Lefamulin for Mycoplasma Genitalium Treatment Failures in the US
Phase: PHASE1
Conditions: Mycoplasma Genitalium Infection
Sponsor: University of Washington

 
 
 
 
 
 
 
 
 
 
 
 
Lefamulin for Mycoplasma genitalium 
treatment failures in the US 
NCT05111002 
6/3/2022 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Lefamulin for Mycoplasma genitalium treatment failures in the US 
Investigator Initiated Study Proposal to Nabriva Therapeutics 
Version 3.0:  06-03-2022 
 
Investigators:   
PI:  Lisa E. Manhart, PhD, University of Washington  
Co-PI:  Lindley Barbee, MD, MPH, University of Washington 
Co-Investigators   
Olusegun Soge, PhD, University of Washington 
Catriona Bradshaw, Melbourne Sexual Health Centre, Melbourne Australia 
Jørgen Skov Jensen, Statens Serum Institute, Copenhagen Denmark 
 
Coordinating Center 
University of Washington 
4333 Brooklyn Ave NE, Box 359472 
Seattle, WA 98195-9472 
 
Physician Referrals to Coordinating Center  
STD Clinical Consultation Network (CCN), National Network of STD Clinical Prevention Training 
Centers (https://www.stdccn.org/render/Public) 
 
Overview 
We are requesting compassionate access to lefamulin for symptomatic patients with 
Mycoplasma genitalium who have failed (a) moxifloxacin and/or (b) other second or third line 
antimicrobials (e.g., minocycline, omadacycline, other), or when moxifloxacin is contraindicated.  
We also request modest funding to cover the costs of prescribing and distributing lefamulin to 
patients across the US who meet criteria for compassionate access, document treatment 
outcomes to estimate the efficacy of lefamulin alone and of pre-treatment with doxycycline 
followed by lefamulin for MG treatment failures, and collect specimens for culture and 
assessment of minimum inhibitory concentrations (MICs). 
Background  
Declining efficacy of standard therapies and the emergence of antimicrobial resistance 
increasingly hinder the management of bacterial sexually transmitted infections (STIs). Although 
antibiotic resistant Neisseria gonorrhoeae (GC) has been classified as an urgent threat by the 
US Centers for Disease Control and Prevention (CDC) since 20131, the prevalence of antibiotic 
resistance in Mycoplasma genitalium (MG) is dramatically higher and multiple cases of 
untreatable MG have emerged2,3. In recognition of this, the CDC’s Antibiotic Resistance Threats 
in the United States, 2019 report includes MG as one of three organisms on a newly created 
Watch List.4  

2 
 
Moxifloxacin is currently recommended as second-line therapy for MG treatment failures, yet 
fluoroquinolone resistance in the US is already estimated at 12.8% (95% CI 0.4-34.2%)5. 
Although pristinamycin6 and combination therapy with doxycycline and sitafloxacin2 have shown 
efficacy in cases of MG treatment failures, neither pristinamycin nor sitafloxacin are available in 
the US. As a result, US providers’ only recourse is to trial older antimicrobials (e.g., minocycline) 
in cases of moxifloxacin treatment failure or when moxifloxacin is contraindicated. This is not 
always successful.  
Lefamulin is a highly potent novel antimicrobial of the pleuromutilin class that is approved by the 
FDA for the treatment of Community Acquired Bacterial Pneumonia (CABP)7. Lefamulin was 
well-tolerated in Phase II and Phase III studies,8-10 and initial in vitro studies demonstrated high 
susceptibility of STI pathogens to lefamulin. Notably, susceptibility of CT (MIC50/90, 0.02/0.04 
mg/liter) and GC (MIC50/90, 0.12/0.5 mg/liter) were good, and susceptibility of MG was excellent 
(MIC range, 0.002 to 0.063 mg/liter for multi-drug resistant strains).11 Given this high degree of 
in vitro susceptibility and its favorable safety profile, lefamulin holds great promise for MG 
treatment failures and/or where moxifloxacin is contraindicated. Although the recommended oral 
dose for CABP is 600mg twice daily for 5 days, MG is a slow growing organism and may require 
longer durations of therapy.12 Therefore, we propose to use lefamulin 600mg orally twice 
daily for 7 days for M. genitalium treatment failures with or without pre-treatment with 
doxycycline 100mg twice daily for 7 days.  
Diagnostic testing for MG in the US is more limited than in Europe and Australia and only two 
nucleic acid amplification tests (NAAT) are currently approved by the FDA: the Hologic Aptima 
MG assay and the Roche TV/MG test. Several large commercial laboratories have also 
validated and offer their own in-house laboratory developed tests. Neither of the two FDA-
approved assays includes the capability to detect macrolide resistance mutations (MRM). The 
SpeeDx ResistancePlus MG assay, which does have this capacity, is not yet FDA-approved 
and not available in the US. As such, the resistance-guided therapy approach developed by 
investigators at the Melbourne Sexual Health Centre13,14 is rarely implemented in the US and 
macrolide resistance is infrequently documented. Instead, US providers infer its presence after 
treatment failure. Additionally, in recognition of increasing macrolide resistance in STI 
pathogens, doxycycline is replacing azithromycin as first line therapy for STI syndromes. Many 
STD clinics in the US now treat first with doxycycline, and then treat empirically with 
moxifloxacin when MG is detected. Not all MG treatment failures have previously received 
azithromycin. Therefore, eligibility for compassionate access to lefamulin will be determined on 
the basis of previous treatment failures. 
Objective 
To estimate the efficacy of lefamulin for the treatment of symptomatic MG treatment failures 
and/or where moxifloxacin is contraindicated. 
Study Design 
We propose to provide compassionate access to lefamulin and estimate the efficacy of 
lefamulin in treating antibiotic resistant MG through a coordinating center at the University of 
Washington (UW). We will enroll a total of 40 symptomatic patients with MG infections who have 
experienced treatment failure after moxifloxacin and/or other second or third line antimicrobials 

