75 years, Neisseria gonorrhoeae (N. gonorrhoeae) infections have 
become increasingly resistant to antimicrobial therapy, first to sulfa-based antibiotics, 
then penicillins, tetracyclines, fluoroquinolones, and now extended-spectrum 
cephalosporins [2]. Prior to the advent of ciprofloxacin-resistant N. gonorrhoeae, 
ciprofloxacin was the primary first-line recommended therapy for N. gonorrhoeae 
infections of the throat, rectum, urethra, and cervix. From 1998 to 2006, ciprofloxacin 
was the Centers for Disease Control and Prevention (CDC) recommended treatment for 
N. gonorrhoeae in all anatomic sites. Prior to widespread ciprofloxacin resistance, the 
efficacy of ciprofloxacin treatment in susceptible N. gonorrhoeae infections was 
estimated at more than 99% [3-4]. In 2007, due to high rates of ciprofloxacin resistance 
in N. gonorrhoeae nationally, the CDC recommended the discontinuation of ciprofloxacin 
treatment for gonorrhea, which was followed by a decline in ciprofloxacin N. 
gonorrhoeae resistance nationally [5]. At this time, the only recommended treatment for 
N. gonorrhoeae infection is dual antibiotic therapy with injectable ceftriaxone and oral 
azithromycin or doxycycline [6]. 
 
For decades, bacterial culture was the standard diagnostic modality for N. gonorrhoeae 
infections. Culture is specific, but studies have demonstrated that the molecular-based 
enzyme immunoassay or nucleic acid amplification test (NAAT) has a higher clinical 
sensitivity than culture [7]. However, there has not been a widely used and reliable 
technology that allows for antibiotic susceptibility testing from non-culture specimens.  
 
It has been recently demonstrated that N. gonorrhoeae-deoxyribonucleic acid (DNA) 
mutations can be detected using modern molecular techniques and real-time 
polymerase chain reaction (PCR) assays can be used to detect reproducible, clinically 
significant resistance [8-10]. A protocol for the detection of alterations in the gyrase A 
gene (gyrA), the target of ciprofloxacin anti-gonococcal activity, has been validated [8]. 
While molecular markers of susceptibility have high concordance, sensitivity and a 
specificity of 93% and 100%, respectively, compared with standard antimicrobial 
susceptibility testing, the clinical performance of the test and the response to therapy 
based on a molecular susceptibility result in N. gonorrhoeae is unknown. 
2.2 
Rationale 
Resistance to extended-spectrum cephalosporins was first identified in Japan and is 
increasing in the western United States and among men who have sex with men [11]. 
Antimicrobial resistance mechanisms have been fairly well described as mutations in 
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Currently, the nationwide frequency of N. gonorrhoeae isolates with decreased 
ciprofloxacin susceptibility, minimum inhibitory concentration (MIC) ≥ 0.125 μg/mL, or 
resistance (MIC ≥ 0.5 μg/mL) is relatively modest at 13.5% [12]. Prior experience with 
changing antibiotic treatment guidelines has demonstrated that major shifts in antibiotic 
use may modify the ecology of drug resistance. For example, restricting erythromycin 
use in Group A streptococcal infections in Finland led to a population-level decrease in 
erythromycin-resistance in that organism [13].  
 
While molecular methods to diagnose N. gonorrhoeae have greatly improved the 
detection of infection [14], they have historically precluded the ability to perform antibiotic 
susceptibility testing. Although regional surveillance data critically inform treatment 
recommendations, those data cannot be used for real-time individualized clinical 
management. The clinical validation of an assay to determine the ciprofloxacin 
susceptibility of N. gonorrhoeae infections could result in increased use of ciprofloxacin 
for ciprofloxacin-susceptible N. gonorrhoeae infections and resultant decreased use of 
extended-spectrum cephalosporins, thereby reducing the selection pressure for 
cephalosporin resistance in N. gonorrhoeae. An immediate benefit to taking ciprofloxacin 
would be for those with cephalosporin allergies who would have to take combination 
therapy that is more difficult to administer.  
2.3 
Potential Risks and Benefits 
2.3.1 Potential Risks 
Performance of the assay 
Clinical specimens will be tested for a molecular marker of ciprofloxacin 
susceptibility. Treatment decisions will be made by the subject’s clinician, per 
standard protocols, based on interpretation of laboratory results and selection of 
the best course of treatment based on available information. There is a small risk 
of a misclassification of susceptibility if the test were to show that the N. 
gonorrhoeae infection is ciprofloxacin-susceptible when in fact, it is resistant, and 
a subject with ciprofloxacin-resistant N. gonorrhoeae infection would not receive 
the appropriate treatment. The risk would be ameliorated if the test of cure visit 
(Visit 2, Day 5-10) displayed a treatment failure and the subject received 
standard treatment. The risk would therefore be that this would result in a delay 
of effective treatment.  
 
The risk of a N. gonorrhoeae false negative test of cure result is estimated to be 
less than 0.5% and would result in inappropriate treatment for a subject with 
ciprofloxacin-resistant N. gonorrhoeae infection [9]. The risks of treatment failure 
include continued symptoms and potential transmission of N. gonorrhoeae to 
partners. Without effective re-treatment, treatment failure might result in 
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infertility, chronic pelvic pain, and increased risk of transmission and HIV 
infection. 
 
Risks from study procedures 
Subjects may become embarrassed, worried, or anxious when discussing their 
sexual practices or ways for protecting against HIV and other infections passed 
during sex. They may also experience anxiety while they await test results. 
Women may expect to feel a little discomfort during the speculum exam. 
Subjects may experience gagging, discomfort, fainting, or bleeding when swabs 
are collected from the throat, rectum, urethra or cervix. 
 
Risks of ciprofloxacin 
Ciprofloxacin may cause dizziness, nervousness, difficulty sleeping, or increased 
sensitivity to sunlight, possibly resulting in sunburn. Like many antibiotics used to 
treat infections, ciprofloxacin may cause nausea, vomiting, stomach pain, 
headaches, tiredness, pale skin or a mild skin rash. Less often, hearing loss, 
kidney, liver or nerve problems, tendon pain, an irregular heartbeat, or fainting 
may occur. It is not known if ciprofloxacin will harm a fetus. Pregnancy tests can 
miss the first 14 days of pregnancy; therefore, fetuses may be exposed to 
ciprofloxacin if a subject’s pregnancy is undetected at enrollment. 
 
Significant side effects of ciprofloxacin 
Significant side effects are rare, estimated to be less than 2%, and may include 
severe skin rash; hives; itching; difficulty breathing or swallowing; swelling of the 
face, throat, tongue, lips, eyes, hands, feet, ankles, or lower legs; hoarseness; 
yellowing of the skin or eyes; and rapid, pounding, or irregular heartbeat. 
 
Unknown risks 
There may be unknown risks that cannot be foreseen.  
2.3.2 Known Potential Benefits 
There are no known benefits to individual subjects. A potential benefit to future N. 
gonorrhoeae-susceptible infected individuals is treatment with a less invasive 
regimen (orally administered vs. intramuscular injection), which is less painful. 
Results from this study may help gonorrhea-infected individuals by reducing drug 
resistance as a result of the use of the most appropriate treatment, which is 
guided by pretreatment determination of ciprofloxacin-susceptible gonococcal 
infection.   
 
The study will help to assess the potential impact of a strategy to address the 
critical problem of emerging drug resistance in N. gonorrhoeae. Specifically, the 
information gained from this study can be used to influence national sexually 
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decrease in extended-spectrum cephalosporin-resistant N. gonorrhoeae 
infection, improving the availability of treatment options for individuals infected 
with N. gonorrhoeae. 
 
This study may provide an alternative regimen for the treatment of gonorrhea in 
cases of cephalosporin allergy or antimicrobial resistance to cephalosporins. It 
may also provide an oral regimen for settings in which injections are not feasible. 
In addition, it may provide a convenient and easy-to-administer patient-delivered 
therapy for the partners of index cases. 


 
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3 
OBJECTIVES 
3.1 
Study Objectives 
3.1.1 Primary Objective 
To determine the efficacy of ciprofloxacin for treatment of uncomplicated N. 
gonorrhoeae infections with gyrA serine 91 genotype 
3.1.2 Secondary Objectives 
1) 
To investigate the efficacy of ciprofloxacin for treatment of uncomplicated 
serine 91 gyrA N. gonorrhoeae infection by anatomic site  
2) 
To determine the sensitivity of the gyrA assay for detection of 
ciprofloxacin-susceptible N. gonorrhoeae infections 
3.1.3 Exploratory Objectives 
1) 
To characterize N. gonorrhoeae isolates and non-gyrA gene-dependent 
mechanisms of ciprofloxacin resistance post-treatment of uncomplicated 
N. gonorrhoeae infection by anatomic site using traditional and molecular 
methods like genotyping and sequencing 
2) 
To investigate the efficacy of ciprofloxacin for treatment of uncomplicated 
serine 91 gyrA N. gonorrhoeae infections by demographic and clinical 
characteristics 
3.2 
Study Outcome Measures 
3.2.1 Primary Outcome Measure 
The proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae 
with microbiological cure at Visit 2 (Day 5-10) 
3.2.2 Secondary Outcome Measures 
1) The proportion of subjects infected with gyrA serine 91 genotype N. 
gonorrhoeae with microbiological cure at each anatomic site (throat, rectum, 
male or female urogenital tract) at Visit 2 (Day 5-10)  
2) The proportion of subjects infected with gyrA serine 91 genotype N. 
gonorrhoeae identified by gyrA gene PCR who have ciprofloxacin-susceptible 
N. gonorrhoeae as identified by culture-based antimicrobial susceptibility 
testing at Visit 1 (Day 1) 
3.2.3 Exploratory Outcome Measures 
1) Identification and characterization of non-gyrA gene-dependent mechanisms 
of ciprofloxacin resistance by genotyping and whole genome sequencing 
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5-10). Genotyping and sequencing may be performed on nucleic acid isolated 
from different anatomic sites. 
2) The proportion of subjects infected with gyrA serine 91 genotype N. 
gonorrhoeae with microbiological cure at Visit 2 (Day 5-10) by demographic 
and clinical characteristics 


 
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4 
STUDY DESIGN 
This study is a multi-center, single-arm, open-label clinical study to assess the efficacy of 
one dose of ciprofloxacin given orally in subjects infected with untreated gyrA serine 91 
genotype N. gonorrhoeae as determined by a real-time PCR assay. The study will enroll 
approximately 381 subjects to obtain a per protocol eligible target of 257 subjects age 18 
years or older regardless of gender identification who are seeking care in STD clinics at 
participating sites in the United States. Subjects who have untreated gyrA serine 91 
genotype N. gonorrhoeae of the rectum, or male or female urogenital tract identified by a 
positive culture or NAAT conducted at a prior visit will be offered enrollment in the study. 
Subjects not consenting to participate in the study will receive treatment per local 
standard of care. 
 
At enrollment, Visit 1 (Day 1), a brief physical exam and medical and sexual history will 
be done. Subjects will have samples collected for N. gonorrhoeae culture and N. 
gonorrhoeae NAAT (to include gyrA serine 91 genotype) from each infected anatomic 
site (throat, rectum, male or female urogenital tract) to verify infection status.  
 
Subjects with gyrA serine 91 genotype rectal or urogenital N. gonorrhoeae will receive 
one dose of directly observed ciprofloxacin 500 mg. Subjects will be observed in the 
clinic for at least 5 minutes after receiving ciprofloxacin and will be instructed to return to 
the clinic or to contact the study site coordinator immediately if they vomit within 1 hour 
of receiving ciprofloxacin. Subjects who vomit within 1 hour of study drug administration 
should be retreated for N. gonorrhoeae infection with an alternative recommended 
regimen per local standard of care.  
 
Subjects will return for clinical and laboratory assessments at Visit 2 (Day 5-10), test of 
cure visit. Subjects will have repeat samples collected for N. gonorrhoeae culture and N. 
gonorrhoeae NAAT from all anatomic sites swabbed at Visit 1 (Day 1).  
 
For Visit 3 (Day 11-14), test results will be provided to subjects by phone call. No further 
follow-up is required for subjects who test culture negative and NAAT negative. Subjects 
who test culture positive or NAAT positive will be referred for standard of care treatment 
for N. gonorrhoeae. 
 
The duration of the study for each subject will be approximately 11-14 days. Study 
enrollment is expected to be completed in 24 months. 


 
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5 
STUDY ENROLLMENT AND WITHDRAWAL 
5.1 
Subject Inclusion Criteria 
Subjects must meet all of the inclusion criteria in order to be eligible to participate in the 
study. Subjects who present with a new N. gonorrhoeae infection may be rescreened for 
eligibility. No exemptions are granted on Subject Inclusion/Exclusion Criteria in DMID-
sponsored studies. 
 
1. Willing and able to give voluntary written informed consent before any study related 
procedure is performed. 
2. 18 years or older on the day of enrollment.  
3. Untreated gyrA serine 91 genotype N. gonorrhoeae of the rectum, or male or female 
urogenital tract*, as determined by the gyrA test assay on a specimen collected 
within 30 days of enrollment. 
*Subjects must have gyrA serine 91 genotype detected for N. gonorrhoeae from at 
least one non-pharyngeal site.  
4. Willing to abstain from sexual intercourse or use condoms during any sexual contact 
until the Test of Cure Visit (Visit 2, Day 5-10) is complete. 
5. Women of childbearing potential* must have no vaginal intercourse 14 days before 
enrollment or use an effective birth control method ** for 30 days before enrollment 
and agree to continue through visit 2.  
*A woman is considered of childbearing potential unless post-menopausal (>2 years) 
or surgically sterilized (tubal ligation >1 year, bilateral oophorectomy, or 
hysterectomy). 
**Acceptable birth control methods for the purposes of this study may include 
abstinence from intercourse with a male partner, monogamous relationship with 
vasectomized partner, male condoms with the use of applied spermicide, intrauterine 
devices, and licensed hormonal methods. A highly effective method of contraception 
is defined as one that results in a low failure rate (i.e., less than 1% per year) when 
used consistently and correctly. 
6. Able to swallow pills. 
7. Willing to comply with protocol requirements, including availability for follow-up for 
the duration of the study. 
8. Agree to avoid systemic or intravaginal antibiotics* with activity against N. 
gonorrhoeae from enrollment through Visit 2 (Day 5-10). *Topical and intravaginal 
antifungals are permitted. 
9. Agree to avoid magnesium/aluminum antacids, sucralfate, didanosine, or highly 
buffered drugs, up to 2 hours after receipt of study drug. 
 


 
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5.2 
Subject Exclusion Criteria 
Subjects meeting any of the following criteria at enrollment will be excluded from the 
study: 
 
1. Known renal insufficiency from clinical history. 
2. Use of systemic or intravaginal antibiotics* with potential activity against N. 
gonorrhoeae within 30 days prior to study drug administration. *Topical and 
intravaginal antifungals are permitted. 
3. Use of systemic corticosteroid drugs or other immunosuppressive therapy within 30 
days prior to enrollment. 
4. Receipt or planned receipt of an investigational product in a clinical trial within 30 
days prior to or 7 days after treatment administration.  
5. Pregnant or breastfeeding. 
6. Clinical diagnosis of pelvic inflammatory disease or genital ulcer. 
7. Confirmed or suspected complicated or systemic gonococcal infection, such as 
abdominal pain, testicular pain, epididymitis, orchitis, arthritis, or endocarditis. 
8. Receipt of magnesium/aluminum antacids, sucralfate, didanosine, or highly buffered 
drugs, within 6 hours before receipt of study drug. 
9. Mutant N. gonorrhoeae gyrA serine 91 genotype from any anatomic site, as 
determined by the gyrA test assay on a specimen collected within 30 days of 
enrollment. 
10. Known allergy or history of adverse reaction to ciprofloxacin. 
11. Known allergy to quinolones. 
12. Previous enrollment in this study. 
13. Medical condition or other factor that in the judgment of the investigator might affect 
ability to comply with procedures.  
 
5.3 
Subject Withdrawal  
5.3.1 Reasons for Withdrawal 
Subjects may voluntarily withdraw their consent for further study participation at 
any time and for any reason, without penalty. 
 
Refer to section 11 for how subjects who withdraw from study participation will be 
handled in study analyses. 
  
Subjects may withdraw or be withdrawn from the study for any of the reasons 
given below. The reason for withdrawal will be recorded in the data collection 
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• 
Subject vomits within 1 hour of study medication administration.  
• 
Subject receives any systemic antibiotic other than the study medication prior 
to Visit 2 (Day 5-10).  
• 
Subject is pregnant or breastfeeding. 
• 
Discretionary decision by the site investigator. 
• 
At the discretion of the IRB, NIH, or other government agency as part of their 
duties to ensure that research subjects are protected. 
5.3.2 Handling of Withdrawals 
Subjects who withdraw voluntarily prior to receiving ciprofloxacin will be offered 
local standard of care treatment for N. gonorrhoeae and followed per clinic 
guidelines.  
 
Subjects who withdraw voluntarily or never return after receiving ciprofloxacin 
and tolerated medication without difficulty will not be contacted for repeat 
gonorrhea testing or treatment. 
 
Subjects who withdraw voluntarily or never return after being found to be positive 
for N. gonorrhoeae at Visit 2 (Day 5-10) will be contacted by phone and by 
certified mail with instructions that they should follow-up for treatment per local 
standard of care and should be followed per clinic guidelines.  
5.3.2.1 Termination of Study  
Although the study sponsor has every intention of completing the study, 
the sponsor reserves the right to terminate the study at any time for 
clinical or administrative reasons. Reasons for termination include, but 
are not limited to, study closure at the discretion of DMID. 


 
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6 
GYRASE A ASSAY/STUDY TREATMENT 
6.1 
Gyrase A Assay Description 
Real-time PCR testing protocol: The laboratories participating in this study will follow the 
testing protocol as described in Siedner et al [15] with modifications. For real-time PCR 
analysis of the gyrA gene, remnant specimens will be subject to nucleic acid (DNA) 
extraction by using automated nucleic acid extraction utilizing either the bioMerieux 
easyMag, or the Qiagen EZ1, or Qiacube platforms, as determined in the optimization 
studies. Extracted samples will be used for real-time PCR. Amplification and melting-
curve analysis of specimens will be performed by using a Roche LightCycler 480 or Light 
Cycler 2.0 platforms (Roche Diagnostics, Pleasanton, CA). Amplified regions of 
the gyrA gene will be assessed for mutations in the Ser 91 codon through use of 
melting-curve analysis with probes specific to that region of the gyrA gene. The probes 
for the serine 91 amplicon (gyrA-ser-Flu and gyrA-ser-LC) are a paired set of FRET 
probes, including a LightCycler Red640 probe and a fluorescein-labeled probe, 
separated by 1 bp. The Red640 oligonucleotide has a maximal absorption and 
emissions of 622 and 638 nm, respectively. Amplification of PCR product will be followed 
by melt-curve analysis to confirm specificity of amplification and genotype. Melting-curve 
analysis will be performed by using LightCycler software (v.4.0). The software will be 
used to plot the negative value of the first derivative of fluorescence per unit time to 
distinguish peak melting temperatures from melting-curve plots. Designation of predicted 
susceptibility is based upon the observed melting curve parameters as previously 
described [15]. 
6.2 
Ciprofloxacin Description 
Ciprofloxacin is a quinolone medication approved by the FDA for the treatment of 
gonorrhea. Ciprofloxacin hydrochloride, USP, a fluoroquinolone, is the 
monohydrochloride monohydrate salt of 1- cyclopropyl-6-fluoro-1, 4-dihydro-4-oxo-7-
(1piperazinyl)-3-quinolinecarboxylic acid. The molecular weight of the ciprofloxacin 
hydrochloride monohydrate is 385.82. It is a faintly yellowish to light yellow crystalline 
substance. 
6.2.1 Ciprofloxacin Formulation 
Ciprofloxacin 500 mg tablets 
 
 


 
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6.2.2 Ciprofloxacin Acquisition 
Ciprofloxacin will be purchased centrally, and upon request by DMID, will be 
transferred to the following address:  
DMID Clinical Agents Repository (CAR) 
XXXXXXXXXX 
 
Ciprofloxacin will be shipped from the DMID CAR to the study site upon request 
and approval by DMID. 
6.2.3 Storage and Stability 
Ciprofloxacin is stable at room temperature. Stability of this medication will be 
maintained by storing the drug below 30°C (86°F). The storage room 
temperature will be monitored on business days. 
6.2.4 Dosage Preparation and Administration 
Ciprofloxacin tablets will be administered orally and can be taken with or without 
food. Subjects will receive 500mg and will be directly observed.  
6.2.5 Accountability Procedures 
Fisher repository will ship packaged ciprofloxacin to the investigational sites. At 
each site, medication packages will be kept in a locked storage cabinet at the 
clinic and administered by the study personnel. Accountability records will be 
maintained by designated site staff (i.e., study personnel or pharmacy staff). 
Unused study treatment will be destroyed or returned to Fisher BioServices at 
the end of the study. Unused study treatment will not be destroyed without DMID 
approval. 
6.2.6 Assessment of Subject Compliance 
Medication will be given and directly observed by the study staff and recorded in 
the subject’s case report form (CRF). Since medication will be directly observed, 
there will be no need for return of study medication packaging or a medication 
diary at the follow-up visit. 
6.2.7 Concomitant Medications 
Administration of any contraindicated medications or new antibiotics after 
enrollment will be recorded on the appropriate data collection form. 
Contraindicated medications will include all medications contraindicated with 
ciprofloxacin (described in section 5.2) taken 30 days prior to signing the 
informed consent form through Visit 2 or early termination, whichever occurs 
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Subjects who have received study medication and are subsequently diagnosed 
with a concomitant infection, which requires systemic antibiotics will receive 
treatment according to the local clinic’s standard of care. 
Use of new medication should prompt evaluation for the presence of a new 
diagnosis of chronic medical disease or condition. 
Oral contraceptives are allowed, as they do not alter the metabolism of 
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7 
STUDY SCHEDULE 
Complete study schedule details listed by study visit day are described below. Refer also to 
Appendix A. 
7.1 
Visit 1, Day 1 (Screening/Enrollment) 
Screening and enrollment will occur at the same clinic visit. Potential subjects will be 
informed about the study and invited to participate. Subjects who are interested in the 
study will be asked to sign a consent form that will describe the purpose of the study, the 
procedures to be followed, the risks and benefits of participating, and will include a 
separate section for consent to store samples for future use. A copy of the consent form 
will be given to the subject and this fact will be documented in the CRF. 
 
