Evaluation of Doxycycline Post-exposure Prophylaxis to Reduce Sexually Transmitted Infections in PrEP Users and HIV-infected Men Who Have Sex With Men
Phase: PHASE4
Conditions: Gonorrhea, Chlamydia, Syphilis
Sponsor: University of California, San Francisco

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PROTOCOL 
 
 
DoxyPEP: Evaluation of doxycycline post-exposure prophylaxis to reduce sexually transmitted infections in 
men who have sex with men and transgender women either on PrEP or living with HIV 
 
 
 
 
Version 9.0 
 
May 27, 2022 
 
 

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TABLE OF CONTENTS 
 
STUDY TEAM ................................................................................................................................................... 4 
GLOSSARY ....................................................................................................................................................... 5 
SCHEMA ........................................................................................................................................................... 6 
1 
BACKGROUND AND SIGNIFICANCE ....................................................................................................... 8 
1.1 
Background ........................................................................................................................................ 8 
1.2 
Rationale .......................................................................................................................................... 10 
2 
STUDY DESIGN ...................................................................................................................................... 13 
3 
OBJECTIVES .......................................................................................................................................... 14 
3.1 
Primary Objectives ........................................................................................................................... 14 
3.2 
Secondary Objectives ...................................................................................................................... 14 
3.3 
Exploratory objectives ...................................................................................................................... 14 
4 
SELECTION AND ENROLLMENT OF PARTICIPANTS .......................................................................... 14 
4.1 
Inclusion criteria ............................................................................................................................... 15 
4.2 
Exclusion criteria .............................................................................................................................. 15 
4.3 
Recruitment ...................................................................................................................................... 15 
4.4 
Co-enrollment guidelines. ................................................................................................................. 16 
5 
STUDY TREATMENT .............................................................................................................................. 16 
5.1 
Study product ................................................................................................................................... 16 
5.2 
Safety of doxycycline ....................................................................................................................... 16 
5.3 
Doxycycline dispensing and administration. ..................................................................................... 17 
5.4 
Concomitant medications ................................................................................................................. 17 
5.5 
HIV pre-exposure prophylaxis (PrEP) and HIV antiretroviral therapy (ART) ..................................... 17 
6 
CLINICAL AND LABORATORY MONITORING ....................................................................................... 18 
6.1 
Schedule of Events .......................................................................................................................... 18 
6.2 
Study visits ....................................................................................................................................... 20 
6.3 
Instructions for evaluations ............................................................................................................... 20 
6.4 
Evaluation at time of presumptive or diagnosed GC, CT and syphilis ............................................... 23 
6.5 
Testing for resistance in setting of STI diagnoses on study .............................................................. 25 
6.6 
Treatment of STIs ............................................................................................................................ 26 
6.7 
Qualitative interviews ....................................................................................................................... 26 
6.8 
Reenrollment of participants enrolled prior to 3/15/2020 ................................................................... 26 
7 
ADVERSE EVENTS (AE) AND STUDY MONITORING ........................................................................... 26 
7.1 
Adverse Event Collection Requirements .......................................................................................... 26 
7.2 
AE and SAE attribution to doxycycline ............................................................................................. 27 
7.3 
Study Monitoring .............................................................................................................................. 27 
8 
CLINICAL MANAGEMENT ISSUES ........................................................................................................ 28 
8.1 
Toxicity ............................................................................................................................................. 28 

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8.2 
Specific Management of Toxicities Related to Study-Provided Drugs ............................................... 28 
9 
CRITERIA FOR DISCONTINUATION ...................................................................................................... 29 
9.1 
Premature Study Treatment Discontinuation .................................................................................... 29 
9.2 
Premature Study Discontinuation ..................................................................................................... 29 
10 
STATISTICAL CONSIDERATIONS ......................................................................................................... 29 
10.1 
Outcome measures .......................................................................................................................... 29 
10.2 
Statistical power and analysis .......................................................................................................... 30 
10.3 
Endpoint adjudication ....................................................................................................................... 31 
10.4 
Post COVID follow-up ...................................................................................................................... 32 
10.5 
Analyses post 5/13/2022 closure to enrollment ................................................................................ 32 
11 
PARTICIPANTS ....................................................................................................................................... 32 
11.1 
Institutional Review Board (IRB) Review .......................................................................................... 32 
11.2 
Informed Consent ............................................................................................................................. 32 
11.3 
Study records ................................................................................................................................... 32 
11.4 
Confidentiality .................................................................................................................................. 33 
12 
BIOHAZARD CONTAINMENT ................................................................................................................. 33 
REFERENCES ................................................................................................................................................ 34 
 
 

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STUDY TEAM 
 
Connie Celum, MD, MPH, co-Principal Investigator 
Annie Luetkemeyer, MD, co-Principal Investigator 
Jared Baeten, MD, PhD 
Ruanne Barnabas, MBChB, DPhil 
Susan Buchbinder, MD, MPH 
Katerina Christopoulos, MD, MPH 
Edwin D. Charlebois, MPH, PhD 
Stephanie Cohen, MD, MPH 
Julie Dombrowski, MD, MPH 
Deborah Donnell, PhD 
Rob Fredericksen, PhD 
 Diane Havlir, MD 
Chaz Langelier, MD,PhD 
Hyman Scott, MD, MPH 
Olusegun Soge, MSc, PhD 
Vivek Jain, MD, MAS 
Emma Bainbridge, MD, MPH 

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GLOSSARY 
 
AE 
Adverse event 
AMR 
Antimicrobial resistance 
ART 
Antiretroviral therapy 
CT 
Chlamydia trachomatis 
GC 
Gonorrea 
HIV 
Human Immunodeficiency virus 
LGV 
Lymphogranuloma venereum 
MG 
Mycoplasma genitalium 
MSM 
Men who have sex with men 
NAAT 
Nucleic acid amplification test 
NGU 
Non-gonococcal urethritis 
PEP 
Post-exposture prophylaxis 
PLWH 
People living with HIV 
PrEP 
Pre-exposure prophylaxis 
RPR 
Rapid Plasma Reagin 
SAE 
Serious Adverse Event 
STI 
Sexually transmitted infection 
TCN 
Tetracycline 
TGW 
Transgender women 
VDRL 
Venereral Disease Research Lab 

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SCHEMA 
 
DoxyPEP: Prospective, randomized, open-label, clinical trial to evaluate the impact of doxycycline post-
exposure prophylaxis on the occurrence of bacterial STIs among men who have sex with men (MSM) and 
transgender women (TGW) PrEP users and people living with HIV 
 
 
Design: 
Open-label randomized clinical trial of doxycyline PEP to reduce bacterial STIs (N. 
gonorrheae [GC], C. trachomatis [CT], and T. pallidum [syphilis]) among MSM and 
transgender women (TGW) living with HIV (PLWH) or on HIV PrEP. 
 
Study Population: Sample size of 780, approximately equal numbers of PLWH and participants taking HIV pre-
exposure prophylaxis (PrEP)  
 
Study Sites: 
1. HIV/AIDS Clinic (“Ward 86”), Zuckerberg San Francisco General Hospital, UCSF, San 
Francisco 
2. San Francisco City Clinic, San Francisco Department of Public Health, San Francisco 
(municipal STD clinic) 
3. Madison HIV/AIDS Clinic, Harborview Medical Center University of Washington, Seattle 
4. Public Health-Seattle & King County Sexual Health Clinic at Harborview Medical Center, 
Seattle 
 
Primary Study Objectives: 
1. Evaluate the effectiveness of doxycycline post-exposure prophylaxis (PEP) to reduce 
STI infections in two populations: a) MSM living with HIV and b) MSM/TGW taking HIV 
PrEP 
2. Investigate the impact of doxycycline PEP on development of culture-based tetracycline 
(TCN) resistance in N. gonorrheae and among nasopharyngeal carriers of S. aureus 
 
Secondary Study Objectives: 
1. Assess the safety, tolerability, and acceptability of doxycycline PEP 
2. Investigate the impact of doxycycline PEP on detection of culture and molecular 
markers of tetracycline (TCN) resistance in C. trachomatis (CT), and T. pallidum 
(syphilis- molecular markers only) 
3. Evaluate the development of phenotypic tetracycline resistance among oropharyngeal 
carriers of commensal Neisseria species 
4. Measure the proportion of sex acts which are covered by doxycycline PEP 
5. Assess the effect of doxycycline PEP on the gut resistome through measuring the 
abundance of tetracycline resistance genes in stool of a subset of 50 MSM living with 
HIV and 50 MSM/TGW on PrEP assigned to receive doxycycline PEP as well as rectal 
swabs from all participants, stored for future evaluation 
 
Exploratory Objectives: 
1. Evaluate the diversity of the gut microbiome and quantity and breadth of drug 
resistance genes in participants on doxycycline PEP and not on PEP 
2. Assess the association between meningococcal vaccination and incident GC infection 
3. Evaluate the incidence of nongonococcal, nonchlamydial urethritis and the proportion 
of urethritis in which Mycoplasma genitalium (MG) is detected 
4. Assess the rate of detection of Mycoplasma genitalium (MG) in urine in each arm and 
the presence of tetracycline and other antimicrobial resistance in MG in each arm. 

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5. Evaluate association of doxycycline use with weight change over time 
6. Evaluate whether doxycycline PEP is associated with PrEP persistence and HIV 
virologic suppression by comparison of arms and within the doxycycline PEP arm by 
adherence to doxycycline PEP. 
7. Evaluate the incidence of lymphogranuloma venereum (LGV) in those diagnosed 
with rectal chlamydia in each arm 
 
 
Approach: 
Eligible participants randomized to receive PEP will receive open-label doxycycline 200 mg 
to be taken ideally within 24 hours but no later than 72 hours after each condomless sexual 
contact (receptive anal, insertive anal, vaginal, or oral, or use of shared sex toys). No more 
than 200 mg will be taken in each 24 hour period. Sexual activity and doxycycline PEP 
usage will be recorded using a smartphone application and assessment at study visits. At 
enrollment and quarterly for 12 months of follow-up, GC and CT testing will be conducted 
on samples from the oropharynx, rectum and urine and a blood specimen for syphilis 
serology will be collected. Resistance testing will be conducted on specimens that test 
positive for GC using phenotypic methods, and molecular techniques for CT and syphilis 
(for syphilis, DNA obtained from mucosal or lesional swabs). Nares and pharyngeal swabs 
will be obtained to evaluate tetracycline resistance among nasopharyngeal carriers of S. 
aureus and commensal Neisseria species (oropharyngeal swab only). Stool samples from 
50 MSM/TGW living with HIV and 50 MSM/TGW on PrEP in the doxycycline PEP arm at 3 
time points will undergo metagenomic sequencing for tetracycline resistance genes. Rectal 
swabs from all participants who consent will be archived for future evaluation of the enteric 
microbiome and resistome, as well as for presence of MG. 
 