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or in whom moxifloxacin is contraindicated. Patients will be followed for 42 or 56 days, 
depending on the regimen they receive.  
There is an increasing global trend to pre-treat MG infections with doxycycline to reduce 
organism load. There have also been several initial reports of treatment failure after a 7-day 
regimen of lefamulin alone, but successes after a regimen in which patients were pre-treated 
with doxycycline in the companion study in Melbourne, Australia. Therefore, we propose to also 
determine if pre-treatment with doxycycline is necessary. To simultaneously assess the efficacy 
of lefamulin alone (600mg orally twice daily for 7 days), and a regimen incorporating pre-
treatment with doxycycline (doxycycline 100mg orally twice daily for 7 days followed by 
lefamulin 600mg orally twice daily for 7 days), we will randomize the first 20 patients to either 
Regimen A (lefamulin alone) or Regimen B (pretreatment with doxycycline followed by 
lefamulin) in a 1:1 ratio.  
An interim analysis will be performed after the first 20 patients are enrolled to assess the 
efficacy of each of these two regimens for futility. Based on the results of this interim analysis, 
we will make one of three possible decisions: 
• 
If neither of the regimens meet criteria for futility, we will continue randomizing patients 
to one of the two regimens until we have reached our target sample size of 40 patients 
(20 randomized per arm).  
• 
If one of the regimens meets criteria for futility but the other regimen does not, we will 
drop the regimen that met futility criteria and continue to administer the other regimen to 
the remaining 20 patients for a total of 30 randomized patients in the retained regimen. 
• 
If both regimens meet criteria for futility, we will halt the study and reassess the 
possibility of using alternative dosing regimens.  
Criteria for futility are outlined in the section on sample size on p. 6. 
Study population:   
Symptomatic patients with MG treatment failure will be eligible. Treatment failure will be defined 
as persistent symptoms and a positive NAAT test after (a) moxifloxacin and/or (b) other second 
or third line antimicrobials (e.g., minocycline, omadacycline, other), or (c) when moxifloxacin is 
contraindicated. Additional inclusion and exclusion criteria are: 
Inclusion Criteria: 
• 
Physician referral  
• 
Persistent symptomatic urogenital MG infection documented by any NAAT 14-90 days 
after completion of the prior antimicrobial regimen for MG 
• 
Low risk of reinfection defined as no unprotected sex with an untreated sex partner since 
completion of the prior antimicrobial regimen 
• 
Male or female sex at birth 
• 
≥18 years of age 
• 
English-speaking 
• 
Able to provide written informed consent 
• 
Able to undergo a test to confirm MG infection at baseline and tests of cure 21-28 days 
and 42-47 days after completing lefamulin 

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• 
Referring physician willing and able to provide needed patient information 
• 
Living in the US 
 