The following will be performed for subjects who give informed consent: 
 
1. Demographic information including age, sex, and gender will be collected from the 
subject  
2. Eligibility criteria will be reviewed with the subject  
3. Discuss pertinent medical history for assessment of specific symptoms that are 
potentially related to fluoroquinolone use as described in section 9, Assessment of 
Safety, and sexual history will be obtained by interview of subjects to assure 
eligibility. Concomitant infections will be reviewed. 
4. Review of signs and symptoms within the past 7 days 
5. All new antibiotics or concomitant medications contraindicated with ciprofloxacin 
taken in the 30 days prior to signing the informed consent will be recorded on the 
appropriate data collection form 
6. Targeted physical exam 
7. Speculum exam for females 
Note: Women diagnosed with BV by local standard test at Visit 1 will receive 
treatment for BV at Visit 2 according to local standard of care. 
8. Urine pregnancy test for females of childbearing potential 
9. One swab for N. gonorrhoeae culture and one swab for NAAT and gyrA serine 91 
genotype from the throat* 
10. One swab for N. gonorrhoeae culture and one swab for NAAT and gyrA serine 91 
genotype from the rectum* 
11. One swab for N. gonorrhoeae culture from the urethra (males)* 
12. Urine specimen for NAAT and gyrA serine 91 genotype (males)* 
13. Cervical swab for N. gonorrhoeae culture (females)*  
14. Cervical or vaginal swab for NAAT and gyrA serine 91 genotype (females)*  
*Note 1: Only at the suspected infected anatomical site based on prior test results or 
other sites as clinically indicated 
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15. Once swabs have been collected, and all eligibility criteria have been assessed, 
subjects will receive one dose of ciprofloxacin 500 mg by mouth under direct 
observation with the date and time of administration documented.  
• 
Subjects will be observed for at least 5 minutes after administration of 
ciprofloxacin. 
• 
Subjects will be instructed to return to the clinic or to contact the study site 
coordinator immediately if they vomit within 1 hour of receiving study medication.  
• 
Subjects who vomit within 1 hour of study drug administration will be retreated for 
N. gonorrhoeae infection with an alternative recommended regimen per the local 
standard of care.  
16. Reminder to abstain from sexual intercourse or use condoms during any sexual 
contact until the Test of Cure Visit (Visit 2, Day 5-10) is complete   
17. Reminder to bring sex partners in for testing and treatment, if needed 
18. Reminder to return for Visit 2 (Day 5-10)  
7.2 
Visit 2, Day 5-10 (Test of Cure Visit) 
Subjects will have the following: 
 
1. Interim medical history for assessment of  specific symptoms that are potentially 
related to fluoroquinolone use as described in section 9, Assessment of Safety, and 
interim sexual history 
2. Review of signs and symptoms at site of infection since the previous visit 
3. Review of new antibiotics or concomitant medications contraindicated with 
ciprofloxacin 
4. Targeted physical exam 
5. One swab for N. gonorrhoeae culture and one swab for NAAT and gyrA serine 91 
genotype from the throat* 
6. One swab for N. gonorrhoeae culture and one swab for NAAT and gyrA serine 91 
genotype from the rectum* 
7. One swab for N. gonorrhoeae culture from the urethra (males)* 
8. Urine specimen for NAAT and gyrA serine 91 genotype (males)* 
9. Cervical swab for N. gonorrhoeae culture (females)* 
10. Cervical or vaginal swab for NAAT and gyrA serine 91 genotype (females)*  
*Note 1: Repeat samples to be collected only from those anatomical sites swabbed 
for N. gonorrhoeae culture or NAAT at Visit 1  
*Note 2: GyrA assay is required only if NAAT is positive 
11. Reminder to bring sex partners in for testing and treatment, if needed 
12. Reminder that test results will be provided to subjects by phone call (Visit 3, Day 11-
14) 
 
Women diagnosed with bacterial vaginosis (BV) will receive treatment according to local 
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7.3 
Visit 3, Day 11 to 14 (Test of Cure Results) 
1. Test results will be provided to subjects by phone call.  
2. Subjects whose Visit 2 (Day 5-10) N. gonorrhoeae culture and NAAT results are 
negative will have completed participation in the study; no further follow-up is 
required. 
3. Subjects who are N. gonorrhoeae culture positive or NAAT positive will be referred 
for standard of care treatment for N. gonorrhoeae. 
4. Reminder to bring sex partners in for testing and treatment, if needed 
7.4 
Unscheduled/Early Termination Visit  
For an unscheduled visit at the subject’s request or the site investigator’s 
recommendation, subjects will have the following:  
 
1. Interim medical history for assessment of specific symptoms that are potentially 
related to fluoroquinolone use as described in section 9, Assessment of Safety, and 
interim sexual history 
2. Review of signs and symptoms at site of infection since the previous visit  
3. Review of new antibiotics or concomitant medications contraindicated with 
ciprofloxacin 
4. Targeted physical exam  
5. Reminder to abstain from sexual intercourse or use condoms during any sexual 
contact until the Test of Cure Visit (Visit 2, Day 5-10) is complete 
6. Reminder to bring sex partners in for testing and treatment, if needed 
7. Reminder to return for follow-up visit 
 
For an early termination visit, subjects will have the following: 
 
1. Interim medical history for assessment of specific symptoms that are potentially 
related to fluoroquinolone use as described in section 9, Assessment of Safety, and 
interim sexual history 
2. Review of signs and symptoms at site of infection since the previous visit  
3. Review of new antibiotics or concomitant medications contraindicated with 
ciprofloxacin 
4. Targeted physical exam  
5. Reminder to bring sex partners in for testing and treatment, if needed 
 


 
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8 
STUDY PROCEDURES/EVALUATIONS 
8.1 
Clinical Evaluations 
Discuss pertinent medical history for assessment of specific symptoms that are 
potentially related to fluoroquinolone use as described in section 9, Assessment of 
Safety, and sexual history (including assessment of signs and symptoms) will be 
obtained by interview of the subjects at Visit 1 prior to study treatment. Subjects will be 
asked if they can swallow pills.  
 
• 
For female cervicovaginal infections, subjects will be classified as symptomatic if 
they report any of the following symptoms: abnormal vaginal discharge, abnormal 
vaginal bleeding, or pain during intercourse.  
• 
For male urethral infections, subjects will be classified as symptomatic if they report 
any of the following symptoms: urethral discharge or pain with urination.  
• 
For testing of rectal swab specimens, subjects will be classified as symptomatic if 
they report any of the following symptoms: anorectal pain, anorectal discharge, or 
anorectal bleeding.  
• 
For testing of pharyngeal swab specimens, subjects will be classified as symptomatic 
if they report having a sore throat.  
• 
For all specimen types, subjects will be considered asymptomatic if they do not 
endorse these symptoms. 
 
At Visit 2 (Day 5-10) and unscheduled visits, an interim medical history will be obtained 
by interview if the subject notes any changes since the previous visit in specific 
symptoms that are potentially related to fluoroquinolone use as described in section 9, 
Assessment of Safety. The interim medical history should include an assessment for 
new medical conditions.  
 
Sexual history including sexual orientation will be obtained by interview of the subjects at 
Visit 1. At Visit 2 (Day 5-10) and unscheduled visits, subjects will be queried regarding 
sexual activity and condom use since the previous clinic visit. 
 
Medications history (concomitant medications contraindicated with ciprofloxacin) will 
include a review of all current medications and medications taken 30 days prior to study 
enrollment. Assessment of eligibility will also include a review of all permitted and 
prohibited medications per the Subject Inclusion and Exclusion Criteria (see section 5). 
 
A targeted physical exam will be performed based on subject’s clinical history. The exam 
will be performed by appropriate study personnel to assess general physical condition 
and will at a minimum include the following areas/systems: throat, genitals, and rectum. 
A speculum exam will be performed on females. All physical examinations will be 
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Visit 1, a targeted physical examination may be conducted based on interim medical 
history. 
 
8.2 
Laboratory Evaluations 
8.2.1 Clinical Laboratory Evaluations 
Prior to the study implementation period, each laboratory will verify the 
performance of the gyrA serine 91 genotype real-time polymerase chain reaction 
with fluorescent hybridization probe detection assay, to meet the CLIA 
requirements, including accuracy, precision, limit of detection, interfering 
substances, and normal values. Full details of the verification protocol and gyrA 
serine 91 genotype assay standard operating procedure (SOP) are in the study’s 
Manual of Procedures.  
 
Specimens positive for gonococcal DNA or RNA from the participating clinical 
sites will be tested by PCR for detection of wild-type gyrA serine 91 genotype. 
Subjects who have been treated empirically (i.e., symptomatic subjects) may opt 
out of this testing, if indicated by the clinical site on the laboratory requisition. 
 
The presence or absence of mutations in the gyrA gene will be determined by 
real-time PCR. For real-time PCR analysis of the gyrA gene, remnant NAAT 
specimens will be extracted, using either a Roche MagNAPure instrument or 
Qiacube, which will then be used for the gyrA real-time PCR, using a Roche 
LightCycler platform. The gyrA assay combines amplification of the gyrA gene in 
the serine 91 coding region and melting-curve analysis of to determine wild-type 
vs. mutation in this region. This is done through use of Fluorescence Resonance 
Energy Transfer (FRET) probes for the serine 91 amplicon.   
8.2.2 Special Assays or Procedures for Enrolled Subjects 
Urine collected at Visit 1 will be analyzed for detecting pregnancies by use of a 
standard rapid urine βhCG assay.  
 
Swabs (non-cotton) will be used to collect specimens at each site (throat, rectal, 
urethral or cervical) for N. gonorrhoeae culture. The swab will be immediately 
smeared onto a modified Thayer Martin plate, which is placed into a candle jar or 
other CO2-rich transport media, at the clinic. These plates will be transported in 
the CO2-rich transport media to the local laboratory for culture for N. 
gonorrhoeae. The local laboratory will culture and isolate the gonococcal strain, 
according to their SOP for N. gonorrhoeae culture. N. gonorrhoeae culture 
specimens will be obtained first; this sequence maximizes the load collected, 
which increases the likelihood of a successful culture. A second swab or urine 
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laboratory SOP, using a collection kit with liquid transport specific to the local 
protocols (e.g. unisex swab specimen collection kit). 
 
For each positive culture (regardless of anatomical site or visit number), a 
subculture of each gonococcal isolate will be subject to antimicrobial 
susceptibility testing using the agar dilution method for azithromycin, cefixime, 
ceftriaxone, ciprofloxacin, gentamicin, penicillin, spectinomycin, and tetracycline. 
M100 Clinical and Laboratory Standards Institute (CLSI) interpretive criteria will 
be used to evaluate susceptibility to each agent, with the exception of 
azithromycin, where CDC criteria will be used [16].  
 
For each positive NAAT, or negative NAAT with a positive culture for the same 
visit, up to two 500 uL aliquots of the specimen will be frozen in screw-top 2.0 mL 
tubes, at -70̊C for discordant resolution, if needed. These frozen remnants will be 
stocked at the local laboratory until they are sent to the central laboratories 
approximately halfway through the study and at study completion. 
 
For subjects who demonstrate culture-based antibiotic resistance to ciprofloxacin 
but are deemed ciprofloxacin-susceptible by the gyrA gene-dependent 
mechanism, or have culture positivity at Visit 2, whole genome sequencing will 
be performed on their N. gonorrhoeae isolates from all visits. DNA samples will 
be extracted from the cultures and multiplexed libraries will be created. 
Sequencing will be performed according to the laboratory SOP using a platform 
such as the MiSeq (Illumina, San Diego, CA). Genomic assembly and annotation 
will be performed using sequenced N. gonorrhoeae strains as reference 
scaffolding and phylogenetic analyses will be conducted based on nucleotide 
polymorphisms [17]. 
 
Specific instructions and numbering schemes for study isolates and specimens are 
described in the study’s Manual of Procedures. 
8.2.3 Specimen Preparation, Handling, and Shipping 
8.2.3.1 Instructions for Specimen Preparation, Handling, and Storage  
 
Stocked clinical isolates of N. gonorrhoeae and remnant specimens will 
be stored at the performing laboratory site until they are sent to the 
central laboratories approximately halfway through the study and at the 
end of the study.  
 
Specific instructions for specimen preparation, handling, and storage 
are described in the study’s Manual of Procedures. 
 
 
 


 
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8.2.3.2 Specimen Shipment 
 
Bacterial isolates will be shipped frozen on dry ice in accordance with 
IATA shipping regulations. N. gonorrhoeae DNA remnant specimens will 
be shipped to the reference laboratory frozen on dry ice at specified 
intervals in accordance with IATA shipping regulations. Specimens will 
be shipped as category B (infectious) substances to meet the 
requirements outlined in 49 CFR 178.609.  
 
 
Specimens and isolates for use/long-term storage will be shipped to: 
 
ATTN: DeeDee Pacheco, Laboratory Manager  
University of California San Diego AVRC  
 
XXXXXXXXXX 
 
Specific instructions for specimen shipment will be described in the 
study’s Manual of Procedures. 
 


 
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9 
ASSESSMENT OF SAFETY 
Ciprofloxacin has a well-established safety profile and has been prescribed to several 
millions of people in the US and worldwide as it was the CDC’s recommended treatment 
regimen for uncomplicated gonorrhea from 1993 to 2007. Therefore, adverse event 
assessment is not required for this study. 
 
In order to address the FDA Drug Safety Communication dated May 12, 2016, regarding 
fluoroquinolone use for certain uncomplicated infections, subjects will be asked at Visit 
1, Visit 2, and any Unscheduled or Early Termination Visit if they have experienced any 
serious side effects related to fluoroquinolone use. These include tendon pain, joint pain, 
muscle pain, tingling or pricking sensation, confusion, and hallucinations. This 
information will be recorded in the study source documents as a change in health status. 
Any subject who experiences such an event will be given instructions on how to submit a 
MedWatch Consumer Voluntary Reporting Form to the FDA if they desire. 
 
 


 
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10 
CLINICAL MONITORING 
10.1 Site Monitoring Plan 
Site monitoring is conducted to ensure that the human subject protections, study and 
laboratory procedures, study intervention administration, and data collection processes 
are of high quality and meet sponsor requirements, ICH/GCP guidelines and applicable 
regulations, and that the study is conducted in accordance with the protocol, protocol-
specific Manual of Procedures and applicable sponsor standard operating procedures. 
DMID, the sponsoring agency, or its designee, will conduct site-monitoring visits as 
detailed in the clinical monitoring plan.  
 
Site visits will be made at standard intervals as defined by DMID and may be made more 
frequently as directed by DMID. Monitoring visits will include, but are not limited to, 
review of regulatory files, accountability records, electronic case report forms (eCRFs), 
informed consent forms, source documents necessary to support the documentation 
entered into the eCRFs, and protocol and GCP compliance. Site monitors will have 
access to the study site, study personnel, and all study documentation according to the 
DMID-approved site monitoring plan. Study monitors will meet with site principal 
investigators to discuss any problems and actions to be taken and will document visit 
findings and discussions. 
 
 


 
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11 
STATISTICAL CONSIDERATIONS 
11.1 Study Hypotheses 
The primary objective of the study is to clinically validate a gyrA assay used to determine 
ciprofloxacin susceptibility in the treatment of uncomplicated gonococcal infection by 
assessing the efficacy of ciprofloxacin for treatment of uncomplicated N. gonorrhoeae 
infections with serine 91 gyrA genotype as identified by the gyrA assay.  
 
The study is designed to test the following hypothesis in the primary efficacy analysis 
conducted in the per-protocol (PP) analysis population: 
 
Null hypothesis: The proportion of ciprofloxacin-susceptible (as identified by the gyrA 
assay) N. gonorrhoeae-infected subjects with microbiological cure 5-10 days after 
receiving ciprofloxacin is less than 0.95. 
 
Alternative hypothesis: The proportion of ciprofloxacin-susceptible (as identified by the 
gyrA assay) N. gonorrhoeae-infected subjects with microbiological cure 5-10 days after 
receiving ciprofloxacin is at least 0.95. 
 
The cut-off of 0.95 was chosen based on the CDC criteria for treatments of 
uncomplicated N. gonorrhoeae infections. The criterion for recommended treatments is a 
cure rate of greater than 95% with a lower bound of the 95% confidence interval of least 
95%.  The criterion for alternative treatments is a cure rate of greater than 95% with a 
lower bound of the 95% confidence interval of at least 90%.  
11.2 Sample Size Considerations 
The primary analysis will compute the proportion of ciprofloxacin-susceptible N. 
gonorrhoeae-infected subjects with microbiological cure 5-10 days after receiving 
ciprofloxacin in the PP analysis population. The confidence interval for the 
microbiological cure proportion will be computed using a one-sided modified Jeffreys 
interval using a significance level of 0.05. Power calculations were performed via a 
simulation study based on 10,000 replications assuming a 98% microbiological cure 
rate.   
 
Figure 11.2 below presents the power available to test that the microbiological cure rate 
is at least 95% (i.e., lower bound of the one-sided confidence interval is at least 95%) 
across a range of evaluable sample sizes. Here, evaluable denotes eligible for the PP 
analysis population. The power reaches 80% at a sample size of 195 evaluable subjects; 
however, since the power curve is not monotonic, sample sizes directly on either side of 
195 are below 80%. Since the exact number of evaluable subjects at the end of the 
study is difficult to predict, an evaluable target of 257 subjects is chosen to ensure at 
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slightly from 257. With a target of 257, the power available is approximately 85% and we 
can fall at most 10 subjects short (sample size of 247 evaluable subjects) and still 
ensure 80% power. Any sample size greater than 257 will ensure at least 80% power.    
 
Figure 11.2: Power Available to Test That the Microbiological Cure Rate Is at Least 95% 
 
To calculate the number of subjects required to enroll to reach 257 subjects in the PP 
analysis population, the following assumptions are made: 
 
• 
25% of enrolled subjects will be culture negative at baseline. 
• 
10% of subjects will be excluded from the PP analysis population (reasons for 
exclusion are stated in section 11.4.1) 
 
Under these assumptions, enrolling 381 subjects will provide 257 subjects in the PP 
analysis population. Since the proportion of subjects who will be culture negative at 
baseline can vary depending on a number of factors, 25% is a rough estimate. The exact 
number of subjects needed to provide 257 subjects in the PP analysis population may 
vary from 381, so 381 is an approximate enrollment target. 


 
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11.3 Planned Analyses 
11.3.1 Planned Futility Review  
The study will be monitored for futility. The number of treatment failures among 
subjects eligible for the PP analysis population will be monitored by a statistician 
independent from the study team.  If, at any point in the trial, 30 subjects eligible 
for the PP analysis population are classified as treatment failures, then the 
statistician will notify DMID to consider termination of the trial. 
 
The cut-off was chosen because 29 or fewer treatment failures among 257 
subjects eligible for the PP analysis population would result in a lower bound of 
the one-sided 95% Jeffreys confidence interval greater than or equal to 85%. 
Under the protocol’s assumptions of the cure rate, a simulation study based on 
50,000 replications found that the operating characteristics (power and type-I 
error) of this futility review do not vary from those described in section 11.2. 
11.4 Final Analysis Plan 
A separate statistical analysis plan document will be generated that will contain the 
details of the analyses. This section outlines the major components of the analyses. 
11.4.1 Analysis Populations 
Per-Protocol (PP) Population: This analysis population includes enrolled subjects 
who met all inclusion/exclusion criteria, have N. gonorrhoeae isolated on Day 1 
culture from the rectum or urogenital site, have an evaluable microbiological 
outcome status (see section 11.4.3.1), complied with study treatment, did not 
receive any contraindicated medication or systemic antibiotic other than the study 
medication for any concomitant infection prior to Visit 2 (Day 5-10), and returned 
for their Visit 2 (Test of Cure) visit within window. 
 
To be compliant with study treatment, a subject must be able to swallow the pill 
and not vomit within 1 hour of administration. 
 
For the primary analysis, subjects need only have N. gonorrhoeae isolated on 
Day 1 culture from the rectum or urethra (male) or cervix/vagina (female). For the 
analysis of secondary objective 1, subjects need to have N. gonorrhoeae isolated 
on Day 1 culture at the particular site being assessed.  
 
In addition, alternate per-protocol analyses which exclude subjects with reported 
concomitant infection/disease/procedure that may interfere with study product, 
use of concomitant medications or products that may interfere with study product, 
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effectiveness or study analyses will be explored.  Details will be described in the 
separate statistical analysis plan.   
 
Microbiological Intent-to-Treat (micro-ITT) Population:  This analysis population 
includes all enrolled subjects who have N. gonorrhoeae isolated from the rectum 
or urogenital site on Day 1 culture.   
 
For the primary analysis, subjects need only have N. gonorrhoeae isolated on 
Day 1 culture from the rectum or urethra (male) or cervix/vagina (female). For the 
analysis of secondary objective 1, subjects need to have N. gonorrhoeae isolated 
on Day 1 culture at the particular site being assessed. 
 
Intent-to-Treat (ITT) Population:  This analysis population includes all enrolled 
subjects.   
 
Subjects who receive any treatment other than the study medication for their N. 
gonorrhoeae infection will be included in all efficacy analyses as treatment 
failures. 
11.4.2 Baseline Characteristics 
Baseline and demographic characteristics will be summarized. For both 
continuous and categorical variables, appropriate summary statistics will be 
applied. For continuous variables, descriptive statistics will include the number of 
non-missing values, mean, standard deviation, median, minimum, and maximum.  
For categorical variables, descriptive statistics will include counts and 
percentages per category. 
11.4.3 Efficacy and Other Analysis Plan 
In this section, the primary and secondary analyses are described. The 
exploratory analysis will be addressed in the statistical analysis plan and is not 
described here. 
11.4.3.1 Primary Analysis 
The primary analysis will test whether the microbiological cure rate of 
ciprofloxacin in subjects infected with gyrA serine 91 genotype N. 
gonorrhoeae is greater than or equal to 95%. The cure rate will be 
estimated by the proportion of subjects infected with gyrA serine 91 
genotype N. gonorrhoeae with microbiological cure at Visit 2 (Day 5-10).   
 
Microbiological outcome status for the primary analysis is evaluated at 
Visit 2 (Day 5-10) and is defined as follows: 
• 
Microbiological Cure: N. gonorrhoeae not detectable by culture from 
all anatomical sites that had detectable N. gonorrhoeae at Visit 1. 


 
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• 
Microbiological Failure: N. gonorrhoeae detectable by culture from at 
least one anatomical site that had detectable N. gonorrhoeae at Visit 
1. 
• 
Non-evaluable: At least one of the following: Subject did not return 
for Visit 2 (Day 5-10), or culture results at Visit 2 (Day 5-10) were not 
available for any reason, or subject could not be evaluated for 
microbiological outcome status for any other reason.  
 
For the PP analysis population, subjects with non-evaluable outcome 
status will be excluded from the analysis. For the micro-ITT and ITT 
analysis populations, subjects with non-evaluable outcome status will be 
included in analyses and classified as treatment failures. Subjects who 
discontinued early from the study due to a lack of treatment effect are 
included in all analysis populations as treatment failures. 
 
The test will be performed by calculating the one-sided 95% modified 
Jeffreys confidence interval and comparing it to the value 0.95. The 
modification to the Jeffreys confidence interval was introduced in Brown, 
Cai, and DasGupta [18]. The lower bound of the confidence interval will 
be calculated as follows: 
 
If the number of cures, denoted X, is less than the number of subjects 
included in the analysis, denoted N, then the lower bound of the one-
sided 95% confidence interval is: 
 
𝐵𝐵(0.95; 𝑋𝑋+ 0.5; 𝑁𝑁−𝑋𝑋+ 0.5)   
 
where 𝐵𝐵(𝛼𝛼; 𝑚𝑚1; 𝑚𝑚2) denotes the α quantile of a Beta(m1, m2) distribution. 
 