 
 
 
Study Schema 

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1 
BACKGROUND AND SIGNIFICANCE 
 
1.1 
Background 
The incidence of bacterial sexually transmitted infection (STI) continues to increase in the US, with more than 2 
million diagnoses of syphilis, gonorrhea (GC) and chlamydia (CT) in 2016.2 This STI epidemic is occurring 
globally and is concentrated among men who have sex with men (MSM) and transgender women (TGW), 
including those living with and without HIV. In the US, MSM accounted for 81% of syphilis infections in 2016 and 
38% of gonorrhea cases; the latter represents a nearly 10-fold increase since 1989. 2 CT is also increasing 
among MSM, with rectal chlamydia rates of 17% and the highest rates of CT diagnosed in STI clinics in MSM ≥ 
25 years old.2 Both MSM living with HIV and MSM without HIV infection on PrEP have very high bacterial STI 
incidence, reaching or exceeding 50% new STI diagnoses per year.3, 4 
 
Increasing STI rates have been associated with a rise in serious morbidity, including blindness secondary to 
syphilitic ocular complications.5 Congenital syphilis rates have increased 28% in the past few years;6 it is likely 
that some of this increase comes from ‘bridging’ from MSM to heterosexual populations.7 Distressingly, drug- 
resistant GC continues to rise globally8-10 and in the US,11 leading to limited oral treatment options; recent cases 
of highly-resistant GC in the UK and Australia required treatment with ertapenem.12, 13 Untreated STIs increase 
the risk of HIV transmission from individuals with HIV infection who are not virologically suppressed,14, 15 as 
occurs in nearly half of those living with HIV nationwide.16 With the recent CDC-endorsed “U=U” campaign (i.e., 
undetectable=untransmittable),17 condom use may further decrease among persons with HIV infection, and may 
impact ‘serosorting’ in selection of sexual partners and decisions to use condoms. Accordingly, there is an urgent 
need for innovative, effective, and acceptable interventions to halt the rise in syphilis, GC, and CT among MSM 
and TGW living with and at-risk for HIV infection. 
 
One potential STI control strategy for these high-risk populations is post-exposure prophylaxis (PEP) 
with doxycycline. Antibiotic prophylaxis against STIs is not a new concept; minocycline was used as PEP for 
GC in the US Navy in the 1940s and showed transient benefits with no clinical harms, but the rapid emergence 
of tetracycline resistance prevented uptake of this approach as a public health strategy 18 A systematic review of 
presumptive periodic treatment of sex workers showed overall 50% reductions in GC and CT without risk 
compensation or increased AMR, and this approach is recommended for populations with high baseline GC and 
CT prevalence 19. The rationale for STI prophylaxis among MSM and TGW is similar, given the high prevalence 
and incidence of bacterial STIs among MSM living with HIV and MSM on PrEP. An effective STI prophylaxis 
strategy could augment frequent STI screening, partner notification and other efforts to reduce STI acquisition 
and transmission among MSM. 
 
 

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Doxycycline has good tolerability, high bioavailability with oral 
dosing, a 20 hour half-life, and excellent tissue penetration. 
Doxycycline is a first line treatment for CT with very high efficacy 
(97-100%). Doxycycline is used to treat syphilis for persons with 
penicillin allergy. Notably, CT and syphilis have not developed TCN 
resistance in spite of decades of doxycycline use to treat these 
infections. Doxycycline is not recommended for GC treatment due 
to baseline resistance and increased TCN resistance will not affect 
GC management. 
 
The IPERGAY study demonstrated efficacy of single dose 
doxycycline PEP after condomless sex among 232 HIV-negative 
MSM taking event-driven PrEP in France.20 Doxycycline PEP 
resulted in a 47% relative reduction in new bacterial STIs (GC, CT, 
or syphilis) over 8.7 months of follow-up (45.9 vs. 79.6 per 100 
person-years in those assigned to doxycycline PEP vs. no PEP 
control, respectively; Figure 1A. Doxycycline PEP reduced the 
incidence of CT and syphilis, but not GC (Figure 1B-D), which was 
not surprising given doxycycline resistance in >50% of GC strains 
in France. MSM in IPERGAY had a median age of 38 years, were 
highly educated, majority Caucasian, and highly adherent to event-
driven HIV PrEP. MSM in the doxycycline arm in IPERGAY took a 
median of 680 mg of doxycycline per month. Adverse events were 
rare and there was no difference in self-reported sexual behavior 
between MSM in the two study arms. 
 
Limitations of generalizability from the IPERGAY study include that 
the sample was small (n=232), and in contrast to MSM in the US 
heavily impacted by STIs, MSM were older (median age 38), highly educated, and majority Caucasian. In addition, 
with respect to adherence to event-driven doxycycline PEP, MSM in the IPERGAY study were highly adherent to 
event-driven HIV PrEP and were already ‘cueing’ their TDF-FTC (Truvada) PrEP dosing to their sexual activity. 
Importantly, uptake and adherence to doxycycline PEP among daily PrEP users are unknown. Additionally, 
IPERGAY did not conduct detailed measurements of the pattern of doxycycline use with sexual practices nor 
evaluate for antibiotic resistance associated with intermittent doxycycline use. Doxycycline PEP may be more 
efficacious for reducing GC incidence in the US than in Europe, due to lower GC TCN resistance in the US (25% 
vs 55% respectively).11, 20 PEP may also be more effective to prevent GC at non-pharyngeal sites, as evidenced 
by the lack of an observed effect on pharyngeal GC incidence, whereas there was a trend toward reduction in 
rectal and urethral GC infections with doxycycline PEP in IPERGAY.21 
 
A small study piloted daily doxycycline among 30 MSM living with HIV with a history of syphilis, and showed a 
73% reduction in composite STIs, without power to assess individual STIs.22 The greater risk of side effects and 
antimicrobial resistance (AMR) with daily dosing of doxycycline have dampened enthusiasm for daily dosing of 
doxycycline as PrEP against STIs. Event-driven doxycycline PEP has not been studied in MSM living with HIV. 
 
Significant scientific knowledge gaps remain about on-demand STI doxycycline PEP in PrEP users and 
MSM living with HIV. MSM in IPERGAY were already ‘cueing’ their Truvada PrEP dosing to sexual activity; 
PEP adherence in daily PrEP users is unknown. IPERGAY did not conduct detailed measurements of the pattern 
of doxycycline use with sexual practices nor report antibiotic resistance associated with intermittent doxycycline 
use. Doxycycline PEP may be more efficacious for reducing GC incidence in the US than in Europe, due to lower 
TCN resistance in GC the US (30% vs 55% respectively).11, 20 PEP may also be more effective to prevent GC at 
non-pharyngeal sites; there was a trend toward reduction in rectal and urethral infections with doxycycline PEP 
in IPERGAY.21 Notably, based on the IPERGAY demonstration of efficacy with doxycycline PEP, providers have 
Figure 1. IPERGAY Study: Time to first STI (panel a), GC 
infection (panel b), CT infection (panel c), and syphilis 
infection (panel d) 1 

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begun to prescribe doxycycline PEP to reduce incident STIs in MSM without a confirmatory study or normative 
guidance. Moreover, the balance of benefits and risks of doxycycline PEP need to be carefully studied in MSM 
living with HIV as well as in PrEP users in a study powered to assess effectiveness for each population. The 
relative benefits and risks of doxycycline PEP may differ in MSM living with HIV and PrEP users due to 
differences in adherence, sexual practices, potential risk compensation, sexual networks, and/or pre-existing 
antibiotic resistance due to higher prior antibiotic exposure among MSM living with HIV. 
 
In summary, a sufficiently-powered, high-quality study is needed to evaluate the effectiveness of 
doxycycline PEP in populations both with and without HIV infection, and to evaluate its impact on drug 
resistance in target bacterial STIs and resident bacterial microbiota. There is a public health need and 
sufficient clinical equipoise to conduct an effectiveness study of doxycycline PEP as an STI reduction strategy 
for a diverse population of MSM in the US to address the following key scientific questions: 1) Effectiveness of 
doxycycline PEP for bacterial STI prevention in MSM and TGW on PrEP, 2) Effectiveness of doxycycline PEP 
in MSM and TGW living with HIV; 3) Differential tolerability and impact on antimicrobial resistance between 
MSM/TGW living with HIV and MSM/TGW on PrEP; 4) TCN resistance in GC, CT and syphilis, 5) TCN resistance 
in commensal Neisseria (which can transfer TCN resistance) and potentially pathogenic Staph Aureus in carriers, 
and 6) effect on the gut resistome in terms of changes in TCN resistance genes. 
 
 
1.2 
Rationale 
The overall goal of this study is to understand the effectiveness of doxycycline PEP on reducing STIs in MSM 
and TGW populations at high risk for STI acquisition and to evaluate its impact on antibiotic resistance. 
 
1.2.1 Doxycycline Safety 
Several features of doxycycline make it an optimal choice for STI PEP. Doxycycline has been used safely and 
for extended durations as prophylaxis against infections such as malaria23 and for non-infectious conditions 
including rosacea24 and acne vulgaris.25 Doxycycline is generally safe and well-tolerated when used chronically. 
Side effects include mild gastrointestinal symptoms, photosensitivity, and rarely pill esophagitis and pseudotumor 
cerebri.26 Reassuringly, doxycycline has a much lower risk than other antibiotics for the antibiotic-associated 
diarrhea caused by C. difficile infection,27, 28 and may even exert a protective effect against C. difficile.29, 30 
Doxycycline is a scalable PEP intervention, as it is generic, inexpensive, and widely available. Doxycycline does 
not require dose adjustment in hepatic or renal failure, including dialysis. In the IPERGAY doxycycline PEP study, 
there was no difference in grade 3 or 4 adverse events between the study arms. As anticipated, there were more 
gastrointestinal side effects in those on PEP (25%) vs. the non-PEP control arm (14%). Discontinuation of 
doxycycline was uncommon with 8 study participants (7%) stopping doxycycyline due to side effects attributed 
to doxycycline, the majority of which were gastrointestinal.1 Given the safety profile of doxycycline and the 
enrollment of participants receiving ongoing clinical care for HIV or HIV PrEP, study-specific monitoring will be 
limited to complete blood count and liver function tests at months 3 and 9 to assess for hematologic and hepatic 
toxicity, which occur rarely with chronic doxycycline use (<1%). Assessment for side effects (eg., pill esophagitis, 
photosensitivity, new onset headaches), with clinical and laboratory testing if indicated if potential serious 
adverse events are suspected. Participants will receive standard of care monitoring through their HIV or PrEP. 
Typical standard of care monitoring for PLHIV includes semi-annual viral load monitoring, renal and liver function 
tests, and annual CBC. Typical standard of care monitoring for PrEP patients includes quarterly HIV tests and 
semi-annual or annual renal monitoring. 
 
1.2.2 Rationale for single dose doxycycline as STI PEP. 
A concern about a single post-sex dose of doxycycline is the long in vivo doubling time of syphilis (approximately 
30-33 hours)31, 32, which is the rationale for treatment of early syphilis with long-acting IM penicillin or oral 
doxycycline for 14 days. However, the incubation time for syphilis is 10-90 days,33and doxycycline PEP 
administered within 72 hours of exposure may deliver sufficient chemoprophylaxis to abort primary infection. 
Notably, in IPERGAY, a 73% reduction in syphilis incidence was observed with single dose doxycycline.1 In 

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addition, single dose doxycycline PEP has been shown to be effective for Lyme disease34 and leptospirosis 35, 36 
– spirochetal diseases that also have slow doubling times.35, 37 An alternative approach is doxycycline PrEP (i.e., 
daily dosing).22 However, daily doxycycline PrEP may have a higher frequency of intolerability due to side effects, 
selection of antimicrobial resistance through higher exposure, and greater costs than doxycycline PEP. 
Importantly, MSM in IPERGAY demonstrated their ability to effectively adhere to peri-coital Truvada PrEP and 
post-coital doxycycline PEP. 
 