Exclusion Criteria: 
• 
Females with PID, pregnancy, or currently breastfeeding 
• 
Females of reproductive age not on a highly effective method of contraception (i.e., IUD, 
Nexplanon, progesterone only depot injection with last injection <3 months, or oral 
contraceptive pill and last menstrual period <28 days prior)  
• 
Known QT prolongation, ventricular arrhythmias including torsades de pointes 
• 
Receiving concurrent drugs known to prolong QT interval (e.g., Class IA or Class III 
antiarrhythmics, antipsychotics, erythromycin, pimozide, moxifloxacin, tricyclic 
antidepressants). 
• 
Receiving strong or moderate CYP3A or P-gp inducers, strong CYP3A or P-gp 
inhibitors, moderate CYP3A or P-gp inhibitors or sensitive CYP3A4 substrates that 
prolong QT interval 
• 
Moderate or severe liver impairment 
• 
Renal failure requiring dialysis 
• 
Known allergy to doxycycline, other tetracyclines, and/or lefamulin 
• 
Known liver disease 
• 
Not willing or unable to undergo a test to confirm MG infection at baseline and tests of 
cure 21-28 days and 42-47 days after completion of lefamulin   
• 
Not fluent in English and/or not able to provide written informed consent 
• 
Referring physician unwilling or unable to provide needed patient information 
• 
At the study physician’s discretion 
• 
Rectal MG infection only 
 
Recruitment 
STI care in the US is decentralized and there is no single clinic where MG treatment failures 
receive care. Instead, cases come to the attention of our team when individual providers and 
patients throughout the country contact us, and through clinical consultation requests submitted 
to the STD Clinical Consultation Network (CCN), National Network of STD Clinical Prevention 
Training Centers (https://www.stdccn.org/render/Public). The study physician, Dr. Barbee, is a 
consulting physician in the CCN and handles requests for consultation. In addition to leveraging 
the CCN to link providers with the study team, we will also post the protocol on clinicaltrials.gov.  
The referring provider for patients with documented symptomatic MG treatment failure will be 
the official point of contact. Patients who contact team members directly will be provided contact 
information for the study team and asked to have their health care provider contact the team.  
Enrollment and consent 
After the referring provider obtains verbal consent from their patient to contact the study team, 
the study physician will conduct an initial telephone or zoom consultation with the referring 
provider to discuss the patient’s case and to determine initial eligibility. The study physician will 
complete the case report form (CRF) as a UW ITHS REDCap form, the referring provider will 

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indicate that verbal consent was obtained in a UW ITHS REDCap form, and sign and date the 
form. The CDC has developed an MG Treatment Failure Case Report Form (CRF) to document 
and track treatment failures that was approved by the OMB in March 2021. We propose to use 
this CRF to document cases of treatment failure, allowing us to link with the eventual CDC 
process for tracking MG treatment failures. The study physician will abstract information on 
concomitant medications, and other relevant medical history, to confirm eligibility and enter this 
information into a UW ITHS REDCap form. Where available, the study physician will also 
abstract Gram stain results and chemistry panel with liver function test results. 
Upon receipt of the CRF, a research coordinator will arrange a zoom discussion between the 
study physician and the patient to explain the study procedures, answer questions, and obtain 
written informed consent, using the UW ITHS REDCap electronic signature process for consent. 
The UW-ITHS-supported version of REDCap meets the FDA’s Part 11 electronic system 
requirements. The additional clinical information and the CRF will be completed by the study 
physician during the discussion with the patient to confirm eligibility and prior to prescribing 
lefamulin (and doxycycline for patients randomized to sequential therapy). 
Dispensing lefamulin (and doxycycline, as warranted) 
Dr. Barbee will be the prescribing physician of record and partner with the UW Harborview 
Medical Center Investigational Drug Services (HMC IDS) to check for drug interactions and/or 
contraindications to lefamulin (and doxycycline for patients randomized to sequential therapy). 
Lefamulin and doxycycline will be stored in and dispensed from the UW HMC IDS Pharmacy, 
which will serve as the pharmacy of record. This is a locked, temperature-controlled facility 
adjacent to the PHSKC Sexual Health Clinic that manages and dispenses all medications for 
research studies conducted at the Harborview campus. HMC IDS will be responsible for 
tracking, documentation, and return/disposal of any unused drug provided by Nabriva. 
Upon receipt of a prescription from Dr. Barbee, HMC IDS will prepare the medication packet(s). 
The research coordinator will ship the medication packet(s) to the patient. Mailing antibiotics 
across state lines is permissible with an IND exemption in place, which is the case here. Per our 
consultation with a clinical trials pharmacist, “when a clinical study is found to be IND exempt 
[21 CFR 312.2(b)], the FDA has granted that study the same permissions as a study with an 
IND (such as placing investigational drug into interstate commerce). … with a documented IND 
exemption, … the drug can be shipped across state lines when a subject has been enrolled in 
the study [21 CFR 312.40].” (full text of letter noting on file in the regulatory binder). The FDA 
has granted this study an IND exemption, cross-referencing Nabriva Therapeutics’ existing IND. 
In addition to the lefamulin tablets, the medication package will include a drug information sheet 
for lefamulin; contact information for any patient questions about the antibiotic, side effects, or 
both; a letter, which provides an overview of the study; a specimen collection instruction sheet 
for each specimen; a return shipment instruction sheet; and materials for patients to collect and 
return two specimens (one specimen for culture and assessment of MICs; the other specimen to 
confirm MG infection at baseline). For patients randomized to sequential therapy, the 
medication package will also contain doxycycline tablets and a drug information sheet for 
doxycycline. 
Culture Specimens 