If the number of cures is equal to the number of subjects included in the 
analysis, denoted N, then the lower bound of the one-sided 95% 
confidence interval is: 
(0.05)1/𝑁𝑁 
 
The primary analysis will be performed in the PP analysis population.  
Secondary analyses of the primary outcome measure will be performed 
in the micro-ITT and ITT analysis populations. Sensitivity analyses may 
be performed to assess the impact of the choice of confidence interval.  
These analyses will be specified in the statistical analysis plan.  
11.4.3.2 Secondary Analyses 
The analysis of the efficacy of by anatomic site (secondary objective 1) 
will proceed as described in section 11.4.3.1 where the modification to 


 
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the definition of microbiological outcome status is provided below.  
Summaries of the cure rate estimate and associated confidence interval 
and hypothesis test will be generated for each individual anatomic site.   
 
For the analysis of secondary objective 1, microbiological outcome 
status at each anatomical site is evaluated at Visit 2 (Day 5-10) and is 
defined for a particular anatomical site as follows: 
 
• 
Microbiological Cure: N. gonorrhoeae not detectable by culture at 
the particular anatomical site that had detectable N. gonorrhoeae at 
Visit 1. 
• 
Microbiological Failure: N. gonorrhoeae detectable by culture at the 
particular anatomical site that had detectable N. gonorrhoeae at Visit 
1. 
• 
Non-evaluable: At least one of the following: Subject did not return 
for Visit 2 (Day 5-10), or culture results at Visit 2 (Day 5-10) were not 
available for any reason, or subject could not be evaluated for 
microbiological outcome status for any other reason.  
 
For the analysis of the sensitivity of the gyrA assay for the detection of 
ciprofloxacin-susceptible N. gonorrhoeae infections (secondary 
objective 2), the sensitivity will be estimated by calculating the 
proportion of enrolled subjects who have ciprofloxacin-susceptible N. 
gonorrhoeae as identified by culture-based antimicrobial susceptibility 
testing at Visit 1.  The proportion of enrolled subjects who do not have 
ciprofloxacin-susceptible N. gonorrhoeae will also be estimated. This 
analysis will be performed in the micro-ITT analysis population. 
Secondary and sensitivity analyses, which will assess the impact of 
analysis population and missing antimicrobial susceptibility testing, may 
be performed. These analyses will be specified in the separate statistical 
analysis plan document. 
11.4.3.3 Exploratory Analysis   
The exploratory analysis will be described in the separate statistical 
analysis plan. 
 
 
 


 
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12 
SOURCE DOCUMENTS AND ACCESS TO SOURCE 
DATA/DOCUMENTS 
Each participating site will maintain appropriate research records for this trial, in 
compliance with ICH E6, Section 4.9 and regulatory and institutional requirements for 
the protection of confidentiality of subjects. As part of participating in a DMID-sponsored 
study, each site will permit authorized representatives of the DMID, its designees, and 
appropriate regulatory agencies to examine (and when required by applicable law, to 
copy) study records for the purposes of quality assurance reviews, audits, and 
evaluation of the study safety and progress. These representatives will be permitted 
access to all study source data. Study source data are all information, original records of 
clinical findings, observations, or other activities in a clinical trial necessary for the 
reconstruction and evaluation of the trial. 
  


 
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13 
QUALITY CONTROL AND QUALITY ASSURANCE 
Following a written DMID-accepted site quality management plan, the participating site is 
responsible for conducting routine quality assurance (QA) and quality control (QC) 
activities to internally monitor study progress and protocol compliance. The site principal 
investigator will provide direct access to all trial-related sites, source data/data collection 
forms, and reports for the purpose of monitoring and auditing by the sponsor, and 
inspection by local and regulatory authorities. The site principal investigator will ensure 
all study personnel are appropriately trained and applicable documentations are 
maintained on site. 
 
The Statistical Data and Coordinating Center (SDCC) will implement quality control 
procedures beginning with the data entry system and generate data quality control 
checks on the database. Any missing data or data anomalies will be communicated to 
the site for clarification and resolution.  


 
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14 
ETHICS/PROTECTION OF HUMAN SUBJECTS 
14.1 Ethical Standard 
This study will be conducted in full conformity with the Declaration of Helsinki, or with the 
ICH-GCP regulations and guidelines, whichever affords the greater protection to the 
subject.  
 
The investigator will also ensure that this study is conducted in full conformity with the 
principles set forth in The Belmont Report: Ethical Principles and Guidelines for the 
Protection of Human Subjects of Research of the US National Commission for the 
Protection of Human Subjects of Biomedical and Behavioral Research (April 18, 1979) 
and codified in 45 CFR Part 46 and/or the ICH E6; 62 Federal Regulations 25691 
(1997). 
14.2 Institutional Review Board 
Each participating institution will provide review and approval of this protocol and the 
associated informed consent documents and recruitment material by an appropriate 
independent ethics committee (IEC) or IRB registered with the Office for Human 
Research Protections (OHRP). Any amendments to the protocol or consent materials 
will also be approved before they are placed into use. In the United States and in other 
countries, only institutions holding a current US Federalwide Assurance issued by OHRP 
may participate. 
14.3 Informed Consent Process 
Informed consent is a process that is initiated prior to the subject agreeing to participate 
in the study and continuing throughout the subject’s study participation.  Extensive 
discussion of risks and possible benefits of this therapy will be provided to the subjects 
and their families. Consent forms describing in detail the study treatment, procedures, 
and risks are given to the subject and written documentation of informed consent is 
required prior to administering study treatment. Consent forms will be IRB-approved and 
the subject will be asked to read and review the document. Upon reviewing the 
document, the investigator will explain the research study to the subject and answer any 
questions that may arise. The subject will sign the informed consent document prior to 
any procedures being done specifically for the study. The subject should have the 
opportunity to discuss the study with his/her surrogates or think about it prior to agreeing 
to participate. The subject may withdraw consent at any time throughout the course of 
the trial.  A copy of the informed consent document will be given to the subject.  The 
rights and welfare of subjects will be protected by emphasizing to them that the quality of 
their medical care will not be adversely affected if they decline to participate in this study. 
 
 
 


 
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14.4 Exclusion of Women, Minorities, and Children (Special Populations) 
 
This trial will be inclusive of all adults who meet the subject inclusion/exclusion criteria, 
regardless of religion, sex, or ethnic background. Should the outcome of this trial be 
deemed acceptable, additional trials may be initiated in other populations. The 
demographic and ethnic distribution of the study population will be generally reflective of 
the distribution of subjects with N. gonorrhoeae within each STD clinic. The following 
populations will be excluded from study participation:  
 
• 
Pregnant women 
Pregnant women are excluded from this study, as it is not known if ciprofloxacin will 
harm a fetus.  
 
• 
Children 
The NIH has mandated that children (defined as anyone under the age of 21) be 
included in research trials when appropriate. This study will enroll children aged 18 to 
20 who are able to give informed consent. This study meets "Justifications for 
Exclusion" criteria for younger children as set forth by the NIH. Specifically, 
"insufficient data are available in adults to judge potential risk in children" and 
"children should not be the initial group to be involved in research studies."  
14.5 Subject Confidentiality 
Subject confidentiality is strictly held in trust by the participating investigators, their staff, 
and the sponsor(s) and their agents. This confidentiality is extended to cover testing of 
biological samples and genetic tests in addition to the clinical information relating to 
participating subjects. 
 
The study protocol, documentation, data, and all other information generated will be held 
in strict confidence. No information concerning the study or the data will be released to 
any unauthorized third party without prior written approval of the sponsor. 
 
To further protect the privacy of study subjects, we have a Certificate of Confidentiality 
from the National Institutes of Health (NIH). This certificate protects identifiable research 
information from forced disclosure. It allows the investigator and others who have access 
to research records to refuse to disclose identifying information on research participation 
in any civil, criminal, administrative, legislative, or other proceeding, whether at the 
federal, state, or local level. By protecting researchers and institutions from being 
compelled to disclose information that would identify research subjects, Certificates of 
Confidentiality help achieve the research objectives and promote participation in studies 
by helping assure confidentiality and privacy to subjects. 
 


 
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Applicable regulatory authorities, such as the FDA, or other authorized representatives 
of the sponsor may inspect all study documents and records required to be maintained 
by the investigator.  The clinical study site will permit access to such records. 
14.6 Study Discontinuation 
If the study is discontinued, subjects will be given appropriate care and treatment for 
gonorrhea under medical supervision until the infection has resolved.  
14.7 Future Use of Stored Specimens 
All gonococcal strains will be stored in a secured location and may be subject to 
additional future testing by authorized staff to better understand resistant gonorrhea. The 
strains will not be stored with any personal identifying information but will include a new 
unique subject ID number so that specimens from the same individual are linked but the 
subject’s identify will remain unknown. The samples will not contain human genetic 
material. Future tests will be limited to those related to the study of N. gonorrhoeae and 
not of any human material. The informed consent process will include appropriate 
consent to obtain and store these samples. At the time of informed consent, subjects 
may choose to withhold permission for storage of their specimens and may continue in 
the study if they decline permission. Specimens from subjects not consenting to storage 
and future research will be destroyed at the end of the study. 


 
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15 
DATA HANDLING AND RECORD KEEPING 
The site principal investigator is responsible to ensure the accuracy, completeness, 
legibility, and timeliness of the data reported.   
 
Data collection forms will be derived from the eCRF and provided by the SDCC to record 
and maintain data for each subject enrolled in the study. All data collection forms should 
be completed in a neat, legible manner to ensure accurate interpretation of data.  Black 
or blue ink is required to ensure clarity of reproduced copies. When making a change or 
correction, cross out the original entry with a single line and initial and date the change.  
DO NOT ERASE, OVERWRITE, OR USE CORRECTION FLUID OR TAPE ON THE 
ORIGINAL. 
 
Data reported in the eCRF derived from the data collection forms should be consistent 
with the data collection forms or the discrepancies should be explained. 
The sponsor and/or its designee will provide guidance to site principal investigators and 
other study personnel on making corrections to the data collection forms and eCRF. 
15.1 Data Management Responsibilities 
All data collection forms and laboratory reports must be reviewed by the clinical team 
and data entry personnel, who will ensure that they are accurate and complete.  
 
Data collection is the responsibility of the study personnel at the participating sites under 
the supervision of the respective site principal investigator. During the study, the site 
principal investigator must maintain complete and accurate documentation for the study. 
 
The Emmes Corporation will serve as the SDCC for this study and will be responsible for 
data management, quality review, analysis, and reporting of the study data.  
15.2 Data Capture Methods 
Clinical (including, but not limited to, concomitant medications, medical history, physical 
assessments, clinical laboratory values) and endpoint data will be entered into a 21 CFR 
11-compliant Internet data entry system provided by the SDCC. The data system 
includes password protection and internal quality checks, such as automatic range 
checks, to identify data that appear inconsistent, incomplete, or inaccurate. Clinical data 
will be entered directly from the data collection forms completed by the study personnel. 
15.3 Types of Data 
Data for this study will include clinical, laboratory, demographic, behavioral variables, 
and outcome measures. 


 
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15.4 Timing/Reports 
A final report will be prepared following the availability of all the safety and laboratory 
data. Interim statistical reports may be generated as deemed necessary and appropriate 
by DMID.   
15.5 Study Records Retention 
Study records and reports, including, but not limited to, CRFs, source documents, 
informed consent forms (except for future use informed consent forms), laboratory test 
results, and medication inventory records, shall be retained for 2 years after the last 
marketing application is approved for the device and until there are no pending or 
contemplated marketing applications. If an application is not approved for the device, 
study documents should be retained at least 2 years after clinical development of the 
device for investigational use is discontinued and the FDA has been so notified. The site 
must contact DMID for authorization prior to the destruction of any study records. No 
records will be destroyed without the written consent of the sponsor. It is the 
responsibility of the sponsor to inform the investigator when these documents no longer 
need to be retained. Informed consent forms for future use will be maintained as long as 
the sample exists. 
15.6 Protocol Deviations 
A protocol deviation is any noncompliance with the clinical trial protocol, GCP, or Manual 
of Procedures requirements. The noncompliance may be either on the part of the 
subject, the investigator, or the study personnel. As a result of deviations, corrective 
actions are to be developed by the site and implemented promptly.  
These practices are consistent with ICH E6: 
4.5 
Compliance with Protocol, sections 4.5.1, 4.5.2, and 4.5.3 
5.1 
Quality Assurance and Quality Control, section 5.1.1 
5.20 Noncompliance, sections 5.20.1, and 5.20.2. 
 
It is the responsibility of the site principal investigator and other study personnel to use 
continuous vigilance to identify and report deviations within 5 working days of 
identification of the protocol deviation, or within 5 working days of the scheduled 
protocol-required activity. All deviations must be promptly reported to DMID, via The 
Emmes Corporation’s AdvantageEDCSM. 
 
All deviations from the protocol must be addressed in study subject source documents.  
A completed copy of the DMID Protocol Deviation Form must be maintained in the 
regulatory file, as well as in the subject’s source document. Protocol deviations must be 
sent to the local IRB/IEC per their guidelines. The site principal investigator and other 
study personnel are responsible for knowing and adhering to their IRB/IEC 
requirements. 


 
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16 
PUBLICATION POLICY 
The NIH Public Access Policy ensures the public has access to the published results of 
NIH funded research. It requires investigators to submit final peer-reviewed journal 
manuscripts that arise from NIH funds to the digital archive PubMed Central upon 
acceptance for publication. Further, the policy stipulates that these papers must be 
accessible to the public on PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/) no later 
than 12 months after publication. 
 
Refer to: 
• NIH Public Access Policy, http://publicaccess.nih.gov/ 
• NIH OER Grants and Funding, http://grants.nih.gov/grants/oer.htm 
 
Following completion of the study, the lead principal investigator is expected to publish 
the results of this research in a scientific journal. The International Committee of Medical 
Journal Editors (ICMJE) member journals have adopted a trials-registration policy as a 
condition for publication. This policy requires that all clinical trials be registered in a 
public trials registry such as ClinicalTrials.gov, which is sponsored by the National 
Library of Medicine [19]. Other biomedical journals are considering adopting similar 
policies. 
 
The ICMJE defines a clinical trial as any research project that prospectively assigns 
human subjects to intervention or comparison groups to study the cause-and-effect 
relationship between a medical intervention and a health outcome. Studies designed for 
other purposes, such as to study pharmacokinetics or major toxicity (e.g., Phase I trials), 
would be exempt from this policy. Results of any exploratory analysis will not be 
published prior to publication of the primary results for this study. 
All clinical trials supported by the NIH must be registered on ClinicalTrials.gov.  As part 
of the result posting, a copy of this protocol (and its amendments) and a copy of the 
Statistical Analysis Plan will be included in the post on ClincialTrials.gov. 
For trials in which DMID is not the investigational new drug/investigational new device 
exemption (IND/IDE) sponsor, or there is no IND/IDE, and DMID does not provide data 
management services, it is the responsibility of the investigator to register the trial and 
post results in compliance with Public Law 110-85, the Food and Drug Administration 
Amendments Act of 2007 (FDAAA). 
 


 
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17 
LITERATURE REFERENCES 
1. 
Centers for Disease Control and Prevention. Sexually Transmitted Disease Surveillance 
2012. http://wwwcdcgov/std/stats12/Surv2012pdf 2012; accessed Aug 13, 2014. 
2. 
Barry PM, Klausner JD. The use of cephalosporins for gonorrhea: the impending 
problem of resistance. Expert Opinion on Pharmacotherapy 2009 Mar; 10(4):555-77. 
[PMID: 19284360]  
3.  
Echols RM, Heyd A, O'Keeffe BJ, Schacht P. Single-dose ciprofloxacin for the treatment 
of uncomplicated gonorrhea: a worldwide summary. Sex Transmitted Diseases. 1994 
Nov-Dec;21(6):345-52. [PMID: 7871449] 
4. 
Hook EW 3rd, Jones RB, Martin DH, Bolan GA, Mroczkowski TF, Neumann TM, Haag 
JJ, Echols R. Comparison of ciprofloxacin and ceftriaxone as single-dose therapy for 
uncomplicated gonorrhea in women. Antimicrobial Agents and Chemotherapy. 1993 
Aug;37(8):1670-3. [PMID:8215281] 
5. 
Centers for Disease Control and Prevention. Cephalosporin susceptibility among 
Neisseria gonorrhoeae isolates, United States, 2000-2010. Morbidity and Mortality 
Weekly Report: 2011 Jul 8;60(26):873-7. [PMID: 21734634]  
6. 
Centers for Disease Control and Prevention. Update to CDC’s Sexually transmitted 
diseases treatment guidelines, 2010: oral cephalosporins no longer a recommended 
treatment for gonococcal infections. Morbidity and Mortality Weekly Report 2012; Aug 
10; 61(31):590-4. [PMID: 22874837]  
7. 
Centers for Disease Control and Prevention. Recommendations for the laboratory-based 
detection of Chlamydia trachomatis and Neisseria gonorrhoeae—2014. Morbidity and 
Mortality Weekly Report (MMWR). Recommendations and Reports. March 14, 
2014/63(RR02);63:1-19. http://www.cdc.gov/mmwr/preview/mmwrhtml/rr6302a1.htm 
8. 
Siedner MJ, Pandori M, et al. Real-time PCR assay for detection of quinolone-resistant 
Neisseria gonorrhoeae in urine samples. Journal of Clinical Microbiology 2007 Apr; 
45(4):1250-4. [PMID: 17267635]  
9.  
Pandori M, Barry PM, et al. Mosaic penicillin-binding protein 2 in Neisseria gonorrhoeae 
isolates collected in 2008 in San Francisco, California. Antimicrobial Agents and 
Chemotherapy 2009 Sept; 53(9):4032-4. [PMID: 19546370]  
10.  
Buono S, Wu A, Hess DC, Carlson JS, Rauch L, Philip SS, et al. Using the Neisseria 
gonorrhoeae multiantigen sequence-typing method to assess strain diversity and 
antibiotic resistance in San Francisco, California. Microbial Drug Resistance 2012 Oct; 
18(5): 510-7. [PMID: 22686196]  
11. 
Bolan GA, Sparling PF, Wasserheit JN. The emerging threat of untreatable gonococcal 
infection. New England Journal of Medicine 2012 Feb 9; 366(6):485-7. [PMID: 
22316442].  
12. 
Kirkcaldy RD, Kidd S, Weinstock HS et al. Trends in antimicrobial resistance in Neisseria 
gonorrhoeae in the USA: the Gonococcal Isolate Surveillance Project (GISP), January 
2006–June 2012. Sexually Transmitted Infections. 2013;89:suppl4:iv5–10. 


 
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13. 
Seppälä H, Klaukka T, Vuopio-Varkila J, Muotiala A, Helenius H, Lager K, Huovinen P. 
The effect of changes in the consumption of macrolide antibiotics on erythromycin 
resistance in group A streptococci in Finland: Finnish Study Group for Antimicrobial 
Resistance. New England Journal of Medicine 1997 Aug 14; 337(7):441-6. [PMID: 
9250845]  
14. 
Dicker LW, Mosure DJ, Steece R, Stone KM. Testing for sexually transmitted diseases 
in U.S. public health laboratories in 2004. Sexually Transmitted Diseases 2007 Jan; 
34(1):41-6. [PMID: 16735955]  
15. 
Siedner MJ, Pandori M, Castro L, Barry P, Whittington WL, Liska S, Klausner JD. Real-
time PCR assay for detection of quinolone-resistant Neisseria gonorrhoeae in urine 
samples. Journal of Clinical Microbiology 2007 Apr;45(4):1250-4. 
16. 
Clinical and Laboratory Standards Institute. Performance Standards for Antimicrobial 
Susceptibility Testing: 12th Informational Supplement. M100-S1727], 124-25. 2007. Ref 
Type: Serial (Book, Monograph) 
17. 
Demczuk w, Lynch T, Martin I, et al. Whole-genome phylogenomic heterogeneity of 
Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in 
Canada between 1989 and 2013. Journal of Clinical Microbiology 2015; 53(1):191-200. 
18. 
Brown L, Cai T, DasGupta A. Interval estimation for a binomial proportion. Statistical 
Science 2001 16(2):101–33. doi:10.1214/ss/1009213286  
19. 
De Angelis C, Drazen JM, Frizelle FA, Haug C, Hoey J, et al. Clinical trial registration: a 
statement from the International Committee of Medical Journal Editors. New England 
Journal of Medicine. 2004 Sep 16;351(12):1250-1. Epub 2004 Sep 8 
 
 
 
 


 
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APPENDIX A: SCHEDULE OF EVENTS 
Evaluation  
Screening/ 
Enrollment  
Visit 1 
Day 1 
Visit 2  
Day 5-10 
(Test of 
Cure) 
Visit 3 
Day 11-143 
(Test of Cure 
Results) 
Unscheduled/ 
Early  
Termination 
Visit5 
Signed consent form 
X 
 
 
 
Confirmation of eligibility criteria 
X 
 
 
 
Medical history for assessment of specific symptoms that 
are potentially related to fluoroquinolone use as 
described in section 9, Assessment of Safety 
X 
X 
 
X 
Signs/symptoms 
X 
X 
 
X 
Concomitant medications 
X 
X 
 
X 
Sexual history  
X 
 
 
 
Interim sexual history  
 
X 
 
X 
Targeted physical examination 
X 
X 
 
X 
Rapid urine βhCG pregnancy test (females) 
X 
 
 
 
Speculum examination (females) 
X 
 
 
 
Cervical swab for N. gonorrhoeae culture (females) 
X2 
X2 
 
 
Cervical or vaginal swab for NAAT and gyrA assay 
(females)1 
X2 
X2 
 
 
Urethral swab for N. gonorrhoeae culture (males) 
X2 
X2 
 
 
Urine specimen for NAAT and gyrA assay (males)1 
X2 
X2 
 
 
Throat swab for N. gonorrhoeae culture and NAAT and 
gyrA assay1 
X2 
X2 
 
 
Rectal swab for N. gonorrhoeae culture and NAAT and 
gyrA assay1 
X2 
X2 
 
 
Study intervention 
X 
 
 
 
Reminder to abstain from sexual intercourse or use 
condoms  
X 
 
 
X5 
Reminder to bring partners in for treatment 
X 
X 
X 
X 
Follow-up for test of cure results  
 
 
 X4 
 
1. GyrA assay required only if NAAT is positive. 
2. Collect specimen at anatomic site of N. gonorrhoeae infection.  
3. Follow-up for test of cure results will be by phone call.  
4. For subjects N. gonorrhoeae culture negative and NAAT negative, no further follow-up required.  
Subjects who are N. gonorrhoeae culture positive or NAAT positive will be referred for standard of care 
treatment for N. gonorrhoeae. 
5. Not required at the Early Termination Visit. 