1.2.3 Potential for drug resistance 
An important consideration with intermittent doxycycline use for STI prophylaxis is selection of drug resistance, 
in both target bacterial STI pathogens as well as in microbiota which are potential pathogens or possible 
reservoirs of antimicrobial resistance, such as S. aureus and commensal Neisseria species. GC has sequentially 
developed resistance to antibiotics in multiple classes, including those previously or currently recommended for 
treatment. Rates of TCN-resistance in GC in the US are 25%-38% in studies of MSM,11 compared with >50%  in 
Europe.20 Doxycycline is not currently recommended as treatment for GC. IPERGAY has not reported on TCN 
resistance in GC and did not address AMR in other bacterial such as S. aureus and commensal Neisseria 
species. Doxycycline is commonly used to treat CT and syphilis, and there have been no documented cases of 
TCN-resistant CT or syphilis. However, TCN resistance from single point mutations has been reported in related 
organisms such as Chlamydia suis38, 39 and Brachyspira spp.40 in antibiotic-exposed pigs, suggesting that 
development of TCN resistance could evolve (or be acquired from a resistant organism such as E. coli 41). 
Azithromycin-resistant Treponema pallidum emerged from a single mutation42 and rapidly became widespread 
in the US west coast and globally,43 serving as a cautionary tale. 
 
Repeated antibiotic exposure can foster drug resistance in the normal commensal flora of the body and impact 
the composition of gut microbiome. The effect of doxycycline use on S. aureus is an important consideration, 
given that ∼30% of the population are S aureus carriers.44 AMR is concerning for community-based MRSA 
infections, for which doxycycline is sometimes used as an alternative to sulfa drugs.45 Similarly, doxycycline 
exposure could also drive development of TCN resistance in commensal Neisseria species, serving as a 
reservoir that potentially can transfer resistance to GC. Antibiotics affect the larger microbiome, with decreased 
diversity of gut flora and shifts in the predominant species, which may fuel a “dysbiotic” environment and may 
contribute to inflammation and complications such as C. difficile.46-48 In sum, a comprehensive assessment of 
doxycycline PEP is needed, including public health benefits, safety, tolerability, adherence, and AMR among 
bacterial STIs and organisms that may can be pathogenic (e.g. S. aureus among carriers) or transfer resistance 
to GC (e.g., from commensal Neisseria). 
 
1.2.4 Rationale for evaluation of meningococcal vaccination status 
A recent report from New Zealand suggests that vaccination with an outer membrane-based Group B Neisseria 
meningitidis vaccine is associated with a reduced risk of gonorrhea in adolescents and adults aged 15-30 years 
of age; the estimated effectiveness of the OMV meningococcal vaccine against gonococcal infection to be 33% 
[ NZ OMV is part of the composition of the 4CMenB vaccine, commercially distributed as BEXSERO49 (GSK). It 
is not known if other meningococcal vaccines are associated with a similar decrease in GC infections. 
Meningococcal vaccination (Serogroup A/C/W/Y) is currently recommended by the ACIP for all PLWH and 
serogroup B vaccination is a consideration for adolescents and young adults50. Meningococcal vaccine status 
will be recorded, with the type of vaccine if known, to evaluate for a potential association of vaccination with 
decreased GC rates. 
 
 

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1.2.5 Rationale for evaluation of nongonoccal urethritis (NGU) and Mycoplasma genitalium (MG) 
Mycoplasma genitalium is a frequent cause of urethritis in men .51 MG can be detected with nucleic acid testing; 
however, many public health programs do not routinely test for MG and instead treat non-gonoccocal urethritis 
(NGU) empirically.52 While azithromycin is superior to doxycycline for treatment of MG, 53, 54 doxycycline does 
have activity against MG and use of doxycycline PEP may potentially impact the prevalence of MG, the incidence 
of MG-associated urethritis and the syndrome of NGU. Therefore, urine will be collected every three months to 
look for the presence of asymptomatic MG as well as at the time of urethral symptoms, to evaluate for MG as 
the etiology of urethritis.53, 54 Specimens with MG detected will be stored for future analysis of resistance to 
tetracycline and other antimicrobials. 
 
1.2.6 Rationale for evaluation of longitudinal weight change 
Tetracyclines have been associated with weight gain in mice,55 as well as in individuals taking tetracycline- 
based combination therapy for Q fever56 and for Helicobacter pylori.57, 58 Therefore, participants in both arms 
will have weight evaluated at regular intervals to evaluate for possible weight gain 
 
1.2.7 Impact of COVID-19 on study conduct 
Study enrollment and the majority of in-person study evaluations were halted in March 2020 due to the COVID- 
19 pandemic and the hold on clinical research required by the participating institutions. As a result, patients 
enrolled 3/2020 or earlier were unable to undergo regular ascertainment for the STI endpoint during the following 
months. Given the need for full endpoint ascertainment and acknowledging potential changes in sexual behavior 
during the COVID pandemic, participants enrolled 3/2020 and earlier will be offered a full 12 months of follow up 
at the time of resumption of follow up after COVID restrictions are lifted. Those who decline a 12 month follow 
up will be discontinued. The team will monitor discontinuation rates in this pre-COVID cohort. If there is a 
differential discontinuation in the active vs. control arm, this will be discussed with DSMB and the team statistician 
with consideration of additional enrollments to ensure adequate power for the primary endpoint 
 
As COVID may continue to impact research activity in the future, the study will allow for electronic consenting 
as an option, and shipment of doxycycline to participant homes, if necessary and if acceptable to study 
participants. In-person visits will be preferred when feasible to allow for STI testing, research labs, and pill 
counts. Home collection of STI testing may be considered, as long as there is sufficient data to support the 
testing platforms for use in home collection, particularly in terms of syphilis testing. 
 
1.2.8 Early closure by the DSMB and revision to study conduct  
Enrollment into the DoxyPEP study was stopped early on 5/13/2022, as a prespecified interim data analysis 
demonstrated that the study had crossed pre-specified effectiveness thresholds. At the time of interimr review 
of  554 participants enrolled,  a single dose of 200 mg doxycycline taken after condomless sex significantly 
reduced the acquisition of gonorrhea, chlamydia and syphilis in men who have sex with men (MSM) and 
transgender women (TGW).  The effectiveness of doxycycline PEP was observed and statistically significant 
both in the cohort of participants living with HIV and the cohort of participants without HIV who were taking 
PrEP. The strategy of doxyPEP was safe and well-tolerated, with no doxycycline-associated Grade 2 or higher 
adverse events and no doxycycline-associated serious adverse events.  
 
Enrolled participants will be notified of the study early closure and of the finding of doxycycline effectiveness 
to reduce STIs. They will also be informed that the impact of doxycycline PEP on antimicrobial resistance in 
STIs, S. aureus, commensal Neisseria and the gut microbiome is still under investigation. This protocol 
modification amends the study to offer doxycycline to enrolled participants assigned to the standard of care 
arm for the remainder of their 12 month participation. Participants who roll over from the control arm into the 
active doxycycline PEP arm will undergo the same evaluations as specified for the active arm (e.g., safety 
labs) per the schedule of events and will continue with quarterly study visits through month 12. At the time of 
roll over onto active doxycycline PEP, a rectal swab to establish the microbiome baseline prior to starting 
doxycycline will be collected.  Participants who decline to roll over into the active doxycycline arm will have the 
option of remaining on study through month 12 following the standard of care arm schedule of events. All 

DoxyPEP protocol Ver 9.0 5/27/2022 
13 
 
 
participants will review and sign a revised informed consent at the time of their next study visit to consent to 
continuation in the study and to receive doxycycline, for those in control arm who chose to roll over to active 
doxyPEP. 
 
The goal of continued follow-up through Month 12 of enrolled participants receiving doxycycline PEP is to 
obtain additional data on the tolerability and acceptability of doxycycline PEP and the impact of intermittent 
doxycycline PEP on antimicrobial resistance and the gut microbiome. This information is critical for 
understanding the risk/benefit profile of doxycycline PEP and to inform guidelines about the doxyPEP strategy 
which will be considered both by individuals, providers, and public health authorities.  
 
 
2 
STUDY DESIGN 
 
Design: The overarching goal is to assess the effectiveness of doxycycline PEP on incidence of STIs and 
tetracycline resistance among STIs and commensal bacteria to inform public health policy. Participants will be 
randomized 2:1 (see Schema), with two-thirds receiving doxycycline PEP and one-third receiving the standard 
of care control, to maximize data on safety, tolerability, adherence coverage of sexual acts, and resistance data 
in participants randomized to doxycycline PEP, without negatively impacting power to measure effectiveness. 
Participants will be counseled about the preliminary effectiveness data from IPERGAY, and the potential for AMR 
in STIs or other bacteria. Possibility of unreported doxycycline use in the control arm (contamination) will be 
monitored through retrospective batch testing of doxycycline metabolites in hair, to detect doxycycline use in the 
prior 3 months. 59 
 
The trial of doxycycline PEP will be powered to separately assess impact for MSM living with HIV and MSM on 
PrEP because of potential differences in safety, tolerability, adherence, sexual networks, sexual practices, 
background AMR, and ultimately, PEP effectiveness. Eligible participants randomized 2:1 to receive PEP will 
receive open-label doxycycline 200 mg to be taken ideally within 24 hours but no later than 72 hours after 
condomless sexual contact (oral or anal). 200 mg of doxycycline will be taken at most once per 24 hour period 
regardless of the number of sexual acts occurring during this time period. the rationale for 2:1 randomization is 
to maximize data on doxycycline PEP safety, tolerability, acceptability, and resistance, while providing sufficient 
power for the primary outcome of the effectiveness of doxycycline PEP. Sexual activity will be recorded for both 
arms of the study (doxycycline PEP and control condition) by the participant using a smartphone application that 
will be adapted for study use; this will enable comparable assessment of risk in the two arms. PEP pill-taking will 
also be measured by the app to enable assessment of coverage of sex acts by PEP. Sexual activity and 
adherence will also be assessed in person at quarterly visits. STI testing will be conducted quarterly from three 
anatomic sites (pharyngeal, rectal, and urinary) and blood obtained for syphilis testing, following CDC guidelines 
for serologic diagnosis of syphilis. Participants with a positive STI test will return for STI treatment and for swabs 
of the affected site for resistance testing; culture based for GC and molecular methods for CT and syphilis. Those 
with signs and symptoms suggestive of syphilis infection and those with a reactive syphilis serologic test that 
indicates a new syphilis infection will have swabs of any current active lesion (if present) as well as mucosal 
swabs from the oropharynx. Swabs from the anterior nares and oropharynx will be obtained at baseline, 6 and 
12 months to evaluate tetracycline resistance in S. aureus among carriers and oropharyngeal swabs will be 
obtained at baseline and 12 months to evaluate tetracycline resistance in commensal Neisseria species. 
 
Stool samples from 100 participants on the doxycycline PEP arm − 50 MSM and TGW living with HIV and 50 
MSM and TGW on PrEP− will be collected at baseline, 6 and 12 months to evaluate effects of intermittent 
doxycycline on the gut resistome, using FLASH targeted metagenomic sequencing to evaluate for tetracycline 
and other resistance genes. Rectal swabs will be collected and archived in all participants at baseline, 6, and 12 
months for future studies of the impact of doxycycline PEP on the enteric microbiome and resistome. 
 