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Each medication package will include one Copan flocked swab, one vial of Copan Universal 
Transport Medium [UTM]), and materials and instructions for returning culture specimens to the 
UW Global Health STI Laboratory. Male patients will be instructed to collect a self-obtained meatal 
swab and place it into the tube containing UTM before the first dose of lefamulin (or doxycycline 
if randomized to sequential therapy) is taken. Female patients will be instructed to take a self-
obtained vaginal swab as described above. Both types of self-obtained swabs have demonstrated 
comparable sensitivity and specificity for diagnostic testing relative to clinician obtained swabs, 
and are acceptable to patients.15,16 Additional culture specimen collection materials and 
instructions will be included along with the Aptima test kits mailed out for tests of cure (see below).  
Upon receipt in the Global Health STI Laboratory at the UW, culture specimens will be stored 
immediately at -70⁰C or colder. They will subsequently be shipped in batches to Dr. Jørgen 
Jensen’s laboratory at Statens Serum Institute. Dr. Jensen’s laboratory is one of only a few 
worldwide with the demonstrated capacity to consistently cultivate M. genitalium and perform 
antimicrobial resistance testing. His laboratory will perform the culture and susceptibility testing 
for lefamulin, as well as for azithromycin and moxifloxacin, under a separate contract. Performing 
culture and MICs will enable us to assess whether there is any pre-existing resistance to lefamulin, 
whether any resistance to lefamulin is selected for during treatment, and whether the efficacy of 
lefamulin differs for azithromycin-resistant and moxifloxacin-resistant strains. 
Tests of cure 
Tests of cure will be performed in the UW Global Health STI Laboratory (laboratory director 
Olusegun Soge). The Hologic Aptima MG assay, which we propose to use for tests of cure, has 
higher sensitivity and specificity than most other assays. Thus, test-of-cure windows when using 
this assay are generally longer (21-28 days) than when other assays are used. Furthermore, 
instances of MG recrudescing after an initial negative test subsequent to treatment have been 
reported,17,18 suggesting that additional follow-up after an initial test of cure is warranted in 
studies of novel antimicrobials. Therefore, we will perform two tests of cure (one at 21-28 days 
and one at 42-47 days after completion of lefamulin).  
The research coordinator will ship Aptima test kits to enrolled patients, one 21-48 days, and one 
42-47 days after completion of Lefamulin. In addition to the Aptima collection kit and instructions 
and shipping materials to return the Aptima tubes to the UW Global Health STI Laboratory, that 
package will also include materials and instructions for culture specimen collection as described 
above. Culture specimens will be shipped at the same time as the test of cure specimens. 
Clinical, symptom, adherence, and side effects data 
In addition to the CDC MG Treatment Failure CRF, the study physician will ask about other 
aspects of the patient medical history and enter this information into a separate UW ITHS 
REDCap form (concomitant medications, other relevant medical history, etc.). Where available, 
the study physician will also obtain Gram stain results and chemistry panel with liver function 
test results.  
We will also program electronic surveys, using the UW ITHS REDCap platform, that will be 
completed by the patient on the start date of the first antibiotic course, upon completion of the 
antibiotic regimen (lefamulin alone or lefamulin and doxycycline), and at the 21-28-day and the 
42-47-day test-of-cure timepoints. The REDCap surveys will collect information on dates of 