SAP_001.pdf: 
CLINICAL RESEARCH IN INFECTIOUS DISEASES 
 
 
 
STATISTICAL ANALYSIS PLAN 
for 
DMID Protocol: 15-0090 
Study Title: 
Clinical Validation of a Molecular Test for 
Ciprofloxacin-Susceptibility in Neisseria gonorrhoeae 
 
NCT02961751 
 
Version 1.0 
 
DATE: 08–April-2019 
 
THIS COMMUNICATION IS PRIVILEGED AND CONFIDENTIAL  
 
 


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STUDY TITLE 
Protocol Number Code: 
DMID Protocol: 15-0090 
Development Phase: 
Clinical Study 
Products: 
Ciprofloxacin 
Form/Route: 
Orally 
Indication Studied: 
Neisseria Gonorrhoeae 
Sponsor: 
Division of Microbiology and Infectious Diseases 
National Institute of Allergy and Infectious Diseases 
National Institutes of Health 
Clinical Trial Initiation Date: 
19OCT2016 
Clinical Trial Completion Date: 
TBD 
Date of the Analysis Plan: 
08APR2019 
Version Number: 
1.0 
This study was performed in compliance with Good Clinical Practice. 
Information contained in this publication is the property of Division of Microbiology and Infectious Diseases and is confidential. This 
information may not be disclosed to third parties without written authorization from Division of Microbiology and Infectious Diseases. This 
report may not be reproduced, stored in a retrieval system or transmitted in any form or by any means - electronic, mechanical, recording or 
otherwise - without the prior authorization from Division of Microbiology and Infectious Diseases. This document must be returned to Division 
of Microbiology and Infectious Diseases upon request. 
 


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TABLE OF CONTENTS 
STUDY TITLE ............................................................................................................................... II 
TABLE OF CONTENTS ...............................................................................................................III 
LIST OF ABBREVIATIONS ....................................................................................................... VI 
1. 
PREFACE .....................................................................................................................1 
2. 
INTRODUCTION ........................................................................................................2 
2.1. 
Purpose of the Analyses ................................................................................................3 
3. 
STUDY OBJECTIVES AND ENDPOINTS ................................................................4 
3.1. 
Study Objectives ...........................................................................................................4 
3.1.1. 
Primary Objectives .......................................................................................................4 
3.1.2. 
Secondary Objectives ...................................................................................................4 
3.1.3. 
Exploratory Objectives .................................................................................................4 
3.2. 
Endpoints ......................................................................................................................4 
3.2.1. 
Primary Outcome Measure ...........................................................................................4 
3.2.2. 
Secondary Outcome Measure .......................................................................................4 
3.2.3. 
Exploratory Outcome Measures ...................................................................................4 
3.3. 
Study Definitions and Derived Variables .....................................................................5 
3.3.1. 
Baseline untreated serine 91 gyrase A genotype N. gonorrhoeae Diagnosis ...............5 
3.3.2. 
Microbiological Outcome Status ..................................................................................5 
3.3.3. 
Sensitivity of the gyrA assay .........................................................................................5 
3.3.4. 
Baseline Value ..............................................................................................................6 
3.3.5. 
Within Window Test of Cure Visit ...............................................................................6 
3.3.6. 
Treatment Compliance ..................................................................................................6 
3.3.7. 
Symptomatic/Asymptomatic Status..............................................................................6 
3.3.8. 
Ciprofloxacin Susceptible Infection .............................................................................7 
4. 
INVESTIGATIONAL PLAN .......................................................................................8 
4.1. 
Overall Study Design and Plan .....................................................................................8 
4.2. 
Discussion of Study Design, Including the Choice of Control Groups ........................8 
4.3. 
Selection of Study Population ......................................................................................9 
4.4. 
Treatments ..................................................................................................................11 
4.4.1. 
Treatments Administered ............................................................................................11 


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4.4.2. 
Identity of Study Product(s)........................................................................................11 
4.4.3. 
Method of Assigning Subjects to Treatment Groups (Randomization) .....................11 
4.4.4. 
Selection and Timing of Dose for Each Subject .........................................................11 
4.4.5. 
Blinding ......................................................................................................................11 
4.4.6. 
Prior and Concomitant Therapy ..................................................................................11 
4.4.7. 
Treatment Compliance ................................................................................................12 
4.5. 
Efficacy and Safety Variables ....................................................................................12 
4.5.1. 
Safety Variables ..........................................................................................................12 
4.5.2. 
Efficacy Variables ......................................................................................................12 
5. 
SAMPLE SIZE CONSIDERATIONS .......................................................................13 
6. 
GENERAL STATISTICAL CONSIDERATIONS ....................................................14 
6.1. 
General Principles .......................................................................................................14 
6.1.1. 
Pseudo Code ...............................................................................................................14 
6.2. 
Timing of Analyses .....................................................................................................15 
6.3. 
Analysis Populations ..................................................................................................15 
6.3.1. 
Safety Analyses ..........................................................................................................15 
6.3.2. 
Efficacy Analyses .......................................................................................................15 
6.3.2.1. 
Intent-to-Treat Analysis (ITT) Population ..................................................................15 
6.3.2.2. 
Microbiological Intent-to-Treat (micro-ITT) Population ...........................................15 
6.3.2.3. 
Per Protocol Population ..............................................................................................16 
6.3.3. 
Considerations for all Analysis Populations ...............................................................16 
6.4. 
Covariates and Subgroups ..........................................................................................17 
6.5. 
Missing Data ...............................................................................................................17 
6.6. 
Interim Analyses and Data Monitoring ......................................................................17 
6.7. 
Multicenter Studies .....................................................................................................17 
6.8. 
Multiple Comparisons/Multiplicity ............................................................................17 
7. 
STUDY SUBJECTS ...................................................................................................18 
7.1. 
Disposition of Subjects ...............................................................................................18 
7.2. 
Protocol Deviations ....................................................................................................18 
8. 
EFFICACY EVALUATION ......................................................................................19 
8.1. 
Primary Efficacy Analyses .........................................................................................19 


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8.1.1. 
Sensitivity Analyses ....................................................................................................19 
8.2. 
Secondary Efficacy Analyses .....................................................................................19 
8.2.1. 
Other Efficacy Analyses .............................................................................................20 
8.3. 
Exploratory Efficacy Analyses ...................................................................................20 
9. 
SAFETY EVALUATION ..........................................................................................21 
9.1. 
Demographic and Other Baseline Characteristics ......................................................21 
9.2. 
Measurements of Treatment Compliance ...................................................................21 
9.3. 
Adverse Events ...........................................................................................................21 
9.3.1. 
Side Effects Related to Fluoroquinolone use ..............................................................21 
9.4. 
Pregnancies .................................................................................................................21 
9.5. 
Physical Evaluations ...................................................................................................21 
9.6. 
Concomitant Medications ...........................................................................................21 
10. 
PHARMACOKINETICS ...........................................................................................22 
11. 
IMMUNOGENICITY ................................................................................................23 
12. 
OTHER ANALYSES .................................................................................................24 
13. 
REPORTING CONVENTIONS ................................................................................25 
14. 
TECHNICAL DETAILS ............................................................................................26 
15. 
SUMMARY OF CHANGES IN THE CONDUCT OF THE STUDY OR 
PLANNED ANALYSES ............................................................................................27 
16. 
REFERENCES ...........................................................................................................28 
17. 
LISTING OF TABLES, FIGURES, AND LISTINGS ..............................................29 
APPENDICES ...............................................................................................................................30 
APPENDIX 1. TABLE MOCK-UPS..........................................................................................31 
APPENDIX 2. FIGURE MOCK-UPS ........................................................................................65 
APPENDIX 3. LISTINGS MOCK-UPS .....................................................................................69 
 


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LIST OF ABBREVIATIONS 
ATC 
Anatomical Therapeutic Chemical Classification System 
CDC 
Centers for Disease Control and Prevention 
CI 
Confidence Interval 
CRF 
Case Report Form 
DMID 
Division of Microbiology and Infectious Diseases 
DNA 
Deoxyribonucleic Acid 
eCRF 
Electronic Case Report Form 
FDA 
The Food and Drug Administration 
FP 
False Positive 
gyrA 
Gyrase A Genotype 
ICH 
International Conference on Harmonization 
ID 
Identification 
IRB 
Institutional Review Board 
ITT 
Intention to Treat 
MIC 
Minimum Inhibitory Concentration 
micro-ITT 
Microbiological Intent-to-Treat 
N 
Number (typically refers to subjects) 
NAAT 
Nucleic Acid Amplification Test 
NIH 
National Institutes of Health 
PCR 
Polymerase Chain Reaction 
PP 
Per Protocol 
PT 
Preferred Term 
SD 
Standard Deviation 
STD 
Sexually Transmitted Disease 
TP 
True Positive 
US 
United States 
WHO 
World Health Organization 
 


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1. 
PREFACE 
The Statistical Analysis Plan (SAP) for “Clinical Validation of a Molecular Test for Ciprofloxacin-
Susceptibility in Neisseria gonorrhoeae” (DMID Protocol 15-0090) describes and expands upon the statistical 
information presented in the protocol. 
This document describes all planned analyses and provides reasons and justifications for these analyses. It 
also includes sample tables, listings, and figures planned for the final analyses. Regarding the final analyses 
and Clinical Study Report (CSR), this SAP follows the International Conference on Harmonisation (ICH) of 
Technical Requirements for Registration of Pharmaceuticals for Human Use ICH Guidelines, as indicated in 
Topic E3 (Structure and Content of Clinical Study Reports), and more generally is consistent with Topic E8 
(General Considerations for Clinical Trials) and Topic E9 (Statistical Principles for Clinical Trials). The 
structure and content of the SAP provides sufficient detail to meet the requirements identified by the Food and 
Drug Administration (FDA) and ICH, while all work planned and reported for this SAP will follow 
internationally accepted guidelines published by the American Statistical Association and the Royal Statistical 
Society for statistical practice.  
This document contains four sections: (1) a review of the study design, (2) general statistical considerations, 
(3) comprehensive statistical analysis methods for efficacy and safety outcomes, and (4) a list of proposed 
tables and figures. Any deviation from this SAP will be described and justified in protocol amendments 
and/or in the CSR, as appropriate. The reader of this SAP is encouraged to also review the study protocol for 
details on conduct of the study and the operational aspects of clinical assessments. 
Genomic analyses are not described in this SAP; a separate SAP for the genomic analyses will be generated. 


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2. 
INTRODUCTION 
Gonorrhea is the second most commonly reported notifiable disease in the United States with more than 
330,000 cases reported in 2012, a rate of 107.5 per 100,000 population [reference 1 in protocol]. Over the past 
75 years, Neisseria gonorrhoeae (N. gonorrhoeae) infections have become increasingly resistant to 
antimicrobial therapy, first to sulfa-based antibiotics, then penicillins, tetracyclines, fluoroquinolones, and 
now extended-spectrum cephalosporins [reference 2 in protocol]. Prior to the advent of ciprofloxacin-resistant 
N. gonorrhoeae, ciprofloxacin was the primary first-line recommended therapy for N. gonorrhoeae infections 
of the throat, rectum, urethra, and cervix. From 1998 to 2006, ciprofloxacin was the Centers for Disease 
Control and Prevention (CDC) recommended treatment for N. gonorrhoeae in all anatomic sites. Prior to 
widespread ciprofloxacin resistance, the efficacy of ciprofloxacin treatment in susceptible N. gonorrhoeae 
infections was estimated at more than 99% [reference 3-4 in protocol]. In 2007, due to high rates of 
ciprofloxacin resistance in N. gonorrhoeae nationally, the CDC recommended the discontinuation of 
ciprofloxacin treatment for gonorrhea, which was followed by a decline in ciprofloxacin N. gonorrhoeae 
resistance nationally [reference 5 in protocol]. At this time, the only recommended treatment for 
N. gonorrhoeae infection is dual antibiotic therapy with injectable ceftriaxone and oral azithromycin or 
doxycycline [reference 6 in protocol]. For decades, bacterial culture was the standard diagnostic modality for 
N. gonorrhoeae infections. Culture is specific, but studies have demonstrated that the molecular-based 
enzyme immunoassay or nucleic acid amplification test (NAAT) has a higher clinical sensitivity than culture 
[reference 7 in protocol]. However, there has not been a widely used and reliable technology that allows for 
antibiotic susceptibility testing from non-culture specimens. 
It has been recently demonstrated that N. gonorrhoeae-deoxyribonucleic acid (DNA) mutations can be 
detected using modern molecular techniques and real-time polymerase chain reaction (PCR) assays can be 
used to detect reproducible, clinically significant resistance [reference 8-10 in protocol]. A protocol for the 
detection of alterations in the gyrase A gene (gyrA), the target of ciprofloxacin anti-gonococcal activity, has 
been validated [reference 8 in protocol]. While molecular markers of susceptibility have high concordance, 
sensitivity and a specificity of 93% and 100%, respectively, compared with standard antimicrobial 
susceptibility testing, the clinical performance of the test and the response to therapy based on a molecular 
susceptibility result in N. gonorrhoeae is unknown. 
While molecular methods to diagnose N. gonorrhoeae have greatly improved the detection of infection 
[reference 14 in protocol], they have historically precluded the ability to perform antibiotic susceptibility 
testing. Although regional surveillance data critically inform treatment recommendations, those data cannot 
be used for real-time individualized clinical management. The clinical validation of an assay to determine the 
ciprofloxacin susceptibility of N. gonorrhoeae infections could result in increased use of ciprofloxacin for 
ciprofloxacin-susceptible N. gonorrhoeae infections and resultant decreased use of extended-spectrum 
cephalosporins, thereby reducing the selection pressure for cephalosporin resistance in N. gonorrhoeae. An 
immediate benefit to taking ciprofloxacin would be for those with cephalosporin allergies who would have to 
take combination therapy that is more difficult to administer. The study will help to assess the potential 
impact of a strategy to address the critical problem of emerging drug resistance in N. gonorrhoeae. 
Specifically, the information gained from this study can be used to influence national sexually transmitted 
disease (STD) treatment policies and, therefore, result in a marked decrease in extended-spectrum 
cephalosporin-resistant N. gonorrhoeae infection, improving the availability of treatment options for 
individuals infected with N. gonorrhoeae. 


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2.1. 
Purpose of the Analyses 
These analyses will assess the efficacy of ciprofloxacin for treatment of uncomplicated Neisseria 
gonorrhoeae infections with gyrA serine 91 genotype and will be included in the clinical study report. 


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3. 
STUDY OBJECTIVES AND ENDPOINTS 
3.1. 
Study Objectives 
3.1.1. 
Primary Objectives 
1. To determine the efficacy of ciprofloxacin for treatment of uncomplicated Neisseria gonorrhoeae 
infections with gyrA serine 91 genotype. 
3.1.2. 
Secondary Objectives 
1. To investigate efficacy of ciprofloxacin for treatment of uncomplicated gyrA serine 91 genotype 
Neisseria gonorrhoeae infection by anatomic site. 
2. To determine the sensitivity of the gyrA assay for detection of ciprofloxacin-susceptible Neisseria 
gonorrhoeae infections. 
3.1.3. 
Exploratory Objectives 
1. To characterize N. gonorrhoeae isolates and non-gyrA gene-dependent mechanisms of ciprofloxacin 
resistance post-treatment of uncomplicated N. gonorrhoeae infection by anatomic site using traditional 
and molecular methods like genotyping and sequencing. 
2. To investigate the efficacy of ciprofloxacin for treatment of uncomplicated serine 91 gyrA N. 
gonorrhoeae infections by demographic and clinical characteristics. 
3.2. 
Endpoints 
3.2.1. 
Primary Outcome Measure 
1. The proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae with 
microbiological cure at Visit 2 (Day 5-10) 
3.2.2. 
Secondary Outcome Measure 
1. The proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae with 
microbiological cure at each anatomic site (throat, rectum, male or female urogenital tract) at Visit 2 
(Day 5-10) 
2. The proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae identified by gyrA 
gene PCR who have ciprofloxacin-susceptible N. gonorrhoeae as identified by culture-based 
antimicrobial susceptibility testing at Visit 1 (Day 1) 
3.2.3. 
Exploratory Outcome Measures 
1. Identification and characterization of non-gyrA gene-dependent mechanisms of ciprofloxacin 
resistance by genotyping and whole genome sequencing (e.g., Illumina) of nucleic acid isolated from 
uncured subjects at Visit 2 (Day 5-10). Genotyping and sequencing may be performed on nucleic acid 
isolated from different anatomic sites. 
2. The proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae with 
microbiological cure at Visit 2 (Day 5-10) by demographic and clinical characteristics. 


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3.3. 
Study Definitions and Derived Variables  
3.3.1. 
Baseline untreated serine 91 gyrase A genotype N. gonorrhoeae Diagnosis 
For a particular anatomical site, a subject who has not been treated for N. gonorrhoeae prior to enrollment 
into the study will be identified as having untreated serine 91 gyrA N. gonorrhoeae if there is: 
• Detectable N. gonorrhoeae at Visit 1 via culture, i.e. positive N. gonorrhoeae culture from the swab 
taken at Visit 1, and 
• Detection of wild type gyrA by the real-time PCR analysis of the gyrA gene from the swab taken at 
Visit 1. 
3.3.2. 
Microbiological Outcome Status 
1 Microbiological outcome status for the primary analysis is evaluated at Visit 2 and is defined as 
follows: 
• Microbiological Cure: N. gonorrhoeae not detectable by culture from all anatomical sites that had 
detectable N. gonorrhoeae at Visit 1. 
• Microbiological Failure: N. gonorrhoeae detectable by culture from at least one anatomical site 
that had detectable N. gonorrhoeae at Visit 1. 
• Non-evaluable: At least one of the following:  
o Subject did not return for Visit 2, or  
o Culture results at Visit 2 were not available for any reason, or  
o Subject could not be evaluated for microbiological outcome status for any other reason. 
2 For the analysis of secondary objective 1, microbiological outcome status at each anatomical site is 
evaluated at Visit 2 and is defined for a particular anatomical site as follows: 
• Microbiological Cure: N. gonorrhoeae not detectable by culture at the particular anatomical site 
that had detectable N. gonorrhoeae at Visit 1. 
• Microbiological Failure: N. gonorrhoeae detectable by culture at the particular anatomical site that 
had detectable N. gonorrhoeae at Visit 1. 
• Non-evaluable: At least one of the following:  
o Subject did not return for Visit 2, or  
o Culture results at Visit 2 were not available for any reason, or  
o Subject could not be evaluated for microbiological outcome status for any other reason. 
3.3.3. 
Sensitivity of the gyrA assay 
For the analysis of the sensitivity of the gyrA assay for the detection of ciprofloxacin-susceptible 
N. gonorrhoeae infections (secondary objective 2), two measures will be estimated.  First, the sensitivity of 
the assay will be estimated using the following (overall and separately for each anatomical site): 
True Positives (TP): the number wild type gyrA infections that are ciprofloxacin-susceptible N. gonorrhoeae 
as identified by culture-based antimicrobial susceptibility testing at Visit 1.  


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False Negatives (FN): the number of non-wild type gyrA infections that are ciprofloxacin-susceptible 
N. gonorrhoeae as identified by culture-based antimicrobial susceptibility testing at Visit 1. 
Sensitivity = TP / (TP + FN) 
Given the design of the study, the estimate of sensitivity may be biased because subjects with no wild type 
infections are not enrolled and thus their samples are not tested for culture-based susceptibility testing.  To 
supplement the estimates of sensitivity, the assay’s positive predictive value (PPV) will also be estimated.  
PPV is calculated using the following (overall and separately for each anatomical site): 
True Positives (TP): the number wild type gyrA infections that are ciprofloxacin-susceptible N. gonorrhoeae 
as identified by culture-based antimicrobial susceptibility testing at Visit 1. 
False Positives (FP): the number of wild type gyrA infections that are not ciprofloxacin-susceptible 
N. gonorrhoeae as identified by culture-based antimicrobial susceptibility testing at Visit 1. 
PPV = TP / (TP + FP).  
3.3.4. 
Baseline Value 
The baseline value for all variables will be defined as the last value obtained prior to the dose of 
ciprofloxacin. 
3.3.5. 
Within Window Test of Cure Visit 
Version 6.0 of the protocol (03 July 2018) was updated to expand the visit window for Visit 2 from Day 5-9 
to Day 5-10.  For subjects enrolled under version 6.0 (or later) of the protocol, the Test of Cure visit will be 
considered within window if the visit occurred between Days 5 and 10 (inclusive).  For subjects enrolled 
under a version prior to version 6.0, Test of Cure visit will be considered within window if the visit occurred 
between Days 5 and 9 (inclusive). 
3.3.6. 
Treatment Compliance 
A subject will be considered compliant with study treatment if the subject is able to swallow the pill and not 
vomit within 1 hour of administration. Otherwise, the subject will be considered non-compliant. 
3.3.7. 
Symptomatic/Asymptomatic Status 
For female subjects with baseline cervicovaginal infection, subjects will be classified as symptomatic if they 
report any of the following symptoms at baseline: abnormal vaginal discharge, abnormal vaginal bleeding, or 
pain during intercourse.  
For male subjects with baseline urethral infection, subjects will be classified as symptomatic if they report any 
of the following symptoms at baseline: urethral discharge or pain with urination.  
For subjects with baseline rectal infection, subjects will be classified as symptomatic if they report any of the 
following symptoms at baseline: anorectal pain, anorectal discharge, or anorectal bleeding.  
For subjects with baseline pharyngeal infection, subjects will be classified as symptomatic if they report 
having a sore throat at baseline.  
For all anatomic locations, baseline infections are those confirmed by culture. Subjects with baseline 
infections will be considered asymptomatic if they do not affirm these symptoms at baseline. 


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3.3.8. 
Ciprofloxacin Susceptible Infection 
Ciprofloxacin susceptibility will be determined via culture-based antimicrobial susceptibility testing.  An 
infection will be deemed susceptible to ciprofloxacin if the reported minimum inhibitory concentration for the 
isolate is < 1 mcg/ml. 