Study population: This study will enroll 780 participants living with HIV and HIV-negative persons taking PrEP. 
An approximately equal number of  PLWH and HIV uninfected persons taking PrEP will be enrolled.  An 
approximately equal number of participants in each of these cohorts (and in each study arm) will be enrolled in 

DoxyPEP protocol Ver 9.0 5/27/2022 
14 
 
 
San Francisco and Seattle. 
 
Current or planned initiation of PrEP use is an eligibility criterion for enrollment, because this population of MSM 
and TGW has high rates of STIs and is typically seen quarterly for PrEP visits. However, participants may opt to 
stop PrEP use at any time during the study without affecting their involvement in the study. Any participants 
without HIV infection who subsequently seroconvert will be managed clinically by the study site according to 
local practice (appropriate counseling, clinical evaluation, and immediate linkage to clinical and psychosocial 
services). These participants will also be retained in the study unless they choose to discontinue study 
participation. 
 
 
3 
OBJECTIVES 
 
3.1 
Primary Objectives 
3.1.1 Evaluate the effectiveness of doxycycline post-exposure prophylaxis (PEP) to reduce STI infections 
in two populations: a) MSM/TGW living with HIV and b) MSM/TGW taking HIV PrEP. 
3.1.2 Investigate the impact of doxycycline PEP on development of culture-based tetracycline (TCN) 
resistance in N. gonorrheae and among nasopharyngeal carriers of S. aureus 
 
3.2 
Secondary Objectives 
3.2.1 Assess the safety, tolerability, and acceptability of doxycycline PEP 
3.2.2 Investigate the impact of doxycycline PEP on detection of culture and molecular markers of tetracycline 
(TCN) resistance in C. trachomatis (CT), and T. pallidum (syphilis- molecular markers only). 
3.2.3 Measure the proportion of sex acts which are covered by doxycycline PEP 
3.2.4 
Evaluate the development of phenotypic TCN-resistance among oropharyngeal carriers of commensal 
Neisseria species 
3.2.5 Assess the effect of doxycycline PEP on the gut resistome through measuring the abundance of 
tetracycline resistance genes in stool of a subset of 50 MSM living with HIV and 50 MSM/TGW 
on PrEP assigned to receive doxycycline PEP as well as rectal swabs from all participants, 
stored for future evaluation 
 
3.3 
Exploratory objectives 
3.3.1 Evaluate the diversity of the gut microbiome and quantity and breadth of drug resistance genes  
in participants on doxycycline PEP and not on PEP 
3.3.2 Assess the association between meningococcal vaccination and incident GC infection 
3.3.3 Evaluate the incidence of urethritis without identified bacterial etiology and the proportion which is 
associated with MG in each arm 
 
3.3.4 Assess the rate of detection of Mycoplasma genitalium (MG) in urine in each arm and the 
presence of tetracycline and other antimicrobial resistance in MG in each arm. 
3.3.5 Evaluate association of doxycycline use with weight change over time 
3.3.6 Evaluate whether doxycycline PEP is associated with PrEP persistence and HIV virologic 
suppression by comparison of arms and within the doxycycline PEP arm by adherence to 
doxycycline PEP. 
3.3.7 Evaluate the incidence of lymphogranuloma venereum (LGV) in those diagnosed with rectal 
chlamydia in each arm 
 
 
 
4 
SELECTION AND ENROLLMENT OF PARTICIPANTS 
 

DoxyPEP protocol Ver 9.0 5/27/2022 
15 
 
 
4.1 
Inclusion criteria 
4.1.1 Willing and able to give written informed consent 
4.1.2 Age > 18 years 
4.1.3 Male sex at birth 
4.1.4 Previously HIV-diagnosed 
OR 
HIV-seronegative at the time of last test within the past three months and a current prescription for 
PrEP (both daily or event-driven PrEP permitted) or plan to start PrEP within 30 days after the 
enrollment visit 
4.1.5 Condomless anal or oral sexual contact with ≥ 1 male sex-at-birth partners in the past 12 months 
4.1.6 Diagnosed with GC, CT or syphilis in the past 12 months. 
Note: self report of STI is acceptable if documentation not available. If the participant reports an incident 
STI in the past year at the same clinic where the participant will be enrolled, this diagnosis should be 
confirmed by chart review prior to enrollment. If the diagnosis from this clinic cannot be confirmed, the 
participant should not be enrolled.  If the STI was reported at a clinical site that is not the study site, and 
records cannot be obtained, self-report will suffice. 
 
Note: Syphilis diagnosis within the last year refers to primary syphilis, secondary syphilis, and 
documented early latent syphilis (< 1 year since last syphilis diagnosis or negative test).  Known late 
latent syphilis or latent syphilis of unknown duration would not qualify. Positive syphilis titers which 
represent serofast status and not active disease do not qualify as a syphilis diagnosis. Clinician 
judgement regarding qualifying syphilis diagnosis should be sought when the diagnosis of syphilis in the 
past year is not clear or if there is a question about serofast status vs. active infection.  
 
 
4.2 
Exclusion criteria 
4.2.1 Allergy to tetracycline class 
4.2.2 Current medications which may impact doxycycline metabolism or that are contraindicated with 
doxycycline, as per the prescribing information. These include systemic retinoids, barbiturates, 
carbamazepine, and phenytoin. 
4.2.3 Current use of warfarin, as intermittent doxycycline use can lead to an unpredictable impact on 
INR 
4.2.4 Anticipated use of doxycycline during the coming 12 months for non-STI prevention use (e.g., 
acne treatment). 
 
4.3 
Recruitment 
Each site has established local recruitment and screening methods that operationalize protocol-specified 
requirements for eligibility determination in a manner that is tailored to and most efficient for the local study 
setting and target study population. Each site will use a variety of recruitment approaches, including direct 
recruitment at clinics, referrals from other providers of PrEP and ART, and use of online and social networking 
websites and apps. Recruitment materials will educate participants about STI prevalence and incidence in their 
community and the pilot study that demonstrated efficacy of doxycycline for reducing incidence of STIs among 
MSM in IPERGAY. 
 
The study will enroll from 4 clinical sites, 2 in Seattle and 2 in San Francisco (Table 1), which have established 
track records of high quality research in MSM and TGW populations integrated into clinical care settings; 
annual retention rates in clinical trials conducted in these sites exceed 80%-90%. The sites have large MSM 
populations that are ethnically and racially diverse. 
 
 
Table 1. Study Sites 

DoxyPEP protocol Ver 9.0 5/27/2022 
16 
 
 
High volume, comprehensive HIV care clinics with 
on-site STI testing & treatment. 
• “Ward 86” HIV Clinic, ZSFG, UCSF, San 
Francsico, CA 
• Madison (HIV) Clinic, Harborview Medical 
Center, UW, Seattle, WA 
 
Municipal STI clinics with integrated on-site HIV 
PrEP programs. 
• San Francisco City Clinic, San Francisco CA 
• Public Health – Seattle & King County 
Sexual Health Clinic, Seattle, WA 
 
4.4 
Co-enrollment guidelines. 
Participants may be co-enrolled in other research studies, provided that these are a) observational studies or b) 
evaluation of an FDA approved intervention which is not an antibiotic, is not intended to treat or prevent an STI, 
and is compatible with coadministration of doxycycline. The study team should be consulted for co-enrollment 
in studies that do not meet this guidance or if there are questions about eligibility for co-enrollment. For any co-
enrolled study, combined blood draws should not exceed current Red Cross phlebotomy guidance. 
 
 
5 
STUDY TREATMENT 
 
5.1 
Study product 
Generic delayed release doxcycyline hyclate 200 mg capsules (Mayne Pharmaceuticals) will be provided by 
the study to participants randomized to open-label PEP, and to participants who choose to roll over to active 
doxycycline PEP following the 5/13/2022 closure of enrollment. Doxycycline DR is bioequivalent to 
doxycycline hyclate IR. 60, 61 Doxycycline hyclate is widely available and FDA approved for the treatment of 
multiple infectious conditions. The full prescribing information can be accessed at: 
https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=cd2ab9b8-9619-4199-8a5d-83377b3274d1 
 
5.2 
Safety of doxycycline 
Doxycycline is an antibiotic that can be used for prolonged periods of several months in the treatment of acne or 
in the prevention of malaria. The tolerance of repeated-dose of doxycycline in this 12 months study should 
therefore be acceptable. 
 
The most common side effects of doxycycline are62, 63 
• 
Gastrointestinal: nausea, diarrhea, epigastric pain, anorexia, glossitis, enterocolitis, anal and genital 
candidiasis 
• 
Esophageal disorders: dysphagia, pill esophagitis, and rarely esophageal ulceration. Risk for 
esophageal irritation can be reduced by taking doxycycline tablets at least one hour before bedtime (to 
avoid lying down during doxycycline intake) at a meal with a large glass of water (100 ml). 
• 
Skin reactions including maculopapular, erythematous and photosensitivity skin reactions. Due to 
concern for photosensitivity, individuals taking doxycycline are advised to avoid excessive exposure to 
sunlight and UV radiation (such as tanning beds). 
 
Other possible but rare adverse effects occurring in < 1% in post-marketing reports include: 
• 
Hypersensitivity reactions: urticarial, anaphylaxis, serum sickness, drug reaction with eosinophilia and 
systemic symptoms (DRESS) 
• 
Skin toxicity: fixed drug eruption. Stevens-Johnson syndrome, toxic epidermal necrolysis, erythema 
multiforme, fixed drug eruptions exacerbation of preexisting lupus erythematosus 
• 
Pericarditis 
• 
Hematological disorders: hemolytic anemia, thrombocytopenia, neutropenia, eosinophilia 
• 
Intracranial hypertension (also known as pseudotumor cerebri) 
 

DoxyPEP protocol Ver 9.0 5/27/2022 
17 
 
 
5.3 
Doxycycline dispensing and administration. 
Doxycycline will be dispensed at each 3-month visit or in shorter intervals per patient preference, with additional 
dispensation as needed to replace lost medication or provide additional medication when needed (see MOPS 
for addition dispensing guidance). Capsules should be stored at room temperature (59-86o F) to the extent 
feasible. Participants will be instructed to take 200 mg of doxycycline within 24 hours after condomless sexual 
contact, and no later than 72 hours after sex. Condomless sexual contact is defined as receptive anal, insertive 
anal, vaginal, or oral sex (which includes oral/anal and oral/genital contact) or use of shared sex toys without a 
condom used for the entire time. For participants reporting multiple sexual encounters, 200 mg of doxycycline 
will be recommended to be taken every 24 hours until after the last sexual encounter. Participants will be 
instructed not to exceed 200 mg of doxycycline in a 24 hour period. Study staff will instruct participants on 
procedures for replacement of lost medication. 
 
Doxycycline may be taken on an empty stomach or with food, and it is advised to take each dose with a large glass 
of water at least 60 minutes before bed to reduce risk of esophageal irritation. All participants randomized to PEP 
will be advised to avoid excessive sun exposure and artificial UV light, such as tanning beds, and to consider 
use of sunscreen if they will be exposed to sun. 
 
5.4 
Concomitant medications 
Participants randomized to doxycycline PEP should report current and new medications to the study team to 
ensure no concern for drug interactions with doxycycline. The prescribing information for doxycycline 
monohydrate should be reviewed to ensure no potential for drug interactions. 
 