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antibiotic use, symptoms, antibiotic adherence, sexual behavior, and side effects. We will also 
program electronic reminders to remind the patient to complete the REDCap surveys and to 
mail in the test of cure and culture specimens.  
Outcomes 
We will assess one primary outcome and five secondary outcomes.  
• 
Primary Outcome 
o Microbiologic cure defined as a negative Aptima MG test 21-28 days after 
completing lefamulin 
• 
Secondary Outcomes 
o Microbiologic cure, as defined above, after lefamulin alone compared to 
microbiologic cure after sequential treatment with doxycycline followed by 
lefamulin  
o Clinical cure defined as absence of symptoms, absence of visible discharge, and 
absence of other clinical signs (<5PMNs/hpf on Gram stained smear where 
available) 21-28 days after completion of the lefamulin  
o Reported adherence to lefamulin (defined by self-reported number of tablets 
taken) 
o Reported adverse events (defined by self-reported adverse events) 
o Sustained microbiologic cure defined as a negative Aptima MG test 42-47 days 
after completing lefamulin 
Criteria for futility 
Given the absence of alternative therapies for M. genitalium treatment failures, even modest 
efficacy of 60% would be useful for some patients. Therefore, futility will be defined as <5% 
probability that true efficacy is 60% (or higher), given the number of treatment failures that occur 
in the first 10 patients. The probability of observing three or fewer cures (e.g., at least 7 
treatment failures) in the first 10 patients if the true efficacy is 60% is 5%. Therefore, if three or 
fewer of the first ten patients in either arm experience microbiologic cure, we would declare 
futility for that regimen. 
Sample size 
We initially estimated the sample size needed based on the precision around efficacy estimates 
for lefamulin in a single arm study and estimated that a total of 30 patients with complete data 
on tests of cure, adherence, and adverse events would provide precision to estimate efficacy 
≥90% with binomial exact 95% CI’s ranging from 73.5% - 99.9%. Assuming loss to follow-up of 
up to 30%, a total of 40 patients will need to be enrolled.  
Because there are fewer people in each arm of a two-arm randomized pilot trial, the statistical 
power and precision will be somewhat than that estimated for a single arm study. Table 2 
compares precision for an arm with 20 randomized persons to one with 30 randomized persons. 
Even in the case where an arm has only 20 randomized persons, the lower bound of the 
confidence intervals is >60%, which would still demonstrate benefit. 

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Table 2:  Precision around estimated cure rates assuming 40 patients are enrolled and outcome 
data are available on either 20 participants randomized per arm (if neither regimen meets 
criteria for futility), or 30 participants randomized to an arm (if one of the regimens meets criteria 
for futility) 
Lefamulin 
failures (n) 
N=20  
N=30 
Estimated cure 
95% confidence 
intervals 
Estimated cure 
95% confidence 
intervals 
3 
85% 
62.11 – 96.79 
90% 
73.5 – 97.9 
2 
90% 
68.30 – 98.77 
93% 
77.9 – 99.2 
1 
95% 
75.13 – 99.87 
96% 
82.8 – 99.9 
Data analysis 
We will calculate and present simple proportions and 95% CIs for each of our outcomes. We will 
not require complete data on all outcomes to be included in analyses. Instead, the denominator 
will be the total number of patients for whom we have complete outcome data for the outcome 
of interest. For example, patients with test of cure data but without clinical cure data will be 
included in the calculation of microbiologic cure but excluded from the calculation of clinical 
cure. 
Side effects 
We will collect data on the following potential side effects of lefamulin and of doxycycline 
through our electronic REDCap surveys upon completion of the regimen and at 21-28 days and 
at 42-47 days after completion of the regimen. 
• 
Gastrointestinal complaints:  diarrhea, nausea, vomiting 
• 
Other systemic complaints: photosensitivity, excess vaginal yeast with itching 
• 
Other (open text field for patients to record other events) 
Ethics Approvals 
The University of Washington Institutional Review Board (IRB) will serve as the IRB of record for 
this study. We will secure IRB approval prior to initiating any study activities. 
Timeline and publication 
We estimate it will take one calendar year to enroll and follow 40 patients. Data analysis and 
preparation of a final report for Nabriva and a peer-reviewed publication will be completed within 
12 weeks of the completion of the last follow-up visit of the final participant. 
 
 

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