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4. 
INVESTIGATIONAL PLAN 
4.1. 
Overall Study Design and Plan 
This study is a multi-center, single-arm, open-label clinical study to assess the efficacy of one dose of 
ciprofloxacin given orally in subjects infected with untreated gyrA serine 91 genotype N. gonorrhoeae as 
determined by a real-time PCR assay. The study plans to enroll approximately 381 subjects to obtain a per 
protocol eligible target of 257 subjects age 18 years or older regardless of gender identification who are 
seeking care in STD clinics at participating sites in the United States. Subjects who have untreated gyrA serine 
91 genotype N. gonorrhoeae of the rectum, or male or female urogenital tract identified by a positive culture 
or NAAT conducted at a prior visit are offered enrollment in the study. Subjects not consenting to participate 
in the study receive treatment per local standard of care.  
At enrollment, Visit 1 (Day 1), a brief physical exam and medical and sexual history is performed. Subjects 
have samples collected for N. gonorrhoeae culture and N. gonorrhoeae NAAT (to include gyrA serine 91 
genotype) from each infected anatomic site (throat, rectum, male or female urogenital tract) to verify infection 
status. 
Subjects with gyrA serine 91 genotype rectal or urogenital N. gonorrhoeae receive one dose of directly 
observed ciprofloxacin 500 mg. Subjects are observed in the clinic for at least 5 minutes after receiving 
ciprofloxacin and are instructed to return to the clinic or to contact the study site coordinator immediately if 
they vomit within 1 hour of receiving ciprofloxacin. Subjects who vomit within 1 hour of study drug 
administration should be retreated for N. gonorrhoeae infection with an alternative recommended regimen per 
local standard of care. 
Subjects return for clinical and laboratory assessments at Visit 2 (Day 5-10), the Test of Cure visit. Subjects 
have repeat samples collected for N. gonorrhoeae culture and N. gonorrhoeae NAAT from all anatomic sites 
swabbed at Visit 1 (Day 1). 
For Visit 3 (Day 11-14), test results are provided to subjects by phone call. No further follow-up is required 
for subjects who test culture negative and NAAT negative. Subjects who test culture positive or NAAT 
positive are referred for standard of care treatment for N. gonorrhoeae. 
The duration of the study for each subject is approximately 11-14 days. Table 1 provides the study schematic. 
Table 2 presents the schedule of events for each visit.  
The study is monitored for futility. The number of treatment failures among subjects eligible for the Per 
Protocol (PP) analysis population is monitored by a statistician independent from the study team. If, at any 
point in the trail, 30 subjects eligible for the PP analysis population are classified as treatment failures, then 
the statistician will notify DMID to consider termination of the trial.  
4.2. 
Discussion of Study Design, Including the Choice of Control Groups 
This study is designed as a multi-center, single-arm, open-label clinical study to clinically validate a gyrA 
assay used to determine ciprofloxacin susceptibility in the treatment of uncomplicated gonococcal infection 
by assessing the efficacy of ciprofloxacin for treatment of uncomplicated N. gonorrhoeae infections with 
serine 91 gyrA genotype as identified by the gyrA assay.  
As the study is designed to assess the ability of the gyrA assay to correctly detect subjects with ciprofloxacin-
susceptible N. gonorrhoeae infections, only subjects with infections positively identified by the assay are 
enrolled and all subjects are treated with ciprofloxacin (i.e. there is no control group for this study). 


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4.3. 
Selection of Study Population 
Subjects must meet all of the inclusion criteria in order to be eligible to participate in the study. Subjects who 
present with a new N. gonorrhoeae infection may be rescreened for eligibility. No exemptions are granted on 
Subject Inclusion/Exclusion Criteria in DMID-sponsored studies. 
1. Willing and able to give voluntary written informed consent before any study related procedure is 
performed. 
2. 18 years or older on the day of enrollment. 
3. Untreated gyrA serine 91 genotype N. gonorrhoeae of the rectum, or male or female urogenital tract*, 
as determined by the gyrA test assay on a specimen collected within 30 days of enrollment. 
*Subjects must have gyrA serine 91 genotype detected for N. gonorrhoeae from at least one non-
pharyngeal site. 
4. Willing to abstain from sexual intercourse or use condoms during any sexual contact until the Test of 
Cure Visit (Visit 2, Day 5-10) is complete. 
5. Women of childbearing potential* must have no vaginal intercourse 14 days before enrollment or use 
an effective birth control method ** for 30 days before enrollment and agree to continue through visit 
2. 
*A woman is considered of childbearing potential unless post-menopausal (>2 years) or surgically 
sterilized (tubal ligation >1 year, bilateral oophorectomy, or hysterectomy). 
**Acceptable birth control methods for the purposes of this study may include abstinence from 
intercourse with a male partner, monogamous relationship with vasectomized partner, male condoms 
with the use of applied spermicide, intrauterine devices, and licensed hormonal methods. A highly 
effective method of contraception is defined as one that results in a low failure rate (i.e., less than 1% 
per year) when 
used consistently and correctly. 
6. Able to swallow pills. 
7. Willing to comply with protocol requirements, including availability for follow-up for the duration of 
the study. 
8. Agree to avoid systemic or intravaginal antibiotics* with activity against N. gonorrhoeae from 
enrollment through Visit 2 (Day 5-10). 
*Topical and intravaginal antifungals are permitted. 
9. Agree to avoid magnesium/aluminum antacids, sucralfate, didanosine, or highly buffered drugs, up to 
2 hours after receipt of study drug. 
Subjects meeting any of the following criteria at enrollment will be excluded from the study: 
1. Known renal insufficiency from clinical history. 
2. Use of systemic or intravaginal antibiotics* with potential activity against N. gonorrhoeae within 30 
days prior to study drug administration. 
*Topical and intravaginal antifungals are permitted. 
3. Use of systemic corticosteroid drugs or other immunosuppressive therapy within 30 days prior to 
enrollment. 


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4. Receipt or planned receipt of an investigational product in a clinical trial within 30 days prior to or 7 
days after treatment administration. 
5. Pregnant or breastfeeding.  
6. Clinical diagnosis of pelvic inflammatory disease or genital ulcer. 
7. Confirmed or suspected complicated or systemic gonococcal infection, such as abdominal pain, 
testicular pain, epididymitis, orchitis, arthritis, or endocarditis. 
8. Receipt of magnesium/aluminum antacids, sucralfate, didanosine, or highly buffered drugs, within 6 
hours before receipt of study drug. 
9. Mutant N. gonorrhoeae gyrA serine 91 genotype from any anatomic site, as determined by the gyrA 
test assay on a specimen collected within 30 days of enrollment. 
10. Known allergy or history of adverse reaction to ciprofloxacin.  
11. Known allergy to quinolones.  
12. Previous enrollment in this study.  
13. Medical condition or other factor that in the judgment of the investigator might affect ability to 
comply with procedures. 
Subjects may withdraw or be withdrawn from the study for any of the reasons given below. The reason for 
withdrawal is recorded in the data collection form. 
• Subject vomits within 1 hour of study medication administration. 
• Subject receives any systemic antibiotic other than the study medication prior to Visit 2 (Day 5-
10). 
• Subject is pregnant or breastfeeding. 
• Discretionary decision by the site investigator. 
• At the discretion of the Institutional Review Board (IRB), National Institutes of Health (NIH), or 
other government agency as part of their duties to ensure that research subjects are protected. 
Subjects who withdraw voluntarily prior to receiving ciprofloxacin are offered local standard of care 
treatment for N. gonorrhoeae and followed per clinic guidelines. 
Subjects who withdraw voluntarily or never return after receiving ciprofloxacin and tolerated medication 
without difficulty are not contacted for repeat gonorrhea testing or treatment. 
Subjects who withdraw voluntarily or never return after being found to be positive for N. gonorrhoeae at Visit 
2 (Day 5-10) are contacted by phone and by certified mail with instructions that they should follow-up for 
treatment per local standard of care and should be followed per clinic guidelines. 
Although the study sponsor has every intention of completing the study, the sponsor reserves the right to 
terminate the study at any time for clinical or administrative reasons.  


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4.4. 
Treatments 
4.4.1. 
Treatments Administered  
Subjects with gyrA serine 91 genotype rectal or urogenital N. gonorrhoeae receive one directly observed dose 
of ciprofloxacin 500 mg. Subjects are observed in the clinic for at least 5 minutes after receiving ciprofloxacin 
and are instructed to return to the clinic or to contact the study site coordinator immediately if they vomit 
within 1 hour of receiving ciprofloxacin. Subjects who vomit within 1 hour of study drug administration 
should be retreated for N. gonorrhoeae infection with an alternative recommended regimen per local standard 
of care. 
The dates of the treatment are presented for subjects in the Safety population by site in Table 3. 
4.4.2. 
Identity of Study Product(s) 
Ciprofloxacin is a quinolone medication approved by the FDA for the treatment of gonorrhea. Ciprofloxacin 
hydrochloride, USP, a fluoroquinolone, is the monohydrochloride monohydrate salt of 1- cyclopropyl-6-
fluoro-1, 4-dihydro-4-oxo-7-(1piperazinyl)-3-quinolinecarboxylic acid. The molecular weight of the 
ciprofloxacin hydrochloride monohydrate is 385.82. It is a faintly yellowish to light yellow crystalline 
substance. 
Ciprofloxacin will be supplied as 500 mg tablets. 
4.4.3. 
Method of Assigning Subjects to Treatment Groups (Randomization) 
Not applicable. 
4.4.4. 
Selection and Timing of Dose for Each Subject 
Subjects with gyrA serine 91 genotype rectal or urogenital N. gonorrhoeae receive one dose of ciprofloxacin 
500 mg by mouth under direct observation with the date and time of administration documented.  
4.4.5. 
Blinding 
Not applicable. This is an unblinded study. 
4.4.6. 
Prior and Concomitant Therapy  
Medications history (concomitant medications contraindicated with ciprofloxacin) include a review of all 
current medications and medications taken 30 days prior to study enrollment. Assessment of eligibility also 
include a review of all permitted and prohibited medications per the Subject Inclusion and Exclusion Criteria 
(see Section 4.3). 
Administration of any contraindicated medications or new antibiotics after enrollment are recorded on the 
appropriate data collection form. 
Contraindicated medications include all medications contraindicated with ciprofloxacin (described in 
Section 4.3) taken 30 days prior to signing the informed consent form through Visit 2 or early termination, 
whichever occurs first. 
Subjects who have received study medication and are subsequently diagnosed with a concomitant infection, 
which requires systemic antibiotics receive treatment according to the local clinic’s standard of care. 


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Use of new medication should prompt evaluation for the presence of a new diagnosis of chronic medical 
disease or condition. 
Oral contraceptives are allowed, as they do not alter the metabolism of ciprofloxacin. 
4.4.7. 
Treatment Compliance 
All subjects with gyrA serine 91 genotype rectal or urogenital N. gonorrhoeae will receive single dose of 
directly observed ciprofloxacin 500 mg in the clinic.  
Subjects are observed for at least 5 minutes after administration of ciprofloxacin and are instructed to return to 
the clinic or to contact the study site coordinator immediately if they vomit within 1 hour of receiving study 
medication. Subjects who vomit within 1 hour of study drug administration are retreated for N. gonorrhoeae 
infection with an alternative recommended regimen per the local standard of care. 
See Section 3.3.6 for the definition of treatment compliance. 
4.5. 
Efficacy and Safety Variables 
General principles for safety and efficacy analyses are to accept multiple observations within a specific visit 
period. In the case of multiple observations within a specific window, the assessment value that is closest to 
the scheduled visit window will be used in the analyses for the post-baseline records. The last observed values 
prior to administration of ciprofloxacin will be used as the baseline value. All the recorded data will be listed. 
If observations have the same distance to the scheduled assessment, the latest one will be used.  
4.5.1. 
Safety Variables 
Ciprofloxacin has a well-established safety profile and has been prescribed to several millions of people in the 
United States (US) and worldwide as it was the CDC’s recommended treatment regimen for uncomplicated 
gonorrhea from 1993 to 2007. Therefore, adverse event assessment is not required for this study. 
In order to address the FDA Drug Safety Communication dated May 12, 2016, regarding fluoroquinolone use 
for certain uncomplicated infections, subjects are asked at Visit 1, Visit 2, and any Unscheduled or Early 
Termination Visit if they have experienced any serious side effects related to fluoroquinolone use. These 
include tendon pain, joint pain, muscle pain, tingling or pricking sensation, confusion, and hallucinations. 
This information is recorded in the study source documents as a change in health status. 
Any subject who experiences such an event is given instructions on how to submit a MedWatch Consumer 
Voluntary Reporting Form to the FDA if they desire. 
Side effects of fluoroquinolone use will be summarized for all enrolled subjects (see Section 9). 
4.5.2. 
Efficacy Variables 
See Section 3.3 for efficacy variable definitions.  


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5. 
SAMPLE SIZE CONSIDERATIONS 
The primary analysis will compute the proportion of ciprofloxacin-susceptible N. gonorrhoeae-infected 
subjects with microbiological cure 5-10 days after receiving ciprofloxacin in the per-protocol analysis 
population. The confidence interval for the microbiological cure proportion will be computed using a one-
sided modified Jeffreys interval using a significance level of 0.05. Power calculations were performed via a 
simulation study based on 10,000 replications assuming a 98% microbiological cure rate. 
Figure 1 presents the power available to test that the microbiological cure rate is at least 95% (i.e., lower 
bound of the one-sided confidence interval is at least 95%) across a range of evaluable sample sizes. Here, 
evaluable denotes eligible for the PP analysis population. The power reaches 80% at a sample size of 195 
evaluable subjects; however, since the power curve is not monotonic, sample sizes directly on either side of 
195 are below 80%. Since the exact number of evaluable subjects at the end of the study is difficult to predict, 
an evaluable target of 257 subjects is chosen to ensure at least 80% even if the exact number of evaluable 
subjects at the end of the study differs slightly from 257. With a target of 257, the power available is 
approximately 85% and we can fall at most 10 subjects short (sample size of 247 evaluable subjects) and still 
ensure 80% power. Any sample size greater than 257 will ensure at least 80% power.  
To calculate the number of subjects required to enroll to reach 257 subjects in the PP analysis population, the 
following assumptions are made: 
• 25% of enrolled subjects will be culture negative at baseline. 
• 10% of subjects will be excluded from the PP analysis population (reasons for exclusion are stated 
in Section 6.3) 
Under these assumptions, enrolling 381 subjects will provide 257 subjects in the PP analysis population. 
Since the proportion of subjects who will be culture negative at baseline can vary depending on a number of 
factors, 25% is a rough estimate. The exact number of subjects needed to provide 257 subjects in the PP 
analysis population may vary from 381, so 381 is an approximate enrollment target. 


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6. 
GENERAL STATISTICAL CONSIDERATIONS 
6.1. 
General Principles 
Tabulations will be used extensively to summarize the data. All continuous variables will be summarized 
using some or all of the following descriptive statistics: n (samples size), mean, standard deviation, median, 
maximum, and minimum. The frequency and percentages (based on the sample size) of observed levels will 
be reported for all categorical measures. Modified Jeffreys confidence intervals (CIs) for binomial proportions 
will be computed for efficacy variables [2]. A 5% one-sided significance level will be used; i.e. one-sided 
95% confidence intervals will be generated. In general, all data will be listed, sorted by site and subject, and 
when appropriate by visit number within subject. All summary tables will be annotated with the total 
population size relevant to that table, including any missing observations. 
Note that in the data listing, Subject ID is the unique subject identifier, not the Study ID used on study, and 
dates will not be included, only Study Day. Study Day 1 will be the day of the dose of treatment.  
6.1.1. 
Pseudo Code 
The following SAS® pseudo code will be used to calculate the following: 
Lower bound of the one-sided 95% Jeffreys CI for proportions/percentages if the number of cures is less than 
the number of subjects included in the analysis: 
proc freq; 
   tables cure / alpha=0.1 binomial(jeffreys); 
run; 
Lower bound of the one-sided 95% Jeffreys CI for proportions/percentages if the number of cures is equal to 
the number of subjects (n) included in the analysis: 
CILower = 0.05**(1/n); 
 
95% Wilson CI for proportions/percentages: 
proc freq; 
Table treatment*analysisvariable / alpha=0.1 binomial(wilson); 
    
ods output binomialcls=outputdsn; 
run; 
 
95% Exact Blaker CI for proportions/percentages: 
proc freq; 
Table treatment*analysisvariable / alpha=0.1 binomial(blaker); 
ods output binomialcls=outputdsn; 
run; 
 
95% Agresti-Coull CI for proportions/percentages: 
proc freq; 
Table treatment*analysisvariable / alpha=0.1 binomial(AC); 
ods output binomialcls=outputdsn; 
run; 
 
 


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6.2. 
Timing of Analyses 
The final analysis will be performed after database lock when all subjects have been followed through Visit 3, 
the final study visit.  
6.3. 
Analysis Populations 
6.3.1. 
Safety Analyses 
There are no formal analyses of safety data (see Section 4.5.1 and Section 9). 
6.3.2. 
Efficacy Analyses 
All efficacy analyses will be performed in the Per Protocol (PP), microbiological Intent-to Treat (micro-ITT) 
and Intent-to-Treat (ITT) analyses populations. 
6.3.2.1. 
Intent-to-Treat Analysis (ITT) Population 
The ITT analysis population includes all enrolled subjects, regardless of whether they received study 
treatment or were compliant with the administration procedures or schedule. 
Subjects with non-evaluable outcome status will be included in the ITT analysis population and classified as 
microbiological failures. Subjects who receive any treatment other than the study medication for their 
N. gonorrhoeae infection will be included in all efficacy analyses as treatment failures. Subjects who 
discontinued early from the study with lack of treatment effect being the documented reason for 
discontinuation will be included as microbiological failures. Subjects who vomited within 1 hour of 
administration will be included as microbiological failures. 
6.3.2.2. 
Microbiological Intent-to-Treat (micro-ITT) Population 
For the primary analysis, the micro-ITT population includes all enrolled subjects who have wild type gyrA 
serine 91 N. gonorrhoeae isolated from the rectum or urogenital site on Day 1 culture. Subjects with 
infections at multiple anatomic sites are included as long as one of the infected sites is the rectum or 
urogenital site. Subjects with infections at multiple anatomic sites must be wild- type at each culture-positive 
site to be included in the primary analysis.   
Subjects with non-evaluable outcome status will be included in the micro-ITT population and classified as 
microbiological failures. Subjects who discontinued early from the study with lack of treatment effect being 
the documented reason for discontinuation will be included as microbiological failures. Subjects who vomited 
within 1 hour of administration will be included as microbiological failures. 
For the analysis of secondary objective 1, subjects need to have wild type gyrA serine 91 N. gonorrhoeae 
isolated on Day 1 culture at the particular anatomical site being assessed. The results at the other anatomical 
sites will not be considered when determining a subject’s eligibility into each of the site-specific populations. 
There will be four micro-ITT populations identified: 
• Primary micro-ITT population 
• Rectal micro-ITT population 
• Urogenital micro-ITT population 
• Pharyngeal micro-ITT population 


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6.3.2.3. 
Per Protocol Population 
For the primary outcome measure, the PP population includes enrolled subjects who met all 
inclusion/exclusion criteria, have wild type gyrA serine 91 N. gonorrhoeae isolated on Day 1 culture from the 
rectum or urogenital site, have an evaluable microbiological outcome status (see Section 3.3.2), complied with 
study treatment, did not receive any contraindicated medication or systemic antibiotic other than the study 
medication for any infection prior to Visit 2, and returned for their Visit 2 (Test of Cure) visit within window. 
Subjects with infections at multiple anatomic sites are included as long as one of the infected sites is the 
rectum or urogenital site.  
In addition, subject who are infected at multiple anatomic sites must meet either of the two following criteria 
to be included in the PP population: 
• wild-type at each culture positive site, or 
• wild-type at the rectum/urogenital site and unknown gyrA status at the pharyngeal site (due to 
indeterminate or missing result).   
For subjects who meet the second criteria above, the pharyngeal results will be ignored in the determination of 
cure status. 
For the PP analysis population, subjects with non-evaluable outcome status will be excluded from the 
analysis. Subjects who discontinued early from the study with lack of treatment effect being the documented 
reason for discontinuation will be included as microbiological failures. 
For the analysis of secondary objective 1, subjects need to have wild type gyrA serine 91 N. gonorrhoeae 
isolated on Day 1 culture at the particular anatomical site being assessed. In addition, alternate per-protocol 
analyses which exclude subjects with reported concomitant infection/disease/procedure that may interfere 
with study product, use of concomitant medications or products that may interfere with study product, 
significant protocol deviations, and other events that may impact study product effectiveness or study 
analyses will be explored. Exclusions from this alternate PP population will be determined on a case-by-case 
basis prior to database lock.  
There will be four PP populations and identified based on wild type gyrA serine 91 N. gonorrhoeae isolation 
at Day 1 for a particular site. The results at the other anatomical sites will not be considered when determining 
a subject’s eligibility into each of the site-specific populations. 
• Primary PP population 
• Rectal PP population 
• Urogenital PP population 
• Pharyngeal PP population 
6.3.3. 
Considerations for all Analysis Populations 
Table 4 summarizes the ITT, micro-ITT, and PP analysis population eligibilities for the analysis of the 
primary outcome measure and reasons excluded. Subjects will be included in the count for a particular reason 
for exclusion if they met that criterion. As subjects may meet more than one criterion for exclusion, the 
“Excluded from…” counts may be less than the sum of the individual reason counts. A listing of the subjects 
excluded from each of the analysis populations and the reasons for exclusion will be provided (Listing 1). 


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6.4. 
Covariates and Subgroups 
The protocol does not define any formal subgroup analyses for the primary endpoint, and the study is not 
adequately powered to perform subgroup analyses. However, the secondary efficacy analyses will be 
performed within each anatomical site and the exploratory analyses will be performed within each 
demographic subgroup and clinical characteristics subgroup (see Section 8.3). In addition, enrollment 
summaries will be presented by clinical site (see Section 6.7).  
6.5. 
Missing Data 
For the primary analysis, subjects with non-evaluable outcome status will be included in the micro-ITT 
analysis population and classified as microbiological failures. Subjects who discontinued early from the study 
with lack of treatment effect being the documented reason for discontinuation will be included as 
microbiological failures. 
For the PP analyses of the primary outcome measure, subjects who have a non-evaluable outcome status, 
including subjects who did not return for Visit 2, whose culture results at Visit 2 were not available for any 
reason, or could not be evaluated for microbiological outcome status for any other reason are excluded. 
For the secondary analysis of microbiological cure at each anatomic site using site-specific micro-ITT 
analysis populations, subjects with non-evaluable outcome status at the particular anatomic site will be 
included in analyses and classified as microbiological failures.  
Subjects who discontinued early from the study due to a lack of treatment effect are counted in all analysis 
populations as microbiological failures. 
For secondary outcome of the sensitivity of the gyrA assay for detection of ciprofloxacin-susceptible 
N. gonorrhoeae infections, only specimens with determinate results for both the gyrA assay and the culture-
based antimicrobial susceptibility test will be included. If either the gyrA assay or the culture-based 
antimicrobial susceptibility test results are indeterminate or missing, the specimen will be excluded from the 
analysis. 
6.6. 
Interim Analyses and Data Monitoring 
There are no planned interim analyses for this study. However, the study is monitored for futility. The number 
of treatment failures among subjects eligible for PP analysis population is monitored by a statistician 
independent from the study team. If, at any point in the trail, 30 subjects eligible for the PP analysis 
population are classified as microbiological failures, then the statistician will notify DMID to consider 
termination of the trail. 
6.7. 
Multicenter Studies 
Data will be pooled across all clinical sites. Center effects are not anticipated because the treatment is self-
administered, the sites are using standardized procedures for assessment of serious side effects related to 
fluoroquinolone use and the collection and testing (via culture and NAAT) of specimens.   
Screening, enrollment, subject demographics, baseline characteristics and disposition, and protocol deviations 
will be summarized by clinical site. 
6.8. 
Multiple Comparisons/Multiplicity 
No adjustments for multiple testing are planned. 