5.4.1 Prohibited medications 
• 
Barbiturates 
• 
Carbamazapine 
• 
Phenytoin 
• 
Methoxyflurane 
• 
Systemic retinoids, such as acitretin and isotretinoin 
 
5.4.2 Precautionary Medications 
• 
Antacids containing aluminum, iron, calcium, or magnesium, or bismuth subsalicyclate products 
(such as Pepto-Bismol) may impair doxycycline absorption and should be separated 2 hours 
before or after doxycycline 
• 
Oral iron supplements may impact doxycycline absorption. Iron should be separated 2 hours 
before or after doxycycline 
 
5.5 
HIV pre-exposure prophylaxis (PrEP) and HIV antiretroviral therapy (ART) 
PrEP and ART will not be provided by the study but will be accessible through local providers following the 
standard of care. Each of the participating sites has a clinical infrastructure in place to assist individuals with 
obtaining ART and PrEP, including for those without insurance or whose insurance status changes. 

DoxyPEP protocol Ver 9.0 5/27/2022 
18 
 
 
6 
CLINICAL AND LABORATORY MONITORING 
 
6.1 
Schedule of Events 
 
Month (+2/-10 week window) 
0 
3 
6 
9 
12 or 
Termination 
visit 
Doxycycline 
initiation visit for 
those in control 
arm 
Informed consent 
√ 
 
 
 
 
√ 
Smartphone app instructions 
√ 
 
 
 
 
 
Review of current medications 
√ 
√* 
√* 
√* 
√* 
√ 
Antibiotic & STI history 
√ 
√ 
√ 
√ 
√ 
 
Meningococcal vaccination history 
√ 
 
 
 
√ 
 
Sexual behavior questionnaire 
√ 
√ 
√ 
√ 
√ 
 
Dispense pills/adherence counseling* 
√* 
√* 
√* 
√* 
 
√ 
Doxycycline pill count and adherence 
recall* 
 
√* 
√* 
√* 
√* 
 
Doxycycline PEP acceptability survey* 
 
 
√* 
 
√* 
 
General symptom assessment 
√ 
√ 
√ 
√ 
√ 
 
Costing questionnaire 
 
√ 
√ 
√ 
√ 
 
Condoms/lubricant 
√ 
√ 
√ 
√ 
√ 
 
Risk reduction counseling 
√ 
√ 
√ 
√ 
√ 
 
GC/CT testing (throat & rectal swab, urine 
collection) 
√ 
√ 
√ 
√ 
√ 
 
Syphilis testing 
√ 
√ 
√ 
√ 
√ 
 
Rectal swabs stored for future microbiome 
testing, all participants 
√ 
 
√ 
 
√ 
√ 
Rectal swab stored for future MG testing 
√ 
√ 
√ 
√ 
√ 
 
Urine stored for future MG testing (also at 
time of symptomatic urethritis) 
√ 
√ 
√ 
√ 
√ 
 
Swabs/urine at time of evaluation for STI 
symptoms or confirmed STIs for 
resistance testing 
 
at time of evaluation for STI symptoms or confirmed STI 
Anterior nares and oropharyngeal swabs 
for Staphylococcus aureus culture 
√ 
 
√ 
 
√ 
 
Oropharyngeal swabs for cultures of 
Neisseria species 
√ 
 
 
 
√ 
 
Stool sample from first 50 PLWH & first 50 
HIV- on PrEP* 
√* 
 
√* 
 
√* 
 
Collection of hair for doxycycline testing 
 
 
√ 
 
√ 
 
 

DoxyPEP protocol Ver 9.0 5/27/2022 
19 
 
 
HIV testing data from local care 
(HIV RNA, CD4) 
√ 
 
 
 
√ 
 
CBC and liver function tests* 
 
√* 
 
√* 
√** 
 
Stored serum for future testing (Optional) 
√ 
 
 
 
√ 
 
Reimbursement 
√ 
√ 
√ 
√ 
√ 
 
Weight 
√ 
√ 
√ 
√ 
√ 
 
Qualitative interviews* 
(subset of participants, optional) 
 
3-12 months 
*Intervention arm only   **Standard of care arm only 
 

DoxyPEP protocol Ver 9.0 5/27/2022 
20 
 
 
6.2 
Study visits 
Specific study procedures are detailed in Table 6.1. Visits will take place at enrollment and quarterly thereafter, 
up to 12 months. Interim visits may be scheduled for diagnosis and treatment of STI and collection of additional 
specimens or for evaluation of possible doxycycline associated adverse events. Participants may also request 
interim STI testing. 
 
6.2.1 Enrollment Visit After confirming eligibility through pre-screening and prior to study procedures, we will 
obtain written informed consent and collect locating information; the latter will be updated at each study 
visit. At enrollment, demographic, behavioral, and clinical information will be collected and a release of 
information obtained to permit access to medical records. STI testing for chlamydia and gonorrhea 
through nucleic acid amplification testing (NAAT) of clinician or self-collected pharyngeal and rectal 
swabs and first void urine will be conducted. Serologic testing for syphilis will be conducted. If required 
STI testing has been conducted within past 30 days, these results may be used for the enrollment 
evaluation. Participants diagnosed with an STI at baseline will be treated; presence of a baseline STI 
will not preclude enrollment but STI’s present at time of enrollment will not count towards study 
endpoints. All STIs will be reported to the local health department as required per local standard 
procedures. 
 
Randomization Within 14 days of enrollment, participants will be randomized in a 2:1 ratio to open- 
label doxycycline PEP or the standard of care control condition (regular STI counseling, screening and 
treatment as indicated). The randomization code and resulting allocation list will be generated and 
maintained by the study statistician. The list will be blocked and stratified by site. While neither 
participants nor study staff will be blind to each participant’s randomization group once assigned, the 
randomization scheme will utilize varying block sizes in order to protect the blind prior to randomization 
of each participant. 
 
6.2.2 Quarterly visits after enrollment. Quarterly visits will be conducted every 90 days, +2 weeks/ -10 
weeks. Participants unable to attend a quarterly visit will be asked to return for an unscheduled visit as 
soon as feasible. The quarterly evaluations should be completed at the time of this visit. Subsequent 
visits should occur on the assigned quarterly scheduled to the extent possible. 
 
6.2.3 Unscheduled interim visits: Participants will be instructed to contact the study site and return for an 
unscheduled visit for any of the following a) new diagnosis of STI, b) concern for possible adverse event 
associated with doxycycline, c) need for additional doxycycline (in participants who were randomized 
to PEP arm), d) difficulty using the smartphone app, or any other study-related concerns. 
Reimbursement will not be provided for unscheduled visits. All interim contacts and visits will be 
documented in participants' study records and on applicable CRFs. 
 
6.2.4 Termination visit: In the event that a participant prematurely discontinues study participation, the 
evaluations for the termination visit should be completed if possible. 
 
6.3 
Instructions for evaluations 
 
6.3.1 Smart phone application: A smartphone application (app), Blackbook, (developed in conjunction 
with UCSF researchers) currently in use to track sexual behavior and PrEP use in young MSM has 
been adapted for use in this study to measure daily sexual risk practices (both study arms) and 
doxycycline PEP administration (intervention arm only). Study staff will assist with obtaining 
smartphones through local available resources such as Lifeline Assist, which make cell phones 
available to qualifying lower income individuals, when needed and feasible 
(https://www.truconnect.com/lifeline/freephone/signup). Participants will be given unique codes to 
permit download of the app from an online resource and guidance on how to use the application. 

DoxyPEP protocol Ver 9.0 5/27/2022 
21 
 
 
 
6.3.2 Review of current medications: All participants will have current medications reviewed at screening 
for possible drug interaction with doxycycline. At subsequent quarterly visits, participants randomized 
to doxycycline PEP will have current medications be reviewed and any new medications will be 
assessed for possible drug interactions. 
6.3.3 STI symptom screen. Participants will be asked about current STI symptoms including dysuria, rash, 
throat pain, rectal pain/discharge, and genital lesions 
6.3.4 Symptom assessment. At each visit, participants in both study arms will be asked about possible 
doxycycline side effects, including esophagitis, rash, gastrointestinal symptoms, photosensitivity, 
headache, and changes in vision (including blurred, double vision, vision loss). Control arm 
participants will be asked about these symptoms to establish a comparator for non-specific symptoms 
which can occur in the absence of doxycycline. 
6.3.5 Antibiotic and STI history: History will be recorded of any non-study provided antibiotics taken in the 
last 3 months and any STI diagnosis in preceding 3 months, including the diagnosis of urethritis 
requiring treatment but without detection of gonorrhea or chlamydia. At study entry, STI history for 
preceding 12 months will be recorded as well as obtained through chart review when possible. 
6.3.6 Meningococcal vaccination history: At study entry and at month 12, receipt of any prior 
meningococcal vaccination and the type (if known) will be recorded, using a checklist that will include 
- 
Serogroup A only (includes MenAfriVa, PsA-TT) 
- 
Serogroup B only (includes Trumenba, Bexsero) 
- 
Serogroup C only (includes Meningitec, NeisVac C) 
- 
Quadrivalent A/C/Y/W (includes Menomune, Menveo,Nimirix, Menactra) 
- 
Or other formulation 
Type of vaccination may be confirmed by chart review if records are available. 
6.3.7 Sexual behavior questionnaire: Participants will be asked to complete a sexual behavior 
questionnaire recording number and type of sexual contacts in the past 3 months at enrollment and 
between visits 
6.3.8 Pill count and doxycycline adherence assessment. Participants assigned to doxycycline PEP or 
who roll over to receive doxycycline in the control arm will be asked to bring their doxycycline bottles 
in at each visit for a pill count. They will be asked what proportion of sex acts were covered by PEP 
in the past month and past 3 months, an estimate of overall adherence, and how many total doses of 
doxycycline were taken in the past 3 months.  
 
Note: any period of 7 or more days in which the participant had condomless sexual activity but did 
not take doxycycline will be recorded as a doxycycline interruption. This includes interruptions due to 
lack of doxycycline, forgetting to take doxycycline, taking medication not compatible with doxycycline, 
or participant decision to temporarily or permanently discontinue study-provided doxycycline.  
6.3.9 Doxycycline PEP acceptability survey. At months 6 and 12, participants assigned to  or now taking 
doxycycline PEP will be given a brief self-administered questionnaire evaluating acceptability of PEP 
6.3.10 Risk reduction counseling and offer to provide of condoms/lubricant. At each visit, staff will 
counsel all participants about STI risk reduction and HIV prevention (if not living with HIV), and the 
importance of adherence to ART and PrEP, according to local standard of care. 
6.3.11 STI testing. 
GC/CT: First void urine and pharyngeal and rectal swabs will be collected for NAAT testing. Swabs 
may be self collected or collected by study staff. GC & CT testing should be conducted at least 14 
days after treatment to avoid false positive nucleic acid results. 
 
Note: If GC or CT have been conducted within 30 days prior to study visit and these results are 
available, these results may be used for the quarterly STI assessment. All available STI results should 
be recorded. 
 
RPR: Blood will be collected for non-treponemal assay (RPR or VDRL) with titer if positive. 
Treponemal assay results should be recorded if RPR or VDRL are positive. Syphilis testing will be 

DoxyPEP protocol Ver 9.0 5/27/2022 
22 
 
 
repeated quarterly after last treatment for syphilis to determine if titers fall or if not, for clinical 
evaluation of treatment failure or reinfection. Titers must be interpreted in the context of prior test 
results and current symptoms and exposure history. The need for treatment will be based on 
the clinical assessment of the site investigator based on the serological data and clinical findings. All 
syphilis endpoints will be determined by the Endpoint Adjudication committee (see 10.3) 
 
Note: It is preferred to not repeat syphilis testing at a quarterly visit if testing has been done less than 
12 weeks before the visit and these tests are available. All available syphilis test results should be 
recorded. 
 
6.3.12 Rectal swab for future M. genitalium and other testing. 
Rectal swab will be collected and stored for future batched M.gen testing, including M.gen antibiotic 
resistance testing, and potential testing for other infectious organisms. Swabs may be self-collected 
or collected by study staff. 
 
6.3.13 Urine for M.genitalium testing 
At the time of urine collection for GC/CT testing, a sample of this urine collection will be stored for 
future batched testing for MG. Remnant urine from GC/CT testing may be used or the initial first catch 
specimen may be divided into two samples, as long as the minimum volume for GC/CT testing is met. 
See the MOPS for more information. Urine should also be collected for M.gen at the time of 
symptomatic urethritis (see Table 6.4.1) 
6.3.14 Nasal and oropharyngeal swab for Staphylococcus aureus: nares and oropharynx will be swabbed 
and cultured for S. aureus, with antibiotic resistance testing if S. aureus growth present 
6.3.15 Oropharyngeal swab for commensal Neisseria species. At baseline and month 12, all participants 
will undergo oropharyngeal swab for Neisseria species and TCN-resistance testing if Neisseria 
species are isolated.  
6.3.16 Stool specimen: Stool samples from the first 50 participants living with HIV and 50 HIV- participants 
on PrEP who consent to collection will be obtained at baseline, 6 and 12 months for metagenomic 
resistome studies using 16sRNA amplification of TCN resistance genes. In the event that participants 
cannot provide a stool sample at the scheduled visit, they will have up to 2 weeks from the enrollment 
and 12-month visit to return the stool specimens for those visits, and up until two weeks after the 9-
month visit to return the stool specimen for the 6-month visit.  
6.3.17 Rectal Swab for microbiome testing: Rectal swabs will be collected and frozen for future 
microbiome analysis. These swabs may be self collected or collected by study staff. 
6.3.18 Hair collection: Hair will be collected from all participants who consent to collection and who meet 
eligibility for hair collection (occipital hair length > 0.5 cm and absence of bleaching in area to be 
collected) See manual of procedures for details on hair collection 
6.3.19 HIV testing and RNA data: 
For PLWH: At entry and month 12, the most recent HIV RNA data available from clinical visits will be 
recorded 
For participants on PrEP: At entry, the most recent HIV antibody or viral test results from clinical care 
will be recorded. If no test results available within the past 3 months, HIV testing should be obtained, 
consistent with standard of care monitoring for PrEP. At month 12, the most recent HIV antibody or 
viral load test results from clinical care will be recorded. 
6.3.20 ART and PrEP status 
For PLWH, current ART regimen and status (taking vs. not taking) will be recorded at each visit. At 
entry and month 12 for PLWH, the most recent HIV RNA and CD4+ cell count available from clinical 
visits will be recorded if available 
For participants on PrEP At each visit for those on PrEP, PrEP status will be assessed (taking vs. 
not taking, and how PrEP is taken- daily vs intermittent ). At entry and month 12, the most recent HIV 
antibody or viral load test results from clinical care will be recorded. 
6.3.21 Hematologic and liver function tests: Complete blood count (CBC) (white count with differential, 
hemoglobin, platelets) and liver function testing (AST, ALT, total bilirubin and alkaline phosphatase) 

DoxyPEP protocol Ver 9.0 5/27/2022 
23 
 
 
will be drawn at months 3 and 9 in those on doxycycline PEP. Testing done through standard of care 
within 30 days of the study visit may also be used if available. For those in the standard of care arm, 
CBC will be done at the month 12 visit. In the event that a CBC cannot be obtained at month 12, an 
available CBC from any time during study participation may be used.  
6.3.22 Serum for storage (Optional): At months 0 and 12, 10 mL of serum will be collected for storage for 
future analysis (non-genetic) in participants who agreed to this. Serum may be collected up to 14 
days after the visit if blood cannot be collected at the time of the visit. 
6.3.23 Reimbursement: Participants will be reimbursed at the enrollment visit, at quarterly visits, and at the 
time of return for treatment of STIs with accompanying collection of swabs. An additional 
reimbursement will be provided for participants who consent to the optional stool sample collection at 
the baseline, 6 month, and 12 month timepoints. No reimbursement will be provided at other 
unscheduled interim visits such as visits to provide additional doxycycline. 
6.3.24 Roll over from standard of care to active doxycycline:  All participants initially assigned to the 
standard care arm will be offered the option to receive doxycycline through the study for the remainder 
of their 12 month follow up period. If a standard of care arm participant elects to initiate doxycycline, 
they will complete a new informed consent at the doxycycline initiation visit, and will be provided with 
instructions and counseling on how to use doxycycline PEP.  If a control arm participant comes in to 
initiate doxycycline at a time that falls within the visit window for the next scheduled study visit, all 
scheduled visit evaluations will be conducted, in addition to a rectal swab for microbiome testing, if 
not already scheduled. Up to three bottles of doxycycline will be dispensed at the initial visit- a 
sufficient quantity to ensure enough doxycycline for daily use until the next quarterly visit or the end 
of study visit. If a control arm participant comes in to initiate doxycycline at a time that is before the 
visit window for the next scheduled study visit, doxycycline will be dispensed and a rectal swab 
obtained for microbiome evaluation. CBC and LFT evaluations for possible doxycycline toxicity will 
occur at the month 3 and month 9 study visits per the SOE.  If there is a delay in the participant’s 
ability to come in for a doxycycline initiation visit, it is acceptable for doxycycline to be provided 
through primary care or other provider in advance of visit. Roll over to doxycycline and the date of 
starting doxycycline will be recorded on a CRF. 
 
6.4 
Evaluation at time of presumptive or diagnosed GC, CT and syphilis 
 
6.4.1 Symptoms suggestive of STI for which presumptive STI treatment will be administered. 
For those who have symptoms of an STI at a study visit given characteristic clinical presentation (such as 
chancre, rash characteristic of syphilis, symptomatic urethritis or proctitis) such that the treating clinician will 
provide empiric STI treatment while awaiting confirmatory testing, standard STI testing should be obtained from 
urine/pharynx/rectum for GC/CT and blood for syphilis testing. In addition, the following specimens should be 
obtained for resistance testing from symptomatic anatomic sites based on the clinical presentation as outlined 
in Table 6.4.1. 
 
NOTE: For specimens collected due to presumptive infection, the resistance testing specimens (swabs/urine 
collection) should be held until definitive STI testing is available. If STI testing indicates no infection, the 
specimens may be discarded. Alternatively, the site may send all specimens for storage. Specimens that are 
not associated with a confirmed STI will be discarded when the data management team confirms absence of 
STI. If there is uncertainty about whether STI if present, the specimens should be sent to the BioHUB for testing. 
 
NOTE: Testing for evidence of resistance to GC, CT and syphilis should be conducted prior to STI treatment.  If 
collection of specimens before treatment is not possible, CT and syphilis testing can be conducted the same 
day of treatment after treatment has been provided. Per the SURRG protocol, GC cultures should only be 
collected before GC treatment.  
 
 

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Table 6.4.1 Specimen collection for resistance testing at time of evaluation for STI and presumptive 
STI treatment 
 
Presumptive 
infection 
 
Specimen collection 
 
Buccal 
Swab 
(Zymo) 
Rectal 
Swab 
(Zymo) 
Urine 
(Zymo) 
Urine 
(Hologic 
urine 
specimen 
for M.gen) 
Swab of 
chancre/ 
mucosal 
lesion 
(Zymo) 
GC culture per local 
protocol (all anatomic 
sites of sexual 
exposure in past 90 
days) 
Urethritis 
 
 
√ 
√ 
 
(urethral discharge) 
Proctitis 
 
√ 
 
 
 
√ 
Syphilis with 
chancre/mucosal 
legion 
 
 
 
 
√ 
 
Syphilis diagnosis 
without 
chancre/mucosal 
lesion 
√ 
 
 
 
 
 
 
 
 

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6.4.2 Documented STI: 
Individuals with positive GC and/or CT NAAT results or with serologic testing indicating a new syphilis infection 
will be contacted to return for STI treatment as well as swabs of affected site for resistance testing or urine 
collection, as outlined in Table 6.4.1 Specifically: 
• 
Those with positive GC NAAT results will have 
1) a swab obtained from the involved anatomic site and other sites of sexual contact in past 90 
days (to include throat, rectum, urine) if indicated for GC culture-based phenotypic testing 
according to local GC culture protocol, and 
2) a swab/urine sample obtained from anatomic site of infection only for molecular resistance 
testing. 
• 
For those with CT infection, a swab or urine specimen will be collected (depending on the site of 
infection) for molecular resistance testing. 
• 
For those with confirmed rectal or pharyngeal CT, a swab will be collected for chlamydia cell culture. 
Please see MOPS for specimen handing instructions.  
• 
For those with syphilis serologies indicating new infection and in whom no chancres/mucosal lesions 
are present, a buccal mucosal swab will be obtained for T. pallidum DNA amplification which, if 
positive, will be used for resistance testing. If suspected syphilitic chancre is present, this should be 
swabbed for molecular testing 
 
Documented STI 
Specimen collection 
 
Buccal 
Swab 
(Zymo) 
Pharyngeal 
Swab 
(Zymo) 
Rectal 
Swab 
(Zymo) 
Rectal or 
pharyngeal 
swab 
(Culture) 
Urine 
Collection 
(Zymo) 
Swab of 
chancre 
(Zymo) 
GC culture per 
local protocol 
(all anatomic 
sites of sexual 
exposure in past 
90 days 
Chlamydia 
 
√* 
√* 
√* 
√* 
 
 
Gonorrhea 
 
√* 
√* 
 
√* 
 
√ 
Syphilis with 
chancre/mucosal 
legion 
 
 
 
 
 
√ 
 
Secondary 
syphilis (rash) 
√ 
 
 
 
 
 
 
 
*Specimen sent from site of confirmed infection only 
 
 
6.5 
Testing for resistance in setting of STI diagnoses on study 
 
6.5.1 Testing for tetracycline resistance among N. gonorroheae 
Positive GC cultures for all participants will be sent to either the University of Washington Neisseria Reference 
laboratory for resistance testing led by our co-investigator, Dr Olusegun Soge at the UW/PHSKC STI program 
or the SFDPH Public Health Laboratory for testing by Dr. Godfred Masinde. Both laboratories participate in the 
Strengthening the US Response to Resistant Gonorrhea (SURRG) program. GC isolates collected in Seattle 
and frozen isolates from San Francisco will be shipped to Dr. Soge on a monthly basis for agar dilution 
antimicrobial susceptibility to a panel of antimicrobials including tetracycline, as part of the Antimicrobial 
Resistance Lab Network (ARLN) supported by CDC. In addition, Dr. Soge’s laboratory will determine whether 
tetracycline MICs increases among the subset with repeat GC infections during follow- up. 
 