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7. 
STUDY SUBJECTS 
7.1. 
Disposition of Subjects 
The disposition of subjects in the study will be tabulated by site and all subjects. Table 5 shows the number of 
subjects who are screen failures and number of subjects that met each inclusion/exclusion criterion. Table 6 
shows the total number of subjects enrolled, treated, compliant with study treatment and completing each visit 
(Visit 1 through Visit 3). A listing of subjects who completed the study, terminated early from study and the 
reason for early termination is included in Listing 2. 
Figure 2 is a flowchart showing the disposition of study subjects in the safety and efficacy analyses, adapted 
from the CONSORT statement [1]. It shows the number of subject eligible, enrolled and randomized, lost to 
follow-up, and analyzed for the safety and efficacy analyses. 
7.2. 
Protocol Deviations 
A summary of subject-specific protocol deviations will be presented by the deviation category and the type of 
deviation for all enrolled subjects (Table 7). All subject-specific protocol deviations and non-subject-specific 
protocol deviations are provided in data listings (Listing 3 and Listing 4, respectively). 


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8. 
EFFICACY EVALUATION 
8.1. 
Primary Efficacy Analyses 
The primary analysis will test whether the microbiological cure rate of ciprofloxacin in subjects infected with 
gyrA serine 91 genotype N. gonorrhoeae at rectum or urogenital site is greater than or equal to 95%. The cure 
rate will be estimated by the proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae 
with microbiological cure at Visit 2. The microbiological outcome status is defined in Section 3.3.2.  
A formal hypothesis test will be performed with null hypothesis that the proportion of ciprofloxacin-
susceptible (as identified by the gyrA assay) N. gonorrhoeae-infected subjects with microbiological cure 5-9 
(or 10) days after receiving ciprofloxacin is less than 0.95 and alternative hypothesis that the proportion is at 
least 0.95. The test will be performed by calculating the one-sided 95% modified Jeffreys confidence interval 
and comparing it to the value 0.95.  
The summary of microbiological cure number, microbiological cure rate, and one-sided 95% modified 
Jeffreys confidence interval by analysis population will be presented (Table 8). See Section 6.1.1 for 
pseudocode to fit the above analyses. Individual efficacy data is presented in Listing 7. 
8.1.1. 
Sensitivity Analyses 
A sensitivity analysis of the primary outcome will be performed to assess the impact of the choice of 
confidence interval. The primary analysis will be repeated using three different kinds of confidence intervals 
for binomial proportions: Wilson, Agresti-Coull, and Blaker intervals [2]. The summary of microbiological 
cure number, microbiological cure rate, and one-sided 95% confidence intervals by analysis population will 
be presented. See Table 9. 
Additional sensitivity analyses of the primary outcome measure will be performed with modifications to the 
definition of the micro-ITT and PP populations. First, the micro-ITT and PP populations will be modified 
such that subjects with culture-positive but unknown (indeterminate or missing) gyrA results will be included 
as well as subjects with wild-type only infections. For each subject, all infected sites (whether the infection is 
wild-type or unknown) will be considered in determining the subject’s cure status. Next, the primary analysis 
will be repeated in the alternate PP population described in Section 6.3.2.3. See Table 10 . 
8.2. 
Secondary Efficacy Analyses 
The analysis of the first secondary endpoint will proceed using the same methods as the primary efficacy 
analysis using the anatomical site-specific definition of microbiological outcome status (see Section 3.3.2). 
Summaries of the cure rate and associated confidence interval will be generated for each individual 
anatomical site and analysis population (Table 11). 
For the analysis of the second secondary endpoint, the sensitivity and positive predictive value of the gyrA 
assay will be estimated as described in Section 3.3.3. This analysis will be performed by anatomic sites in the 
ITT analysis population. See Table 12.  
The summaries of N. gonorrhoeae culture results, NAAT testing results and gyrA assay results will be 
presented by each anatomical site and visit (Table 13, Table 14, and Table 15). Listing 5 and Listing 6 provide 
a complete listing of individual microbiological results. 


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8.2.1. 
Other Efficacy Analyses 
An analysis of the in vitro minimum inhibitory concentrations against Ciprofloxacin of gonococcal isolates 
from cultures taken at Visit 1 and Visit 2 will be conducted. The number of urogenital, rectal and pharyngeal 
susceptible isolates for a number of antimicrobials, including Azithromycin, Cefixime, Ceftriaxon, 
Ciprofloxacin, Gentamicin, Penicillin, Tetracycline, and Spectinomycin will be summarized for each visit and 
subject’s microbiological outcome status.  
The Median (MIC50), minimum, maximum and 90th percentile (MIC90) MICs to each antimicrobial will also 
be reported at Visit 1 and Visit 2. Beta-lactamase results will be summarized, as well. See Table 16, Table 17, 
Table 18, Table 19, and Table 20. The distribution of MICs in histogram for each antimicrobial by Visit and 
specimen will be shown in Figure 3, Figure 4, Figure 5, Figure 6, Figure 7 and Figure 8. This analysis will be 
performed in the micro-ITT and PP populations. 
8.3. 
Exploratory Efficacy Analyses 
The proportion of subjects infected with gyrA serine 91 genotype N. gonorrhoeae with microbiological cure at 
Visit 2 will be summarized by demographic (sex, age, race, ethnicity) and clinical characteristics 
(symptomatic status and re-exposure status at follow up by anatomic sites). Age will be broken into two 
categories based on the median age: Age < median and Age >=median for each analysis population. The 
microbiological cure rate will be calculated separately for each category. See Table 21 and Table 26. The 
analyses by demographics will be repeated on the infection level, as well (see Table 22, Table 23, Table 24, 
and Table 25).  
The genomic analyses of identification and characterization of non-gyrA gene-dependent mechanisms of 
ciprofloxacin resistance by genotyping and whole genome sequencing of nucleic acid isolated from uncured 
subjects at Visit 2 will be described in a separate statistical analysis plan. 


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9. 
SAFETY EVALUATION 
9.1. 
Demographic and Other Baseline Characteristics 
Summaries of age, sex, ethnicity, and race will be presented by site for all enrolled subjects (ITT population) 
and PP population (Table 27, Table 28). Ethnicity is categorized as Hispanic or Latino, or not Hispanic and 
not Latino. Race is categorized as American Indian or Alaska Native, Asian, Native Hawaiian or Other 
Pacific Islander, Black or African American, White, Multi-Racial, or Unknown. In accordance with NIH 
reporting policy, subjects may self-designate as belonging to more than one race (Multi-Racial) or may refuse 
to identify a race (Unknown), the latter reflected in the electronic Case Report Form (eCRF) as “No” to each 
racial option. Age will be summarized by site for all enrolled subjects and PP population (Table 29, Table 30). 
A summary of signs and symptoms of N. gonorrhoeae will be presented by visit (Table 31). 
Baseline and follow-up sexual history will be summarized for all enrolled subjects (ITT population) 
(Table 32, Table 33). 
Individual subject listings (Appendix 3) will be presented for all demographics and baseline characteristics 
(Listing 8), sexual history (Listing 9, Listing 10, Listing 11), and N. gonorrhoeae symptomatology 
(Listing 12). 
9.2. 
Measurements of Treatment Compliance 
The number of subjects not compliant with study treatment will be presented as part of the subject disposition 
(Table 6). Individual subject listing will be presented for treatment compliance data (Listing 13). 
9.3. 
Adverse Events 
9.3.1. 
Side Effects Related to Fluoroquinolone use 
Summary of side effects related to fluoroquinolone use will be presented by visits (Table 34). Individual 
subject listing will be presented for all side effects related to fluoroquinolone use (Listing 14). 
9.4. 
Pregnancies 
Female subjects who are pregnant at enrollment are excluded from the study. Urine pregnancy testing is 
conducted for females of childbearing potential. Urine collected at Visit 1 is analyzed for detecting 
pregnancies by use of a standard rapid urine βhCG assay (Listing 15).  
9.5. 
Physical Evaluations 
A targeted physical examination is performed at enrollment Visit 1 and Visit 2. The following body systems 
are assessed: Abdomen, Cardiovascular/heart, Extremities, General Appearance, Genitourinary, HEENT, 
Lymph nodes, Musculoskeletal, Neck, Neurological, Pulmonary/Chest, and Skin. Individual subject listings 
will be provided for physical exam findings (Listing 16). 
9.6. 
Concomitant Medications 
Summaries of concomitant medications contraindicated with ciprofloxacin that were taken 30 days prior to 
study enrollment and after enrollment will be presented by the World Health Organization (WHO), 
Anatomical Therapeutic Chemical Classification System (ATC) Level 1 and Level 2 for all enrolled subjects. 
(Table 35). Individual subject listing will be presented for concomitant medication (Listing 17). 


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10. 
PHARMACOKINETICS 
Not applicable.  


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11. 
IMMUNOGENICITY 
Not applicable. 


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12. 
OTHER ANALYSES 
No other analyses are planned.  


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13. 
REPORTING CONVENTIONS 
P-values ≥0.001 and ≤0.999 will be reported to three decimal places; p-values less than 0.001 will be reported 
as “<0.001”; p-values greater than 0.999 will be reported as “>0.999”. The mean, median, standard deviation, 
and other statistics other than quantiles, will be reported to one decimal place greater than the original data. 
Quantiles other than the median will use the same number of decimal places as the original data. Proportions 
will be presented as two decimal places; values greater than zero but <0.01 will be presented as “<0.01”. 
Percentages will be reported to the nearest whole number; values greater than zero but < 1% will be presented 
as “<1”; values greater than 99% but less than 100% will be reported as >99%. Estimated parameters, not on 
the same scale as raw observations (e.g. regression coefficients) will be reported to three significant figures. 


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14. 
TECHNICAL DETAILS 
SAS version 9.4 or above will be used to generate all tables, figures, and listings. 


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15. 
SUMMARY OF CHANGES IN THE CONDUCT OF THE STUDY OR 
PLANNED ANALYSES 
There are no changes in the planned analyses. 


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16. 
REFERENCES 
1. Drummond R. CONSORT Revised: Improving the Reporting of Randomized Clinical Trials. JAMA. 
2001; 285(15):2006-2007. 
2. Brown L, Cai T, DasGupta A. Interval estimation for a binomial proportion. Statistical Science 2001 
16(2):101–33. doi:10.1214/ss/1009213286   


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17. 
LISTING OF TABLES, FIGURES, AND LISTINGS  
Table, figure, and listing shells are presented in Appendices 1, 2, and 3, respectively. 
 


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APPENDICES 


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APPENDIX 1. TABLE MOCK-UPS 
LIST OF TABLES 
Table 1: 
Study Design ...............................................................................................................33 
Table 2: 
Schedule of Study Procedures ....................................................................................34 
Table 3: 
Dates of Treatment by Site .........................................................................................35 
Table 4: 
Analysis Population Eligibilities for Primary Outcome Measure ..............................36 
Table 5: 
Ineligibility Summary of Screen Failures ...................................................................37 
Table 6: 
Subject Disposition – All Enrolled Subjects ..............................................................38 
Table 7: 
Distribution of Protocol Deviations by Category and Type .......................................39 
Table 8: 
Microbiological Cure Rate by Analysis Population ...................................................41 
Table 9: 
Microbiological Cure Rate by Analysis Population and Alternate Confidence 
Interval ........................................................................................................................42 
Table 10: Microbiological Cure Rate by Analysis Population (Alternate Definitions)..............43 
Table 11: Microbiological Cure Rate by Anatomical Site and Analysis Population .................44 
Table 12: Summary of gyrA Assay Results and Culture-Based Antimicrobial 
Susceptibility Testing at Visit 1—ITT population .....................................................45 
Table 13: Culture Results by Time Point and Anatomical Sites ................................................46 
Table 14: NAAT Results by Time Point and Anatomical Sites .................................................47 
Table 15: gyrA Assay Results by Time Point and Anatomical Sites ..........................................48 
Table 16: Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type 
at Visit 1—Micro-ITT population ..............................................................................49 
Table 17: Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type 
at Visit 1—PP population ...........................................................................................50 
Table 18: Beta-lactamase Susceptibility of N. Gonorrhoeae Isolates by Analysis 
Population, Specimen Type, and Visit 1 ....................................................................51 
Table 19: Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type 
and Microbiological Outcome at Visit 2—Micro-ITT population .............................52 
Table 20: Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type 
and Microbiological Outcome at Visit 2—PP population ..........................................53 
Table 21: Microbiological Cure Rate by Demographic Characteristics and Analysis 
Population ...................................................................................................................54 
Table 22: Microbiological Cure Rate by Demographic Characteristics and Analysis 
Population — All Infections .......................................................................................55 
Table 23: Microbiological Cure Rate by Demographic Characteristics and Analysis 
Population — Urethral Infections ...............................................................................55 


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Table 24: Microbiological Cure Rate by Demographic Characteristics and Analysis 
Population — Rectal Infections ..................................................................................55 
Table 25: Microbiological Cure Rate by Demographic Characteristics and Analysis 
Population — Pharyngeal Infections ..........................................................................55 
Table 26: Microbiological Cure Rate by Clinical Characteristics—Micro-ITT 
Population ...................................................................................................................56 
Table 27: Summary of Categorical Demographic and Baseline Characteristics by 
Site—All Enrolled Subjects ........................................................................................57 
Table 28: Summary of Categorical Demographic and Baseline Characteristics by 
Site—PP population....................................................................................................57 
Table 29: Summary of Continuous Demographic and Baseline Characteristics by 
Site—All Enrolled Subjects ........................................................................................58 
Table 30: Summary of Continuous Demographic and Baseline Characteristics—PP 
Population ...................................................................................................................58 
Table 31: Signs and Symptoms of N. Gonorrhoeae by Visit .....................................................59 
Table 32: Summary of Baseline Categorical Sexual History—ITT population .........................60 
Table 33: Summary of Follow-up Categorical Sexual History—All Enrolled Subjects ............61 
Table 34: Side Effects of Fluoroquinolone Use ..........................................................................63 
Table 35: Number and Percentage of Subjects with Prior and Concomitant 
Medications Contraindicated with Ciprofloxacin or Systemic Antibiotics by 
WHO Drug Classification–All Enrolled Subjects ......................................................64 
 


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Table 1: 
Study Design 
 
 


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Table 2: 
Schedule of Study Procedures 
Evaluation  
Screening/ 
Enrollment  
Visit 1 
Day 1 
Visit 2  
Day 5-10 
(Test of Cure) 
Visit 3 
Day 11-143 
(Test of Cure 
Results) 
Unscheduled/ 
Early  
Termination 
Visit5 
Signed consent form 
X 
 
 
 
Confirmation of eligibility criteria 
X 
 
 
 
Medical history for assessment of specific symptoms that are 
potentially related to fluoroquinolone use as described in section 
9, Assessment of Safety 
X 
X 
 
X 
Signs/symptoms 
X 
X 
 
X 
Concomitant medications 
X 
X 
 
X 
Sexual history  
X 
 
 
 
Interim sexual history  
 
X 
 
X 
Targeted physical examination 
X 
X 
 
X 
Rapid urine βhCG pregnancy test (females) 
X 
 
 
 
Speculum examination (females) 
X 
 
 
 
Cervical swab for N. gonorrhoeae culture (females) 
X2 
X2 
 
 
Cervical or vaginal swab for NAAT and gyrA assay (females)1 
X2 
X2 
 
 
Urethral swab for N. gonorrhoeae culture (males) 
X2 
X2 
 
 
Urine specimen for NAAT and gyrA assay (males)1 
X2 
X2 
 
 
Throat swab for N. gonorrhoeae culture and NAAT and gyrA 
assay1 
X2 
X2 
 
 
Rectal swab for N. gonorrhoeae culture and NAAT and gyrA 
assay1 
X2 
X2 
 
 
Study intervention 
X 
 
 
 
Reminder to abstain from sexual intercourse or use condoms  
X 
 
 
X5 
Reminder to bring partners in for treatment 
X 
X 
X 
X 
Follow-up for test of cure results  
 
 
X4 
 
1. GyrA assay required only if NAAT is positive. 
2. Collect specimen at anatomic site of N. gonorrhoeae infection.  
3. Follow-up for test of cure results will be by phone call.  
4. For subjects N. gonorrhoeae culture negative and NAAT negative, no further follow-up required.  Subjects who are N. gonorrhoeae culture 
positive or NAAT positive will be referred for standard of care treatment for N. gonorrhoeae. 
5. Not required at the Early Termination Visit. 
 


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Table 3: 
Dates of Treatment by Site 
[Note:  Dates will be categorized by breaking the calendar year into quarters.]  
Dates of Dosing 
AIDS 
Healthcare 
Foundation 
(N=X) 
Los Angeles 
LGBT Center 
(N=X) 
San Francisco 
Department of 
Public Health 
(N=X) 
Philadelphia 
Department of 
Public Health 
(N=X) 
University of 
Mississippi 
Medical Center 
(N=X) 
Louisiana State 
University 
(N=X) 
University of 
California, San 
Diego Antiviral 
Research 
Center (N=X) 
Whitman-
Walker Health 
(N=X) 
All Subjects 
(N=X) 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
Total (Entire period of 
enrollment) 
x 
xx 
x  
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
DDMMMYYYY-
DDMMMYYYY 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
DDMMMYYYY-
DDMMMYYYY 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
DDMMMYYYY-
DDMMMYYYY 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
DDMMMYYYY-
DDMMMYYYY 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
N= Number of subjects enrolled at each site. 
 


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Table 4: 
Analysis Population Eligibilities for Primary Outcome Measure 
Analysis Populations 
Eligibility Category 
Reason Subjects Excluded 
All Subjects 
(N=X) 
n 
% 
Intent-to-Treat (ITT) Population Eligible for ITT 
 
x 
xx 
Primary Microbiological Intent-
to Treat (Micro-ITT) Population 
Eligible for Primary Micro-
ITT 
 
x 
xx 
Excluded from Primary 
Micro-ITT 
Any Reason 
x 
xx 
Did not meet inclusion/exclusion criteria 
x 
xx 
Did not have rectum/urogenital N. gonorrhoeae 
on Day 1 culture 
x 
xx 
Primary Per-Protocol (PP) 
Population 
Eligible for Primary PP 
 
x 
xx 
Excluded from Primary PP 
Any Reason 
x 
xx 
Did not meet inclusion/exclusion criteria 
x 
xx 
Did not have rectum/urogenital N. gonorrhoeae 
on Day 1 culture 
x 
xx 
Was not compliant with study product 
x 
xx 
Received other contraindicated medication or 
systemic antibiotic other than the study 
medication for any concomitant infection prior 
to Visit 2 (Day 5-10) 
x 
xx 
Did not complete Visit 2 (Test of Cure) visit 
within window 
x 
xx 
Did not have an evaluable microbiological 
outcome status 
x 
xx 
Denominator of percentages is the number of all enrolled subjects (N). 
 


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Table 5: 
Ineligibility Summary of Screen Failures 
 
 
Screen Failures (N=xx) 
Inclusion/Exclusion Category 
Inclusion/Exclusion Criterion 
na 
%b 
Inclusion and Exclusion 
Number of subjects failing any eligibility criterion 
x 
100 
Inclusion 
Any inclusion criterion 
x 
xx 
 
[inclusion criterion 1] 
x 
xx 
 
[inclusion criterion 2] 
x 
xx 
 
[inclusion criterion 3] 
x 
xx 
Exclusion 
Any exclusion criterion 
x 
xx 
 
[exclusion criterion 1] 
x 
xx 
 
[exclusion criterion 2] 
x 
xx 
 
[exclusion criterion 3] 
x 
xx 
Declined Enrollment 
Any Reason 
x 
xx 
 
Time commitment 
x 
xx 
 
Concern of potential risks 
x 
xx 
 
Number of procedures 
x 
xx 
 
Unable to contact subject 
x 
xx 
 
Other 
x 
xx 
a More than one criterion may be marked per subject. 
b Denominator for percentages is the total number of screen failures. 
 


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Table 6: 
Subject Disposition – All Enrolled Subjects 
Subject 
Disposition  
All Subjects 
(N=X) 
n 
% 
Screened 
x 
-- 
Enrolled 
x 
100 
Enrolled with Positive Baseline rectum/urogenital N. gonorrhoeae culture result and with Wild 
type gyrA detected by gyrA assay 
x 
xx 
Enrolled and Received Treatment 
x 
xx 
Complied with Treatment 
x 
xx 
Completed Visit 2, Day 5-10 (Test of Cure) a 
x 
xx 
Completed Visit 3, Day 11-14 (Test of Cure Results)a 
x 
xx 
N = Number of enrolled subjects. 
a Refer to Listing 1 for reasons subjects terminated early. 
 
 


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Table 7: 
Distribution of Protocol Deviations by Category and Type 
Category 
Deviation Type 
All Subjects 
(N=X) 
No. of Subj. 
No. of Dev. 
Eligibility/enrollment 
Any type 
x 
x 
 
Did not meet inclusion criterion 
x 
x 
 
Met exclusion criterion 
x 
x 
 
ICF not signed prior to study procedures 
x 
x 
 
Other 
x 
x 
Treatment administration schedule 
Any type 
x 
x 
 
Out of window visit 
x 
x 
 
Missed visit/visit not conducted 
x 
x 
 
Missed treatment administration 
x 
x 
 
Delayed treatment administration 
x 
x 
 
Other 
x 
x 
Follow-up visit schedule 
Any type 
x 
x 
 
Out of window visit 
x 
x 
 
Missed visit/visit not conducted 
x 
x 
 
Other 
x 
x 
Protocol procedure/assessment 
Any type 
x 
x 
 
Incorrect version of ICF signed 
x 
x 
 
Blood not collected 
x 
x 
 
swab not collected 
x 
x 
 
Urine not collected 
x 
x 
 
Other specimen not collected 
x 
x 
 
Too few aliquots obtained 
x 
x 
 
Specimen result not obtained 
x 
x 
 
Required procedure not conducted 
x 
x 


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Table 7: 
Distribution of Protocol Deviations by Category and Type (Continued) 
Category 
Deviation Type 
All Subjects 
(N=X) 
No. of Subj. 
No. of Dev. 
 
Required procedure done incorrectly 
x 
x 
 
Study product temperature excursion 
x 
x 
 
Specimen temperature excursion 
x 
x 
 
Other 
x 
x 
Treatment administration 
Any type 
x 
x 
 
Required procedure done incorrectly 
x 
x 
 
Study product temperature excursion 
x 
x 
 
Other 
x 
x 
 


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Table 8: 
Microbiological Cure Rate by Analysis Population 
Analysis Population 
Statistic 
All Subjects 
Intent-to-Treat (ITT) Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects, N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% CI, % 
xx.x, 100 
 
 
 
Microbiological Intent-to-Treat (micro-ITT) Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects, N  
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% CI, % 
xx.x, 100 
 
 
 
Per Protocol (PP) Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects, N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% CI, % 
xx.x, 100 
 


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Table 9: 
Microbiological Cure Rate by Analysis Population and Alternate Confidence Interval 
Analysis Population 
Statistic 
All Subjects 
Intent-to-Treat (ITT) Population 
Number of Subjects with Microbiological Cure. n 
x 
 
Number of Subjects, N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% Jeffreys CI*, % 
xx.x, 100 
 
95% Wilson CI, % 
xx.x, 100 
 
95% Agresti-Coull CI, % 
xx.x, 100 
 
95% Blaker CI, % 
xx.x, 100 
Microbiological Intent-to-Treat (micro-ITT) Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects. N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% Jeffreys CI, % 
xx.x, 100 
 
95% Wilson CI, % 
xx.x, 100 
 
95% Agresti-Coull CI, % 
xx.x, 100 
 
95% Blaker CI, % 
xx.x, 100 
Per-Protocol (PP) Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects, N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% Jeffreys CI, % 
xx.x, 100 
 
95% Wilson CI, % 
xx.x, 100 
 
95% Agresti-Coull CI, % 
xx.x, 100 
 
95% Blaker CI, % 
xx.x, 100 
*95% Modified Jeffrey CI is the primary confidence interval. 
 