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6.5.2 Molecular testing for tetracycline resistance genes in C. trachomatis, T. pallidum and N. gonorrhoeae. 
DNA from positive NAAT tests for C. trachomatis and N. gonorrhoeae and from buccal or chancre/mucosal lesion 
swabs from those with newly diagnosed syphilis will be evaluated using established CRISPR/Cas9 techniques 
to screen against a comprehensive library of antibiotic resistance mutationsin order to establish rapid throughput 
methodology for the multicenter study. Tetracycline resistance will be assessed using FLASH (Finding Low 
Abundance Sequences by Hybridization)) targeted sequencing of antimicrobial resistance genes that will then 
be compared to an established antibiotic resistance database as well as evaluated for known tetracycline 
mutations that have been documented in the target STIs or closely related organisms64. Molecular resistance 
testing will conducted at the San Francisco Chan-Zuckerberg Biohub under the supervision of collaborating 
investigator Dr. Langlier, who has extensive expertise in molecular diagnosis of mutations associated with 
antibiotic resistance. Any TCN-resistance mutations in C. trachomatis or T. pallidum will be investigated further, 
as clinically relevant tetracycline resistance has not been reported to date. The results will not be reported for use 
in clinical care as these methods are experimental and have not been validated for clinical care. 
 
6.6 
Treatment of STIs 
Local clinic standards will be followed for the treatment of STIs diagnosed by laboratory tests or when identified 
syndromically. If doxycycline is used for treatment of an STI for an individual in the PEP arm, doxycycyline PEP 
will be held during treatment and resumed when treatment completed. 
 
6.7 
Qualitative interviews 
A qualitative interview will be offered to a subset of participants assigned to take doxycycline, approximately 
20 per site, during months 3-12, and up to one month after study completion. Qualitative interviews will also 
be offered to 10-20 providers at each of the sites A separate consent will be provided for these interviews.  
 
6.8 
Reenrollment of participants enrolled prior to 3/15/2020 
Participants enrolled prior to the COVID pandemic will be re-enrolled starting 7/2020 with the same initial 
assignment. At time of re-enrollment, these participants will undergo all day 0 evaluations with the exception of 
the following 
• Meningoccal vaccine history 
• Medical & STI history 
• Stool sample collection from first 50 PLWH and HIV uninfected on PrEP 
 
 
7 
ADVERSE EVENTS (AE) AND STUDY MONITORING 
 
7.1 
Adverse Event Collection Requirements 
 
All AEs must be recorded on eCRFs if any of the following criteria have been met: 
• 
All grade 2 and higher hematologic and hepatic laboratory abnormalities that are attributed to 
doxycycline in the opinion of the site investigator 
• 
All AEs meeting SAE definition 
• 
All grade 3 and 4 adverse events judged to be associated with doxycycline (possibly, 
probably, or definitely related) 
 
Serious Adverse Events (SAEs) 
An SAE is defined as any untoward medical occurrence that: 
• 
Results in death 
• 
Is life-threatening 
• 
Requires inpatient hospitalization or prolongation of existing hospitalization 
• 
Results in persistent or significant disability/incapacity 
• 
Is an important medical event that may not be immediately life-threatening or result in death or 

DoxyPEP protocol Ver 9.0 5/27/2022 
27 
 
 
hospitalization but may jeopardize the patient or may require intervention to prevent one of the 
other outcomes listed in the definition above) 
 
All AEs that are recorded must have their severity graded. To grade AEs, sites should refer to the Division 
of AIDS Table for Grading the Severity of Adult and Pediatric Adverse Events (DAIDS AE Grading Table), 
corrected Version 2.1, July 2017, which can be found on the DAIDS RSC website at https://rsc.tech- 
res.com/docs/default-source/safety/division-of-aids-(daids)-table-for-grading-the-severity-of-adult-and- 
pediatric-adverse-events-corrected-v-2-1.pdf 
 
7.2 
AE and SAE attribution to doxycycline 
In those randomized to receive doxycycline PEP, all AEs and SAEs should have attribution recorded as 
doxycycline-related or not doxycycline-related, in the judgment of the site investigator. 
 
7.3 
Study Monitoring 
 
7.3.1 Study Team Monitoring 
The study team will monitor the conduct of the study through monthly summary reports of arms of accrual, and 
baseline characteristics and quarterly reports of data pooled over treatment arms of data completeness, specimen 
collection, and AEs. The study will review individual participant-level safety data frequently to assess the relation 
of all reported AEs to study treatment. On a monthly basis, the study team will review by- arm summaries of 
premature study discontinuations and premature study treatment discontinuations (and reasons) and AEs. 
 
7.3.2 Independent Monitor 
Study conduct will be monitored by an independent monitor. Monitors will visit participating clinical research sites 
to review the individual participant records, including consent forms, eCRFs, supporting data, laboratory specimen 
records, and endpoints through laboratory and medical records (physicians’ progress notes, nurses’ notes, 
individuals’ hospital charts), to ensure protection of study participants, compliance with the protocol, and 
accuracy and completeness of records. The monitors also will inspect sites’ regulatory files to ensure that 
regulatory requirements are being followed and sites’ pharmacies to review product storage and management. 
 
7.3.3 Data safety and monitoring board (DSMB) 
An independent data safety and monitoring board (DSMB) will be convened for this study with expertise in STIs, 
PrEP, and HIV care and a biostatistician. The purpose of the DSMB is to monitor the study for operational futility, 
social harms, and efficacy. The DSMB will evaluate the progress of the project, including periodic assessments 
of accrual, retention, safety, performance and variation of the project sites, and other factors that can affect 
project implementation. The DSMB will review the study after 1/2 of follow- up time with pre-specified stopping 
rules in terms of the efficacy of doxycycline PEP in reducing the incidence of gonorrhea, chlamydia, and syphilis 
overall, and the ability of the study to meet its objectives. The DSMB will review STI endpoints which have been 
adjudicated by the STI Endpoints Committee. The DMSB will consider factors external to the project when 
relevant information becomes available, such as policy changes or scientific developments that may have an 
impact on project implementation, safety, and integration of STI PEP in the STI and HIV care clinics. 
 
The DSMB will conduct reviews every six month and convene by teleconference. Open reports containing 
accrual and retention rates, participant characteristics, serious adverse events, and social, will be sent to the 
protocol team and DSMB members the week prior to the DSMB meeting. Only the DSMB members and the 
unblinded biostatistician will receive password-protected closed reports of STI endpoints by randomization arm. 
 
 

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8 
CLINICAL MANAGEMENT ISSUES 
 
8.1 
Toxicity 
Only toxicities related to study medications provided through the study will be considered in the toxicity 
management section. 
 
Grade 1 or 2 
Participants who develop Grade 1 or 2 toxicity (per DAIDS toxicity table) felt to be related to 
doxycycyline may continue study treatment at the discretion of the site investigator with close follow-
up. If a participant chooses to discontinue study treatment, the site should notify the study 
protocol team within 7 days.These participants will remain on study, off study treatment and have all 
evaluations performed per the SOE. 
 
Grade 3 
• 
Participants who develop a Grade 3 toxicity thought by the site investigator to be related to study 
drug should have doxycycline PEP withheld and the site should consult with the core protocol 
team. The participant should be reevaluated weekly until the AE returns to Grade ≤2, at which 
time study drug may be reintroduced at the discretion of the site investigator in consultation with 
the protocol team. 
• 
Participants experiencing Grade 3 toxicity requiring permanent discontinuation of doxycycline 
PEP should be followed weekly until resolution of the toxicity. Participants will have premature 
study treatment discontinuation evaluations performed as noted on the SOE. These participants 
will remain on study, off study treatment and have all evaluations performed per the SOE. 
 
Grade 4 
• 
Participants with Grade 4 asymptomatic laboratory abnormalities may continue doxycycline PEP 
if the site investigator has compelling evidence that the toxicity is NOT related to study drug. 
• 
Participants who develop a Grade 4 symptomatic toxicity will have doxycycline PEP 
permanently discontinued and the site should notify study team within 72 hours. 
• 
Participants experiencing Grade 4 toxicity requiring permanent discontinuation of doxycycline 
PEP should be followed weekly until resolution of the AE or return to baseline. These 
participants will remain on study, off study treatment and have all evaluations performed per the 
SOE. 
• 
 
8.2 
Specific Management of Toxicities Related to Study-Provided Drugs 
Possible intracranial hypertension (IH) 
Participants taking doxycycline who report new or worsening headaches, visual changes, or vision loss should 
have doxycycline temporarily discontinued and evaluated for IH if these symptoms persist, including a 
fundoscopic exam to look for papilledema. If IH is ruled-out or an alternate etiology identified, doxycycline may 
be restarted, at the discretion of the site investigator. 
 
Skin erythema 
Increased photosensitivity is a known possible side effect of doxycycline. Doxycycline may be discontinued if 
skin erythema develops at the discretion of the site investigator and may reinstituted when resolved at the 
discretion of the site investigation. Any serious skin reaction judged by the local investigator to be related to 
doxycycline should lead to permanent discontinuation of doxycycline . 
 
Fixed drug eruption 
Suspected fixed drug eruption should be evaluated for possible etiologies – if a doxycycline fixed drug eruption 
is suspected, doxycycline should be stopped. 
 
Allergic reactions 

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29 
 
 
Doxycycline should be discontinued permanently if a serious allergic reaction is suspected. These participants 
will remain on study, off study treatment and have all evaluations performed per the SOE. 
 
 
9 
CRITERIA FOR DISCONTINUATION 
 
9.1 
Premature Study Treatment Discontinuation 
 
• 
Requirement for prohibited concomitant medications or other contraindication to doxycycline 
• 
Occurrence of an adverse event requiring discontinuation of doxycycline 
• 
Request by participant to terminate study treatment 
• 
Clinical reasons believed life threatening by the physician, even if not addressed in the toxicity 
section of the protocol 
• 
Requirement for chronic tetracycline use ( >14 days) 
 
Participants who stop doxycycline PEP should be continued on study, off doxycycline PEP with 
continued evaluations as per the SOE. The reason for doxycycline discontinuation should be 
recorded. 
 
9.2 
Premature Study Discontinuation 
 
• 
Request by the participant to withdraw 
• 
Request of the primary care provider if she or he thinks the study is no longer in the best 
interest of the participant 
• 
Participant judged by the investigator to be at significant risk of failing to comply with the 
provisions of the protocol as to cause harm to self or seriously interfere with the validity of the 
study results 
• 
At the discretion of the IRB/EC, NIAID, Office for Human Research Protections (OHRP), other 
government agencies as part of their duties, investigator, or industry supporter 
 
 
10 STATISTICAL CONSIDERATIONS 
 
10.1 Outcome measures 
 
10.1.1 Primary outcome: 
Combined incidence of GC, CT, or early syphilis infection by laboratory- based diagnosis (e.g., positive GC or CT 
based on NAAT, syphilis based on four-fold increase in non- treponemal titers or positive darkfield on exudate 
from a lesion). Incident STI diagnoses will be ascertained through the study through periodic testing, interim visits 
for STI symptoms, as well as STI surveillance from the San Francisco and King County Departments of Health 
and by medical records provided for participants who receive their care from other clinical sites. 
 
10.1.2 Secondary outcomes: 
• Safety of doxycycline PEP, measured by evaluation of all Grade 3 and 4 AEs attributed to study medication. 
• Tolerability, measured using a brief quarterly questionnaire administered to both intervention and control groups 
evaluating side effects commonly associated with doxycycline as well as recording any discontinuations of 
doxycycline by participants and their reasons. 
• Acceptability, assessed through a brief questionnaire for all PEP recipients administered at month 6 and 12 and 
in-depth structured qualitative interviews for a subset, conducted within 6 months of month 12 visit. A separate 
consent will be provided for the in-depth qualitative interview at the time of this interview. 
• Doxycycline coverage of sexual contacts in the prior 3 months, ascertained by sexual behavior and doxycycline 

DoxyPEP protocol Ver 9.0 5/27/2022 
30 
 
 
use from the web-based app, augmented by quarterly adherence questionnaires and pill counts. 
• Longitudinal exposure to doxcycyline will be assessed using hair collection, with a semiquantitive evaluation in 
the control arm (doxycycline present vs. absent) and in the PEP arm (doxycycline concentration high vs. low). 
• Adherence to HIV medications as reflected in viral suppression among participants living with HIV, assessed 
by chart review of HIV RNA levels conducted as standard clinical care. 
• Discontinuation of PrEP, based on self-report 
• Residual hair samples of participants without HIV infection on PrEP will be archived for future tenofovir testing 
to measure adherence to Truvada PrEP. 
 
10.2 Statistical power and analysis 
 
Primary endpoint: We selected a sample size for each cohort (MSM/TGW living with HIV and MSM/TGW on 
PrEP) to achieve 80% power with 0.05 two-sided Type 1 error, for the endpoint of any lab-detected incident early 
syphilis, GC and/or CT infection, based on quarterly assessments for each person, 10% annual loss to follow-up 
and an intra-class correlation of 0.2, reflecting the high prevalence of STI re-infection that has been observed in 
these populations. With these assumptions, a cohort of approximately 390 of MSM/TGW living with HIV and 390 
of MSM/TGW on PrEP (130 in the control and 260 in the intervention for each cohort) will provide 80% power to 
detect a decrease in quarterly STI prevalence from 10% to 5%, which corresponds to an annual reduction in 
combined STI incidence from 34% to 19% (Table 10.2.1). With allowance for 10% lost to follow-up, the sample 
size for each cohort will be approximately 390 participants, for a total sample size of 780. Based on 2017 STI 
incidence data from San Francisco and Seattle PrEP cohorts for both GC and CT, we expect in the control arm in 
each quarter approximately 5% of participants to have GC, 5% CT and 2% early syphilis, acknowledging some 
will be diagnosed with more than one infection. Based on the higher susceptibility of GC to TCN in the US vs 
France (75% vs < 50%11, 20) and the 70% reduction of CT and syphilis with PEP in IPERGAY,1 we anticipate 
effectiveness of doxycycline PEP to be 35% for GC, 65% for CT and 65% for syphilis. Given these assumptions, 
with a 2:1 randomization we expect to see 61 vs 47 GC infections, 47 vs 33 CT infections and 19 vs 13 syphilis 
infections in the doxycycline PEP and control arms respectively, some of which will occur in the same individuals. 
Sample sizes were computed using nQuery for repeated measures for two proportions. The analysis will compare 
time-averaged proportion of infections in each quarter between arms, using repeated measure methods. 
 
Table 10.2.1:  Power Table for N = 390; 2:1 randomization doxycycline PEP: SOC. Sample size 
assumes 370 fully evaluable participants. 
  
Control arm quarterly 
prevalence 
Intervention arm 
quarterly 
prevalence 
Power to detect 50% reduction 
Power to detect 65% reduction 
ICC = 0.2 
ICC = 0.1 
ICC = 0.2 
ICC = 0.1 
10% 
5% 
80% 
87% 
96% 
99% 
7.5% 
3.75% 
68% 
76% 
90% 
95% 
5% 
2.5% 
51% 
59% 
77% 
85% 
3% 
1.5% 
35% 
41% 
57% 
65% 
2% 
1% 
26% 
30% 
43% 
50% 
 
 
 
 

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31 
 
 
Within the total enrollment of 780, we will not require the enrollment of HIV-infected and uninfected participants 
to be equal. Anticipating the possibility of lower enrollment but possibility of equivalent or higher STI rates in the 
HIV-infected cohort, Table 10.2.2 assesses the power characteristics of the study with a cohort that contributes 
from 30% to 50% of the total enrolled, with quarterly events rates of 10% and 12%. With a higher event rate or 
a lower intraclass correlation, the smaller cohort retains reasonable power to detect a 50% reduction.  
 
 
Table 10.2.2: Power characteristics for reduced sample size in a cohort, assuming event rate of 10% 
and 12% STIs occurring each quarter in SOC arm 
 
Total Evaluable  
sample size in cohort 
ICC 
Doxy: SOC 
Power to detect 
50% reduction 
(10% in SOC) 
Power to detect 
50% reduction 
(12% in SOC) 
370 (50% of total) 
0.1 
246:123 
87% 
92% 
370 
0.2 
246:123 
80% 
86% 
296 (40% of total) 
0.1 
196:98 
79% 
86% 
296  
0.2 
196:98 
71% 
78% 
259 (35% of total) 
0.1 
174:87 
74% 
82% 
259 
0.2 
174:87 
66% 
74% 
222 (30% of total) 
0.1 
148:74 
68% 
76% 
222 
0.2 
148:74 
60% 
67% 
 
 
Secondary endpoints include evaluation of PEP effectiveness on incidence of each specific STI and on time to 
first STI, as well as by site of STI infection (oral, rectal, urethral). Impact of risk practices and sexual activity on STI 
incidence will be compared between arms. Survey data will be analyzed to understand factors impacting 
acceptability of doxycycline PEP, including demographic factors, socioeconomic status, substance use, history 
of STIs, HIV infection status, and experience with PEP. The qualitative interviews will be coded using inductive 
(i.e., codes arise from careful reading of the text) and deductive (i.e., codes arise a priori from topics covered by 
the interview guide) approaches, which when employed together have proven useful in health services research. 
Interviews will be coded by at least two research team members who will practice on a selection of transcripts 
until >90% agreement is reached. Dedoose, a web-based program, will be used to facilitate indexing, coding, and 
searching. The qualitative team will meet regularly to group codes into categories and develop major and minor 
themes. 
 
For resistance we will assess the proportion with tetracycline resistance in visits with N. gonorrheae and S. 
aureus. Exploratory endpoints include incidence of tetracycline resistance in C. trachomatis and T. pallidum 
using molecular techniques (e.g., CRISPR and CAS-9), for which the molecular technologies are new and the 
clinical significance of resistance mutations is less clear. Stool samples from 50 participants living with HIV and 
50 participants on PrEP will be obtained at baseline, 6 and 12 months for metagenomic evaluation targeting TCN 
genes. Overall TCN resistance gene abundance (expressed as dpM/patient) and the number of distinct TCN 
resistance genes present per participant will be assessed at baseline and evaluated for change over time during 
doxycycline use. Rectal swabs will be collected and stored for future evaluation of shifts in the fecal microbiome, 
decrease in flora diversity, and quantification of TCN-resistant abundance and diversity 
 
 
10.3 Endpoint adjudication 
All STI endpoints will be reviewed by a blinded, independent Endpoint Adjudication Committee, following CDC 
guidelines for the diagnosis of STIs.52 Incidence of individual STIs and tetracycline resistance will also be 
evaluated. 
 

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32 
 
 
10.4 Post COVID follow-up 
The team will monitor discontinuation rates in the participants enrolled prior to the COVID epidemic (3/15/2020). 
If there is a differential discontinuation in the active vs. control arm, this will be discussed with DSMB and the 
team statistician with consideration of additional enrollments to ensure adequate power for the primary endpoint. 
 
10.5 Analyses after 5/13/2022 closure to enrollment 
Analyses after 5/13/2022 closure to enrollment and doxycycline provision to control will include the following: 
 
STI incidence:  
- Comparison of STI incidence per quarter in control arm before and after doxycycline initiation 
- Comparison of STI incidence per quarter in all participants receiving doxycycline (including those in 
control arm after rolled over to receive doxycycline) compared to incidence on control arm prior to 
doxycycline roll over 
 
Antimicrobial resistance  
- 
Evaluation of tetracycline resistance in Staphylococcus aureus, commensal Neisseria in comparison 
to the control arm and to individual baseline 
- 
Evaluation of genotypic or phenotypic tetracycline resistance in bacterial STIs in all participants who 
receive doxycycline compared to control arm participants, prior to receipt of doxycycline.  
- 
Evaluation of changes in the gut microbiome and total gut burden of tetracycline resistance before and 
after taking doxycycline PEP  
 
Adherence 
- Evaluation of doxycycline coverage of qualifying sex before and after study closure 5/13/2022 
 
Acceptability 
- Proportion of control arm participants who opt to take study provided doxycycline. Control arm 
participants who terminate study participation will have the reason for termination recorded to 
determine if stopping to receive doxycycline outside of the study.  
 
 
11 PARTICIPANTS 
 
11.1 Institutional Review Board (IRB) Review 
The study protocol, site-specific informed consent forms, participant education and recruitment materials, and 
other requested documents—including any subsequent modifications—will be reviewed and approved by the 
UCSF IRB, as the single IRB of record responsible for oversight of research conducted at the study sites. 
Subsequent to initial review and approval, the UCSF IRB will review the study at least annually. 
 
11.2 Informed Consent 
A signed consent form will be obtained from the participant.The consent form will describe the purpose of the 
study, the procedures to be followed, and the risks and benefits of participation. A copy of the consent form will 
be given to the participant and this fact will be documented in the participant’s record. Electronic consenting will 
be an option to reduce face to face exposure during the COVID epidemic. 
 
11.3 Study records 
Each study site will establish a standard operating procedure for confidentiality protection. Each site will ensure 
that study records including administrative documentation and regulatory documentation as well as 
documentation related to each participant enrolled in the study, including informed consent forms, locator forms, 
case report forms, notations of all contacts with the participant, and all other source documents are stored in a 
secure manner. 
 

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11.4 Confidentiality 
Participants’ study information will not be released without their written permission, except as necessary for 
oversight by: 
- 
The Protocol co-Chairs or designees 
- 
Study funders 
- 
University of California, San Francisco IRB 
- 
University of Washington IRB 
 
All laboratory specimens, evaluation forms, reports, and other records that leave the site will be identified by 
coded number only to maintain participant confidentiality. The exceptions are STI testing results which are 
subject to local and state reporting which is names-based. Local public health may contact participants 
diagnosed with STIs for the purpose of surveillance and partner notification. Participants will be informed prior 
to STI testing that results are reportable and may lead to contact by local public health if results are positive for 
infection. In addition, GC culture specimens will be evaluated for drug resistance as part of an existing GC 
program evaluating clinical isolates and may contain patient identifiers such as MRN, name or date of visit, 
according to local laboratory requirements and practice. 
 
All records will be kept locked. All computer entry and networking programs will be done with coded numbers only. 
Clinical information will not be released without written permission of the participant, except as necessary for 
monitoring by the IRB/EC, NIAID, OHRP, other local, US, and international regulatory entities as part of their 
duties, or the industry supporters or designees. 
 
 
12 BIOHAZARD CONTAINMENT 
 
As the transmission of HIV and other blood-borne pathogens can occur through contact with contaminated 
needles, blood, and blood products, appropriate blood and secretion precautions will be employed by all 
personnel in the drawing of blood and shipping and handling of all specimens for this study, as currently 
recommended by the CDC and the National Institutes of Health. 
 
All dangerous goods and materials, including diagnostic specimens and infectious substances, must be 
transported using packaging mandated by CFR 42 Part 72. Please refer to instructions detailed in the 
International Air Transport Association (IATA) Dangerous Goods Regulations. 
 
 

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