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Table 10: 
Microbiological Cure Rate by Analysis Population (Alternate Definitions) 
Analysis Population 
Statistic 
All Subjects 
Modified micro-ITT Population 
Number of Subjects with Microbiological Cure. n 
x 
 
Number of Subjects, N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% Jeffreys CI*, % 
xx.x, 100 
Modified PP Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects. N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% Jeffreys CI, % 
xx.x, 100 
Alternate PP Population 
Number of Subjects with Microbiological Cure, n 
x 
 
Number of Subjects. N 
x 
 
Microbiological Cure Rate, % 
xx.x 
 
95% Jeffreys CI, % 
xx.x, 100 
 
 


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Table 11: 
Microbiological Cure Rate by Anatomical Site and Analysis Population 
Analysis Population 
Statistic 
Urethral/Cervical 
Rectal 
Pharyngeal 
All Anatomical Sites 
Intent-to-Treat (ITT) Population 
Number of Infections with Microbiological Cures, n 
x 
x 
x 
x 
 
Number of Infections, N 
x 
x 
x 
x 
 
Microbiological Cure Rate, % 
xx.x 
xx.x 
xx.x 
xx.x 
 
95% CI, % 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
 
 
 
 
 
 
Microbiological Intent-to-Treat (micro-
ITT) Population 
Number of Infections with Microbiological Cure, n 
x 
x 
x 
x 
 
Number of Infections, N 
x 
x 
x 
x 
 
Microbiological Cure Rate, % 
xx.x 
xx.x 
xx.x 
xx.x 
 
95% CI, % 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
 
 
 
 
 
 
Per-Protocol (PP) Population 
Number of Infections with Microbiological Cure, n 
x 
x 
x 
x 
 
Number of Infections, N 
x 
x 
x 
x 
 
Microbiological Cure Rate, % 
xx.x 
xx.x 
xx.x 
xx.x 
 
95% CI, % 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
 
Implementation Notes: The ITT Population, Micro-ITT Population and PP Population will be based on the anatomical site. 


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Table 12: 
Summary of gyrA Assay Results and Culture-Based Antimicrobial Susceptibility Testing at Visit 1—ITT population 
 
 
 
Culture-Based Antimicrobial Susceptibility Testing 
gyrA Assay 
Anatomic Site 
 
Susceptible 
Not Susceptible 
Total 
n 
% 
n 
% 
n 
% 
All Sites 
Wild Type gyrA detected 
xx  
xx 
xx  
xx 
xx  
xx 
Mutant gyrA detected 
xx  
xx 
xx  
xx 
xx  
xx 
Total 
xx  
xx 
xx  
xx 
xx  
100 
Urethral 
Wild Type gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Mutant gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Total 
xx  
xx  
xx  
xx  
xx  
100 
Cervical 
Wild Type gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Mutant gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Total 
xx  
xx  
xx  
xx  
xx  
100 
Rectal 
Wild Type gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Mutant gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Total 
xx  
xx  
xx  
xx  
xx  
100 
Pharyngeal 
Wild Type gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Mutant gyrA detected 
xx  
xx  
xx  
xx  
xx  
xx  
Total 
xx  
xx  
xx  
xx  
xx  
100 
The denominator for percentages is based on the number of instances in which swabs taken from a subject at Visit 1 resulted in a determinate gyrA Assay result and a determinate culture-based 
antimicrobial susceptibility test result. If either gyrA Assay result or culture-based antimicrobial susceptibility test result is indeterminate or missing, both results will be excluded.  Susceptible is defined 
as an MIC of < 1 ug/ml as reported by the antimicrobial susceptibility testing. 
 
Implementation Notes: The ITT Population will be based on the anatomical site. 


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Table 13: 
Culture Results by Time Point and Anatomical Sites 
Time Point 
Result 
Urethral 
(N=X) 
Cervical 
(N=X) 
Rectal 
(N=X) 
Pharyngeal 
(N=X) 
n 
% 
n 
% 
n 
% 
n 
% 
Visit 1 (Day 1) 
Number of Subjects tested 
x 
- 
x 
- 
x 
- 
x 
- 
Positive 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Negative 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Indeterminate 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Visit 2 (Day 5-10) 
Number of Subjects tested 
x 
- 
x 
- 
x 
- 
x 
- 
Positive 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Negative 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Indeterminate 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
N=Number of subjects with culture results at the respective anatomical site. 
The denominator of the percentages is the number of subjects tested at the specified anatomical site and visit. 
 


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Table 14: 
NAAT Results by Time Point and Anatomical Sites 
Time Point 
Result 
Urethral 
(N=X) 
Cervical 
(N=X) 
Rectal 
(N=X) 
Pharyngeal 
(N=X) 
n 
% 
n 
% 
n 
% 
n 
% 
Visit 1 (Day 1) 
Number of Subjects tested 
x 
- 
x 
- 
x 
- 
x 
- 
Positive 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Negative 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Indeterminate 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Visit 2 (Day 5-10) 
Number of Subjects tested 
x 
- 
x 
- 
x 
- 
x 
- 
Positive 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Negative 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Indeterminate 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
N=Number of subjects with NAAT results at the specified anatomical site. 
The denominator of the percentages is the number of subjects tested at the specified anatomical site and visit. 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 15: 
gyrA Assay Results by Time Point and Anatomical Sites 
Time Point 
Result 
Urethral 
Cervical 
Rectal 
Pharyngeal 
n 
% 
n 
% 
n 
% 
n 
% 
Visit 1 (Day 1) 
Number of Subjects tested 
x 
-- 
x 
-- 
x 
-- 
x 
-- 
Wild Type gyrA detected 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Mutant gyrA detected 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Indeterminate 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Visit 2 (Day 5-10) 
Number of Subjects tested 
x 
-- 
x 
-- 
x 
-- 
x 
-- 
Wild Type gyrA detected 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Mutant gyrA detected 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Indeterminate 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
N=Number of subjects with gyrA assay results at the specified anatomical site. 
The denominator of the percentages is the number of subjects with a gyrA assay result at the specified anatomical site and visit. 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
- 49 - 
PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 16: 
Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type at Visit 1—Micro-ITT population 
Specimen 
Antimicrobial 
Number of Subjects 
MIC50 
(µg/ml) 
MIC90 
(µg/ml) 
Range 
(µg/ml) 
Urethral/Cervical 
Azithromycin 
x 
x 
x 
x.x, x.x 
Cefixime 
x 
x 
x 
x.x, x.x 
Ceftriaxone 
x 
x 
x 
x.x, x.x 
Ciprofloxacin 
x 
x 
x 
x.x, x.x 
Gentamicin 
x 
x 
x 
x.x, x.x 
Penicillin 
x 
x 
x 
x.x, x.x 
Tetracycline 
x 
x 
x 
x.x, x.x 
Spectinomycin 
x 
x 
x 
x.x, x.x 
Rectal 
Azithromycin 
x 
x 
x 
x.x, x.x 
Cefixime 
x 
x 
x 
x.x, x.x 
Ceftriaxone 
x 
x 
x 
x.x, x.x 
Ciprofloxacin 
x 
x 
x 
x.x, x.x 
Gentamicin 
x 
x 
x 
x.x, x.x 
Penicillin 
x 
x 
x 
x.x, x.x 
Tetracycline 
x 
x 
x 
x.x, x.x 
Spectinomycin 
x 
x 
x 
x.x, x.x 
Pharyngeal 
Azithromycin 
x 
x 
x 
x.x, x.x 
Cefixime 
x 
x 
x 
x.x, x.x 
Ceftriaxone 
x 
x 
x 
x.x, x.x 
Ciprofloxacin 
x 
x 
x 
x.x, x.x 
Gentamicin 
x 
x 
x 
x.x, x.x 
Penicillin 
x 
x 
x 
x.x, x.x 
Tetracycline 
x 
x 
x 
x.x, x.x 
Spectinomycin 
x 
x 
x 
x.x, x.x 
 
Implementation Notes: The Micro-ITT Population will be based on the anatomical site. 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Tables with similar format: 
Table 17: 
Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type at Visit 1—PP population 
Implementation Notes: The PP Population will be based on the anatomical site. 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 18: 
Beta-lactamase Susceptibility of N. Gonorrhoeae Isolates by Analysis Population, Specimen Type, and Visit 1 
Analysis Population 
Visit 
Specimen 
Number of Subjects 
Positive 
Negative 
n 
% 
n 
% 
Micro-ITT 
1 
Urethral/Cervical 
x 
x 
xx 
x 
xx 
Rectal 
x 
x 
xx 
x 
xx 
Pharyngeal 
x 
x 
xx 
x 
xx 
2 
Urethral/Cervical 
x 
x 
xx 
x 
xx 
Rectal 
x 
x 
xx 
x 
xx 
Pharyngeal 
x 
x 
xx 
x 
xx 
Per-Protocol 
1 
Urethral/Cervical 
x 
x 
xx 
x 
xx 
Rectal 
x 
x 
xx 
x 
xx 
Pharyngeal 
x 
x 
xx 
x 
xx 
2 
Urethral/Cervical 
x 
x 
xx 
x 
xx 
Rectal 
x 
x 
xx 
x 
xx 
Pharyngeal 
x 
x 
xx 
x 
xx 
 
Implementation Notes: The Micro-ITT Population and PP Population will be based on the anatomical site. 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 19: 
Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type and Microbiological Outcome at Visit 2—Micro-ITT 
population 
Specimen 
Subject Microbiological Outcome 
Antimicrobial 
Number of 
Subjects 
MIC50 
(µg/ml) 
MIC90 
(µg/ml) 
Range 
(µg/ml) 
Urethral/Cervical 
Microbiological Cure 
Azithromycin 
x 
x 
x 
x.x, x.x 
Cefixime 
x 
x 
x 
x.x, x.x 
Ceftriaxone 
x 
x 
x 
x.x, x.x 
Ciprofloxacin 
x 
x 
x 
x.x, x.x 
Gentamicin 
x 
x 
x 
x.x, x.x 
Penicillin 
x 
x 
x 
x.x, x.x 
Tetracycline 
x 
x 
x 
x.x, x.x 
Spectinomycin 
x 
x 
x 
x.x, x.x 
Microbiological Failure 
Azithromycin 
x 
x 
x 
x.x, x.x 
Cefixime 
x 
x 
x 
x.x, x.x 
Ceftriaxone 
x 
x 
x 
x.x, x.x 
Ciprofloxacin 
x 
x 
x 
x.x, x.x 
Gentamicin 
x 
x 
x 
x.x, x.x 
Penicillin 
x 
x 
x 
x.x, x.x 
Tetracycline 
x 
x 
x 
x.x, x.x 
Spectinomycin 
x 
x 
x 
x.x, x.x 
Overall 
Azithromycin 
x 
x 
x 
x.x, x.x 
Cefixime 
x 
x 
x 
x.x, x.x 
Ceftriaxone 
x 
x 
x 
x.x, x.x 
Ciprofloxacin 
x 
x 
x 
x.x, x.x 
Gentamicin 
x 
x 
x 
x.x, x.x 
Penicillin 
x 
x 
x 
x.x, x.x 
Tetracycline 
x 
x 
x 
x.x, x.x 
Spectinomycin 
x 
x 
x 
x.x, x.x 
Etc. for other sites (Rectal and Pharyngeal) 
The denominator for rate estimates is based on the number of subjects enrolled and eligible for the micro-ITT population for the particular anatomical site and microbiological outcome. 
Implementation Notes: The Micro-ITT Population will be based on the anatomical site. 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Tables with similar format: 
Table 20: 
Antimicrobial Susceptibility of N. Gonorrhoeae Isolates by Specimen Type and Microbiological Outcome at Visit 2—PP 
population 
Implementation Notes: The Micro-ITT Population will be based on the anatomical site. 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 21: 
Microbiological Cure Rate by Demographic Characteristics and Analysis Population 
Characteristic 
Analysis Population 
ITT Population 
micro-ITT Population 
PP Population 
Number of 
Subjects with 
Microbiological 
Cure, n 
Number 
of 
subjects, 
N 
Cure 
Rate, % 
Cure Rate 95% 
CI, % 
Number of 
Subjects with 
Microbiological 
Cure. n 
Number 
of 
subjects, 
N 
Cure 
Rate, % 
Cure Rate 
95% CI, % 
Number of 
Subjects with 
Microbiological 
Cure, n 
Number 
of 
subjects, 
N 
Cure 
Rate, % 
Cure Rate 
95% CI, % 
Male 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Female 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Age < Median 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Age >= median 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
American 
Indian/ 
Alaskan Native 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx. 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Asian 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Hawaiian/ 
Pacific Islander 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
White 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Multi-Racial 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Other/Unknown 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Non-Hispanic 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Hispanic 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
Not Reported/ 
Unknown 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
x 
x 
xx.x 
xx.x, 100 
 
 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Tables with similar format: 
Table 22: 
Microbiological Cure Rate by Demographic Characteristics and Analysis Population — All Infections 
Table 23: 
Microbiological Cure Rate by Demographic Characteristics and Analysis Population — Urethral Infections 
Table 24: 
Microbiological Cure Rate by Demographic Characteristics and Analysis Population — Rectal Infections 
Table 25: 
Microbiological Cure Rate by Demographic Characteristics and Analysis Population — Pharyngeal Infections 
Implementation Notes: The analysis populations will be based on the anatomical site. 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 26: 
Microbiological Cure Rate by Clinical Characteristics—Micro-ITT Population 
Statistics 
Cervical 
Urethral 
Rectal 
Pharyngeal 
All Anatomical Sites 
Symptomatic Status 
Symptomatic Status 
Symptomatic Status 
Symptomatic Status 
Symptomatic Status 
Symptomatic 
Asymptomatic 
Symptomatic 
Asymptomatic 
Symptomatic 
Asymptomatic 
Symptomatic 
Asymptomatic 
Symptomatic 
Asymptomatic 
Number of 
Infections with 
Microbiological 
Cure, n 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Number of 
Infections, N 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Microbiological 
Cure Rate 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
Microbiological 
Cure Rate 95% CI, 
%  
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
 
 
 
 
 
 
 
 
 
 
 
 
Re-exposure at Follow up 
Re-exposure at Follow up 
Re-exposure at Follow up 
Re-exposure at Follow up 
Re-exposure at Follow up 
 
Sex with 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Sex without 
Protection 
Number of 
Infections with 
Microbiological 
Cure, n 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Number of 
Infections, N 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Microbiological 
Cure Rate, % 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
Microbiological 
Cure Rate 95% CI, 
% 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
xx.x, 100 
 
Implementation Notes: The Micro-ITT Population will be based on the anatomical site. 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
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PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 27: 
Summary of Categorical Demographic and Baseline Characteristics by Site—All Enrolled Subjects 
Variable 
Characteristic 
AIDS 
Healthcare 
Foundation 
(N=X) 
Los Angeles 
LGBT Center 
(N=X) 
San Francisco 
Department of 
Public Health 
(N=X) 
Philadelphia 
Department of 
Public Health 
(N=X) 
University of 
Mississippi 
Medical Center 
(N=X) 
Louisiana State 
University 
(N=X) 
University of 
California, San 
Diego Antiviral 
Research Center 
(N=X) 
Whitman-
Walker 
Health (N=X) 
All Subjects 
 (N=X) 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
n 
% 
Sex  
Male 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Female 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Ethnicity  
Not Hispanic or 
Latino 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Hispanic or Latino 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Not Reported 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Unknown 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
Race  
American Indian or 
Alaska Native 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Asian 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Native Hawaiian or 
Other Pacific 
Islander 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Black or African 
American 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
White 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Multi-Racial 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
 
Unknown 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
x 
xx 
N= Number of subjects enrolled at each site. 
Tables with similar format: 
Table 28: 
Summary of Categorical Demographic and Baseline Characteristics by Site—PP population 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
- 58 - 
PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 29: 
Summary of Continuous Demographic and Baseline Characteristics by Site—All Enrolled Subjects 
Variable 
Statistic 
AIDS 
Healthcare 
Foundation 
(N=X) 
Los Angeles 
LGBT Center 
(N=X) 
San Francisco 
Department of 
Public Health 
(N=X) 
Philadelphia 
Department of 
Public Health 
(N=X) 
University of 
Mississippi 
Medical Center 
(N=X) 
Louisiana State 
University 
(N=X) 
University of 
California, San 
Diego Antiviral 
Research 
Center (N=X) 
Whitman-
Walker Health 
(N=X) 
All Subjects 
 (N=X) 
Age 
Mean 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
 
Standard Deviation 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
 
Median 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
xx.x 
 
Minimum 
x 
x 
x 
x 
x 
x 
x 
x 
x 
 
Maximum 
x 
x 
x 
x 
x 
x 
x 
x 
x 
N=Number of subjects enrolled at each site. 
Tables with similar format: 
Table 30: 
Summary of Continuous Demographic and Baseline Characteristics—PP Population 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
- 59 - 
PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 31: 
Signs and Symptoms of N. Gonorrhoeae by Visit  
Summary 
Visit 1 
(N = x) 
Visit 2 
(N = x) 
Visit 3* 
(N=x) 
n 
% 
n 
% 
n 
% 
Males assessed for signs/symptoms 
x 
- 
x 
- 
x 
- 
Females assessed for signs/symptoms 
x 
- 
x 
- 
x 
- 
Subjects with any symptoms of gonorrhea 
x 
xx 
x 
xx 
x 
xx 
Signs/Symptoms for Males and Females 
 
 
 
 
 
 
Sore Throat1 
x 
xx 
x 
xx 
x 
xx 
Anorectal Pain1 
x 
xx 
x 
xx 
x 
xx 
Anorectal Discharge (subject-reported) 1 
x 
xx 
x 
xx 
x 
xx 
Anorectal Discharge (observed) 1 
x 
xx 
x 
xx 
x 
xx 
Anorectal Bleeding1 
x 
xx 
x 
xx 
x 
xx 
Pharyngeal Erythema (observed) 1 
x 
xx 
x 
xx 
x 
xx 
Signs/Symptoms for Males Only 
 
 
 
 
 
 
Urethral Discharge (subject-reported)2 
x 
xx 
x 
xx 
x 
xx 
Urethral Discharge (observed) 2 
x 
xx 
x 
xx 
x 
xx 
Pain with Urination2 
x 
xx 
x 
xx 
x 
xx 
Signs/Symptoms for Females Only 
 
 
 
 
 
 
Abnormal Vaginal Discharge (subject-reported)3 
x 
xx 
x 
xx 
x 
xx 
Abnormal Cervical Discharge (observed) 3 
x 
xx 
x 
xx 
x 
xx 
Abnormal Vaginal Bleeding3 
x 
xx 
x 
xx 
x 
xx 
Pain during Intercourse3 
x 
xx 
x 
xx 
x 
xx 
 N is the number of subjects assessed for signs/symptoms at the particular visit. 
‘n’ represents the number of subjects who reported each sign or symptom at the Visit(s) indicated. 
The same subject may be counted at all visits;  
*Only some subjects have data at Visit 3 due to the protocol amendment. 
1 The denominator of the percentage is the number of subjects for each visit. 
2 The denominator of the percentage is the number of males for each visit. 
3 The denominator of the percentage is the number of females for each visit. 
 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
- 60 - 
PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 32: 
Summary of Baseline Categorical Sexual History—ITT population 
Sexual History Interview Question 
Value 
All Subjects 
(N=X) 
n 
% 
1. 
What is your gender identity? 
Man 
x 
xx 
Woman 
x 
xx 
Trans male/Trans man 
x 
xx 
Trans female/Trans woman 
x 
xx 
Genderqueer/Gender non-conforming 
x 
xx 
Multiple 
x 
xx 
Other 
x 
xx 
Refused to Answer 
x 
xx 
2. 
What is your sexual orientation? 
Heterosexual/Straight 
x 
xx 
Homosexual/gay/lesbian 
x 
xx 
Bisexual 
x 
xx 
Other 
x 
xx 
Refused to Answer 
x 
xx 
3. 
Do you have sex with men, women, transgender men, transgender 
women, or multiple genders? 
Men 
x 
xx 
Women 
x 
xx 
Trans male/Trans man 
x 
xx 
Trans female/Trans woman 
x 
xx 
Multiple 
x 
xx 
Refused to Answer 
x 
xx 
4. 
Have you had sex (vaginal, anal, or oral) in the past 30 days? 
Yes 
x 
xx 
No 
x 
xx 
Refuse to answer 
x 
xx 
N=Number of all enrolled subjects 


Statistical Analysis Plan - DMID Protocol: 15-0090  
Version 1.0 
08APR2019 
- 61 - 
PRIVILEGED AND CONFIDENTIAL COMMUNICATION 
Table 33: 
Summary of Follow-up Categorical Sexual History—All Enrolled Subjects 
Sexual History Interview 
Question 
Value 
Visit 2 
(N=X) 
Unscheduled Visit 
(N=X) 
All Subjects 
(N=X) 
n 
% 
n 
% 
n 
% 
1. 
Have you had sex 
(vaginal, anal, or oral) 
since the last visit? 
Yes 
x 
xx 
x 
xx 
x 
xx 
No 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
2. 
Have you had vaginal 
intercourse since the last 
visit? 
Yes 
x 
xx 
x 
xx 
x 
xx 
No 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
If Yes for question 2, did you 
use a condom with vaginal 
intercourse1 
No 
x 
xx 
x 
xx 
x 
xx 
Always 
x 
xx 
x 
xx 
x 
xx 
Sometimes 
x 
xx 
x 
xx 
x 
xx 
Unknown 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
3. 
Have you given oral 
intercourse since the last 
visit? 
Yes 
x 
xx 
x 
xx 
x 
xx 
No 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
If Yes for question 3, did you 
use a condom or barrier with 
oral intercourse?2 
No 
x 
xx 
x 
xx 
x 
xx 
Always 
x 
xx 
x 
xx 
x 
xx 
Sometimes 
x 
xx 
x 
xx 
x 
xx 
Unknown 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
4. 
Have you received oral 
intercourse since the last 
visit? 
Yes 
x 
xx 
x 
xx 
x 
xx 
No 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
If Yes for question 4, did you 
use a condom or barrier with 
oral intercourse?3 
No 
x 
xx 
x 
xx 
x 
xx 
Always 
x 
xx 
x 
xx 
x 
xx 
Sometimes 
x 
xx 
x 
xx 
x 
xx 
Unknown 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
5. 
Have you had receptive 
'bottom' anal intercourse 
since the last visit? 
Yes 
x 
xx 
x 
xx 
x 
xx 
No 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 


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Table 33: 
Summary of Follow-up Categorical Sexual History — All Enrolled Subjects (Continued) 
Sexual History Interview 
Question 
Value 
Visit 2 
(N=X) 
Unscheduled Visit 
(N=X) 
All Subjects 
(N=X) 
n 
% 
n 
% 
n 
% 
If Yes for question 5, did you 
use a condom with receptive 
anal intercourse?4 
No 
x 
xx 
x 
xx 
x 
xx 
Always 
x 
xx 
x 
xx 
x 
xx 
Sometimes 
x 
xx 
x 
xx 
x 
xx 
Unknown 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
6. 
Have you had insertive 
‘top’ anal intercourse 
since the last visit? 
(Males only)5 
No 
x 
xx 
x 
xx 
x 
xx 
Yes 
x 
xx 
x 
xx 
x 
xx 
Refused to answer 
x 
xx 
x 
xx 
x 
xx 
N/A (if female) 
x 
xx 
x 
xx 
x 
xx 
If Yes for question 6, did you 
use a condom with insertive 
anal intercourse?6 
No 
x 
xx 
x 
xx 
x 
xx 
Always 
x 
xx 
x 
xx 
x 
xx 
Sometimes 
x 
xx 
x 
xx 
x 
xx 
Unknown 
x 
xx 
x 
xx 
x 
xx 
Refuse to answer 
x 
xx 
x 
xx 
x 
xx 
N=Number of enrolled subjects at the specific visit. 
1 The denominator of the percentage for this question is the number of subjects answered “yes” for question 2 at each visit. 
2 The denominator of the percentage for this question is the number of subjects answered “yes” for question 3 at each visit. 
3 The denominator of the percentage for this question is the number of subjects answered “yes” for question 4 at each visit. 
4 The denominator of the percentage for this question is the number of subjects answered “yes” for question 5 at each visit. 
5 The denominator of the percentage for this question is the number of male subjects at each visit. 
6 The denominator of the percentage for this question is the number of male subjects answered “yes” for question 6 at each visit. 
 


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Table 34: 
Side Effects of Fluoroquinolone Use 
Summary 
Visit 1 
(N = x) 
Visit 2 
(N = x) 
Visit 3* 
(N = x) 
n 
% 
n 
% 
n 
% 
Tendon Pain 
x 
xx 
x 
xx 
x 
xx 
Joint Pain 
x 
xx 
x 
xx 
x 
xx 
Muscle Pain 
x 
xx 
x 
xx 
x 
xx 
Tingling or Pricking Sensation 
x 
xx 
x 
xx 
x 
xx 
Confusion 
x 
xx 
x 
xx 
x 
xx 
Hallucinations 
x 
xx 
x 
xx 
x 
xx 
N is the number of subjects whose assessments were collected at the particular visit. 
‘n’ represents the number of subjects who reported each sign or symptom at the Visit(s) indicated. 
The denominator of the percentage is the number of subjects whose assessments were collected at the particular visit. 
The same subject may be counted at all visits. 
*Only some subjects have data at Visit 3 due to the protocol amendment. 


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Table 35: 
Number and Percentage of Subjects with Prior and Concomitant Medications 
Contraindicated with Ciprofloxacin or Systemic Antibiotics by WHO Drug 
Classification–All Enrolled Subjects 
WHO Drug Code 
Level 1, Anatomic Group 
WHO Drug Code 
Level 2, Therapeutic Subgroup 
All Subjects 
(N=X) 
n 
% 
Any Level 1 Codes 
Any Level 2 Codes 
x 
x 
[ATC Level 1 - 1] 
Any  
x 
x 
 
[ATC 2 - 1] 
x 
x 
 
[ATC 2 - 2] 
x 
x 
 
[ATC 2 - 3] 
x 
x 
[ATC Level 1 – 2] 
Any 
x 
x 
 
[ATC 2 - 1] 
x 
x 
 
[ATC 2 - 2] 
x 
x 
 
[ATC 2 - 3] 
x 
x 
N= Number of all enrolled subjects 
n=Number of subjects reporting taking at least one medication in the specific WHO Drug Class. 
 


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APPENDIX 2. FIGURE MOCK-UPS 
LIST OF FIGURES 
Figure 1: 
Sample Size/Probability Estimates .............................................................................66 
Figure 2: 
CONSORT Flow Diagram .........................................................................................67 
Figure 3: 
Histogram: MIC distribution for Antimicrobials by Visit— 
Urethral/Cervical— Micro-ITT population ................................................................68 
Figure 4: 
Histogram: MIC distribution for Antimicrobials by Visit— Rectal— Micro-
ITT population ............................................................................................................68 
Figure 5: 
Histogram: MIC distribution for Antimicrobials by Visit— Pharyngeal — 
Micro-ITT population .................................................................................................68 
Figure 6: 
Histogram: MIC distribution for Antimicrobials by Visit— Urethral/Cervical 
— PP population .........................................................................................................68 
Figure 7: 
Histogram: MIC distribution for Antimicrobials by Visit— Rectal— PP 
population ...................................................................................................................68 
Figure 8: 
Histogram: MIC distribution for Antimicrobials by Visit— Pharyngeal — 
Micro-ITT population .................................................................................................68 
 


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Figure 1: 
Sample Size/Probability Estimates  
 
 


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Figure 2: 
CONSORT Flow Diagram 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Received intervention (n=x) 
Did not receive intervention (n=x) 
♦   [Reason 1] (x) 
♦   [Reason 2] (x) 
Intervention 
Primary Analysis 
Follow-Up 
Enrollment 
Assessed for Eligibility (n=x) 
Excluded* (n=x) 
♦   See Table 5 for reasons for screen 
failures 
♦   Concern of potential risk (n=x) 
Completed Follow-up (n=x) 
Terminated Early (n=x) 
♦[Reason 1] (x) 
♦[Reason 2] (x) 
Included in Primary ITT analysis (n=x) 
Included in Primary micro-ITT analysis (n=x) 
♦Excluded from primary micro-ITT analyses (n=x) 
[Reason 1] (x) 
[Reason 2] (x) 
Included in Primary PP analysis (n=x) 
♦Excluded from primary PP analyses (n=x) 
[Reason 1] (x) 
[Reason 2] (x) 
Analyzed for safety (n=x) 
♦Excluded from safety analyses (n=x) 
[Reason 1] (x), [Reason 2] (x) 


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Figure 3: 
Histogram: MIC distribution for Antimicrobials by Visit— 
Urethral/Cervical— Micro-ITT population  
 
Implementation notes: 
The figure will be a paneled figure with specimen as columns and visits as rows.  
 
Figures with similar format:  
Figure 4: 
Histogram: MIC distribution for Antimicrobials by Visit— Rectal— Micro-
ITT population  
Figure 5: 
Histogram: MIC distribution for Antimicrobials by Visit— Pharyngeal — 
Micro-ITT population 
Figure 6: 
Histogram: MIC distribution for Antimicrobials by Visit— 
Urethral/Cervical — PP population 
Figure 7: 
Histogram: MIC distribution for Antimicrobials by Visit— Rectal— PP 
population 
Figure 8: 
Histogram: MIC distribution for Antimicrobials by Visit— Pharyngeal — 
Micro-ITT population 
 


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APPENDIX 3. LISTINGS MOCK-UPS 
LISTINGS 
Listing 1: Subject Disposition .....................................................................................................70 
Listing 2: Subjects Excluded from Primary Analysis Populations .............................................71 
Listing 3: Subject-Specific Protocol Deviations .........................................................................72 
Listing 4: Non-Subject-Specific Protocol Deviations .................................................................73 
Listing 5: Microbiological Results ..............................................................................................74 
Listing 6: Clinical Laboratory Results – Urine Pregnancy Test .................................................75 
Listing 7: Individual Efficacy Data .............................................................................................76 
Listing 8: Demographic and Baseline Characteristics Data—All Enrolled Subjects .................77 
Listing 9: Sexual History at Baseline Visit—All Enrolled Subjects ...........................................78 
Listing 10: Sexual History at Follow-up Visit—All Enrolled Subjects ........................................79 
Listing 11: Sexual History at Follow-up Visit—All Enrolled Subjects ........................................80 
Listing 12: N. Gonorrhoeae Symptomatology..............................................................................81 
Listing 13: Compliance Data ........................................................................................................82 
Listing 14: Side Effects Related to Fluoroquinolone ....................................................................83 
Listing 15: Baseline Pregnancy Test Results ................................................................................84 
Listing 16: Physical Exam Findings .............................................................................................85 
Listing 17: Concomitant Medications ...........................................................................................86 
 


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Listing 1: 
Subject Disposition 
Subject ID 
Category 
Study Day Corresponding to Early 
Termination/Protocol Completion 
Reason for Early Termination  
xxxxxx 
Protocol completed/ 
Early termination 
x 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 
xxxxxx 
Protocol completed/ 
Early termination 
x 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 
xxxxxx 
Protocol completed/ 
Early termination 
x 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 
 
Implementation Notes: 
1. Sort order will be by Subject ID, Category. 
2. Category will be “Early Termination” or “Protocol Completed”.  
3. In the “Reason for Early Termination” column, concatenate any “specify” fields, including the DV number. 
 


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Listing 2: 
Subjects Excluded from Primary Analysis Populations 
Subject ID 
Analyses in which 
Subject is Included 
Analyses from which  
Subject is Excluded 
Results Available? 
Reason Subject Excluded 
xxxxxx 
[e.g., ITT, micro-ITT, PP] 
[e.g., ITT, micro-ITT, PP] 
Yes/No 
xxxxx 
xxxxxx 
[e.g., ITT, micro-ITT, PP] 
[e.g., ITT, micro-ITT, PP] 
Yes/No 
xxxxx 
xxxxxx 
[e.g., ITT, micro-ITT, PP] 
[e.g., ITT, micro-ITT, PP] 
Yes/No 
xxxxx 
xxxxxx 
[e.g., ITT, micro-ITT, PP] 
[e.g., ITT, micro-ITT, PP] 
Yes/No 
xxxxx 
xxxxxx 
[e.g., ITT, micro-ITT, PP] 
[e.g., ITT, micro-ITT, PP] 
Yes/No 
xxxxx 
Note: “Yes” in the “Results available” column indicates that available data were removed from the primary analysis. “No” indicates that no data were available for inclusion in the analysis. 
 
Implementation Notes: 
1. Sort order will be Subject ID. 
2. Reasons Subject excluded should match the same verbiage that is used on the analysis population tables. 
 


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Listing 3: 
Subject-Specific Protocol Deviations 
DV Number 
Study Day 
Deviation 
Deviation 
Category 
Reason for 
Deviation 
Deviation Resulted in 
Subject Termination? 
Deviation 
Resolution 
Comments 
Subject ID:  
xx 
x 
xxxxxxxxxxx 
xxxxxxxxxxxx 
xxxxxxxxxxx 
Yes/No 
xxxxxxxxx 
xxxxxxxxxxxxxxxxxxxxxxxxxxxx 
xx 
x 
xxxxxxxxxxx 
xxxxxxxxxxxx 
xxxxxxxxxxx 
Yes/No 
xxxxxxxxx 
xxxxxxxxxxxxxxxxxxxxxxxxxxxx 
 
Implementation Notes: 
1. Sort order will be by Subject ID, DV number. 
2. In the “Deviation Category” column concatenate any specify fields.  
3. In the “Reason for Deviation” column concatenate any “specify” fields. 
 


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Listing 4: 
Non-Subject-Specific Protocol Deviations 
Site 
Deviation 
Start Date  
End Date 
Reason for 
Deviation 
Deviation Resulted in 
Subject Termination? 
Deviation 
Category 
Deviation 
Resolution 
Comments 
xxxx 
xxxxxxx 
x 
x 
xxxxxxx 
Yes/No 
xxxx 
xxxxxxxx 
xxxxxxxxxxxxxxx 
xxxx 
xxxxxxx 
x 
x 
xxxxxxx 
Yes/No 
xxxx 
xxxxxxxx 
xxxxxxxxxxxxxxx 
 
Implementation Notes: 
1. Sort order will be by Site Name, Start Date. 
2. In the “Deviation Category” column concatenate any specify fields.  
3. In the “Reason for Deviation” column concatenate any “specify” fields. 
 


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Listing 5: 
Microbiological Results  
Study Visit 
Actual 
Study Day  
Sex  
Age (years) 
N. gonorrhoeae 
Culture Result 
NAAT Testing 
Result 
gyrA Assay Results 
Culture-Based Antimicrobial 
Susceptibility Testing 
Anatomical Site 
Subject ID:  
Visit 1 (Day 1) 
x 
xxxxx 
xx 
Negative/ 
Positive/ 
Indeterminate/ 
Not Done 
Negative/ 
Positive/ 
Indeterminate/ 
Not Done 
Wild type gyrA detected/ 
Mutant gyrA detected/ 
Indeterminate/ 
Not Done 
Susceptible/ 
Not susceptible 
Urethral/Cervical/ 
Rectal/Pharyngeal 
Visit 2 (Day 5-
10) 
x 
xxxxxx 
xx 
Negative/ 
Positive/ 
Indeterminate/ 
Not Done 
Negative/ 
Positive/ 
Indeterminate/ 
Not Done 
Wild type gyrA detected/ 
Mutant gyrA detected/ 
Indeterminate/ 
Not Done 
Susceptible/ 
Not susceptible 
Urethral/Cervical/ 
Rectal/Pharyngeal 
 
Implementation Notes: 
1. Sort order will be Subject ID, Study Visit. 
2. Subject may have multiple rows for different anatomical sites. 
 


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Listing 6: 
Clinical Laboratory Results – Urine Pregnancy Test 
Subject ID  
Study Day of Assessment  
Collection Day  
Was a Urine Pregnancy Test 
Performed? 
Result 
xxxxxx 
x 
x 
Yes/No 
Negative/ 
Positive 
xxxxxx 
x 
x 
Yes/No 
Negative/ 
Positive 
xxxxxx 
x 
x 
Yes/No 
Negative/ 
Positive 
xxxxxx 
x 
x 
Yes/No 
Negative/ 
Positive 
 
Implementation Notes: 
1. Sort order will be Subject ID. 
 


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Listing 7: 
Individual Efficacy Data 
Anatomical Site 
N. gonorrhoeae Culture Result at Visit 1 
N. gonorrhoeae Culture Result at Visit 2 
Microbiological Outcome Status 
Subject ID:  
Urethral/ 
Cervical/ 
Rectal/ 
Pharyngeal 
Negative/ 
Positive/ 
Indeterminate/ 
Not Done 
Negative/ 
Positive/ 
Indeterminate/ 
Not Done 
Microbiological Cure/ 
Microbiological Failure/ 
Non-evaluable 
 
Implementation Notes: 
1. Sort order will be Subject ID. 
 


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Listing 8: 
Demographic and Baseline Characteristics Data—All Enrolled Subjects 
Subject ID 
Sex 
Age at Enrollment (years) 
Ethnicity 
Race 
xxxxxx 
xxxxxx 
xx 
xxxxxxx 
xxxxxxx 
xxxxxx 
xxxxxx 
xx 
xxxxxxx 
xxxxxxx 
xxxxxx 
xxxxxx 
xx 
xxxxxxx 
xxxxxxx 
xxxxxx 
xxxxxx 
xx 
xxxxxxx 
xxxxxxx 
 
Implementation Notes: 
1. Sort order will be Subject ID. 
2. For the “Race” column, if a subject is Multi-Racial, all races will be listed, separated by a comma. 
 


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Listing 9: 
Sexual History at Baseline Visit—All Enrolled Subjects 
Subject 
ID 
What is your gender 
identity? 
 What is your sexual 
orientation? 
Do you have sex with men, women, transgender men, 
transgender women, or multiple genders? 
Have you had sex (vaginal, anal, or oral) in the 
past 30 days? 
xxxxxx 
xxxxx 
xxxxxx 
xxxxxxx 
Yes/No/Refused to answer 
xxxxxx 
xxxxx 
xxxxxx 
xxxxxxx 
Yes/No/Refused to answer 
 
Implementation Notes:   
1. Sort order will be by Subject ID 
2. Includes data from Visit 1 
3. Note: Specify fields will be concatenated with a “:”. 
 
 


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Listing 10: 
Sexual History at Follow-up Visit—All Enrolled Subjects 
Subject ID 
Study Day 
1. Have you had sex 
(vaginal, anal, or oral) 
since the last visit 
2. Have you had vaginal 
intercourse since the last 
visit 
If Yes for question 2, did you use 
a condom with vaginal 
intercourse? 
3.Have you given oral 
intercourse since the last 
visit 
If Yes to question 3, did you 
use a condom or barrier with 
oral intercourse? 
xxxxxx 
xx 
Yes/No/Refused to answer 
Yes/No/Refused to answer 
No/Always/Sometimes/Unknown/
Refused to answer 
Yes/No/Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
xxxxxx 
xx 
Yes/No/Refused to answer 
Yes/No/Refused to answer 
No/Always/Sometimes/Unknown/
Refused to answer 
Yes/No/Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
 
Implementation Notes:   
1. Sort order will be by Subject ID, Study Day 
2. For questions that are parented, if the parent question is “No” and the subsequent fields are not required, fill the cell with “—“ 
 


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Listing 11: 
Sexual History at Follow-up Visit—All Enrolled Subjects 
Subject 
ID 
Study 
Day 
4. Have you 
received oral 
intercourse since 
the last visit 
If Yes to question 4, 
did you use a condom 
or barrier with oral 
intercourse? 
5.Have you had 
receptive 
'bottom' anal 
intercourse since 
the last visit 
If Yes to question 5, 
did you use a condom 
with receptive anal 
intercourse 
If Yes to question 5, 
did you use a condom 
with insertive anal 
intercourse 
6. Have you had 
insertive ‘top’ anal 
intercourse since the 
last visit? (Males 
only) 
If Yes to question 6, did 
you use a condom with 
insertive anal 
intercourse? 
xxxxxx 
xx 
Yes/No/ 
Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
Yes/No/ 
Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
No/Yes/ Refused to 
answer/ 
NA (if female) 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
xxxxxx 
xx 
Yes/No 
/Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
Yes/No/ 
Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
No/Yes/ Refused to 
answer/ 
NA (if female) 
No/Always/Sometimes/ 
Unknown/ 
Refused to answer 
 
Implementation Notes:   
1. Sort order will be by Subject ID, Study Day 
2. For questions that are parented, if the parent question is “No” and the subsequent fields are not required, fill the cell with “—“ 
 


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Listing 12: 
N. Gonorrhoeae Symptomatology 
Subject 
ID  
Study Visit 
Sex 
Symptoms of Gonorrhea  
Gender specific Symptoms of Gonorrhea 
Signs of Gonorrhea 
Gender specific Sign of Gonorrhea 
xxxxxx 
Visit 1 (Day 1)/ 
Visit 2 (Day 5-10) xxxxxx 
Sore throat/Anorectal 
pain/Anorectal 
discharge/Anorectal bleeding 
Urethral discharge/Pain with urination (Males Only) 
Abnormal vaginal discharge/Abnormal vaginal 
bleeding/pain during intercourse (Female Only) 
Pharyngeal 
erythema/Anorectal 
discharge 
Urethral discharge (Males Only) 
Abnormal cervical discharge (Females Only) 
xxxxxx 
Visit 1 (Day 1)/ 
Visit 2 (Day 5-10) xxxxxx 
Sore throat/Anorectal 
pain/Anorectal 
discharge/Anorectal bleeding 
Urethral discharge/Pain with urination (Males Only) 
Abnormal vaginal discharge/Abnormal vaginal 
bleeding/pain during intercourse (Female Only) 
Pharyngeal 
erythema/Anorectal 
discharge 
Urethral discharge (Males Only) 
Abnormal cervical discharge (Females Only) 
xxxxxx 
Visit 1 (Day 1)/ 
Visit 2 (Day 5-10) xxxxxx 
Sore throat/Anorectal 
pain/Anorectal 
discharge/Anorectal bleeding 
Urethral discharge/Pain with urination (Males Only) 
Abnormal vaginal discharge/Abnormal vaginal 
bleeding/pain during intercourse (Female Only) 
Pharyngeal 
erythema/Anorectal 
discharge 
Urethral discharge (Males Only) 
Abnormal cervical discharge (Females Only) 
 
Note: Only some subjects have data at Visit 3 due to the protocol amendment. 
1. Implementation Notes: 
2. Sort order will be Subject ID, Study Visit. 
 


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Listing 13: 
Compliance Data 
Subject ID  
Dose Taken?  
Vomit Within 1 Hour of Study Drug Administration? 
Compliance Status 
xxxxxx 
Yes/No 
Yes/No 
Compliant/Non-compliant 
xxxxxx 
Yes/No 
Yes/No 
Compliant/Non-compliant 
xxxxxx 
Yes/No 
Yes/No 
Compliant/Non-compliant 
xxxxxx 
Yes/No 
Yes/No 
Compliant/Non-compliant 
 
Implementation Notes: 
1. Sort order will be Subject ID. 
 


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Listing 14: 
Side Effects Related to Fluoroquinolone 
Subject ID  
Study Visit 
Serious Side Effects Related to Fluoroquinolone 
xxxxxx 
Visit 1 (Day 1)/ 
Visit 2 (Day 5-10) 
Tendon pain/Joint pain/Muscle pain/Tingling or pricking 
sensation/Confusion/Hallucinations 
xxxxxx 
Visit 1 (Day 1)/ 
Visit 2 (Day 5-10) 
Tendon pain/Joint pain/Muscle pain/Tingling or pricking 
sensation/Confusion/Hallucinations 
xxxxxx 
Visit 1 (Day 1)/ 
Visit 2 (Day 5-10) 
Tendon pain/Joint pain/Muscle pain/Tingling or pricking 
sensation/Confusion/Hallucinations 
Note: Only some subjects have data at Visit 3 due to the protocol amendment. 
 
Implementation Notes: 
1. Sort order will be Subject ID, Study Visit. 
 


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Listing 15: 
Baseline Pregnancy Test Results 
Subject ID  
Was a urine pregnancy test performed? 
Pregnancy Test Result 
xxxxxxxx 
Yes/No/NA 
Negative/Positive 
xxxxxxxx 
Yes/No/NA 
Negative/Positive 
 
Implementation Notes: 
1. Sort order is Subject ID 
 


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Listing 16: 
Physical Exam Findings 
Study Visit 
Actual Study Day 
Body System 
Abnormal Finding 
Visit 1 (Day 1) 
x 
xxx 
xxxxxxxxxxxxxxxxxxxxx 
Visit 2 (Day 5-10) 
x 
xxx 
xxxxxxxxxxxxxxxxxxxxx 
 
Implementation Notes: 
1. Sort order will be Subject ID, Study Visit. 
2. Only abnormal findings will be presented. 
 


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Listing 17: 
Concomitant Medications 
Subject ID 
CM 
Number 
Medication 
Medication Start 
Day 
Medication End 
Day 
Indication 
ATC 1/ ATC2 
xxxxxx 
xx 
xxxxxxxx 
xx 
xx 
xxxxxxxx 
 
xxxxxx 
xx 
xxxxxxxx 
xx 
xx 
xxxxxxxx 
 
xxxxxx 
xx 
xxxxxxxx 
xx 
xx 
xxxxxxxx 
 
 
Implementation Notes: 
1. Sort order will be Subject ID, CM Number.