Syphilis, caused by the spirochete Treponema pallidum subsp. pallidum (TPA), is resurging globally, particularly in low- and middle-income countries. However, TPA genomic diversity and population structure in these settings remain poorly characterized. We investigated the global genetic diversity of syphilis spirochetes, sequencing 298 new TPA genomes from 11 countries across five continents, including underrepresented areas such as Argentina, Colombia, Malawi, Sri Lanka, and Vietnam. Combined with 1,409 public genomes, our dataset comprised 1,707 genomes. Hierarchical clustering identified six Nichols and five SS14-lineage subpopulations, with distinct subpopulations concentrated in Africa, East Asia, and the Americas, as well as previously unrecognized diversification within the globally dominant SS14 lineage. Concordance analysis showed that widely used multilocus sequencing typing methods recapitulate major Nichols-lineage subpopulations but have reduced discriminatory power for the SS14 lineage. Genome-wide Fixation index scans and targeted analyses of genes encoding outer membrane proteins prioritized for vaccine development demonstrated lineage- and subpopulation-specific patterns of genetic structure and selection. We observed strong diversifying selection acting on cell envelope assembly factors (BamA, LptD), selected FadL-like transporters, members of the T. pallidum repeat (Tpr) family, and efflux-associated outer membrane factors, alongside strictly conserved β-barrel scaffolds. Macrolide resistance and reduced beta-lactam susceptibility marker prevalence varied by lineage and geographical region. These findings refine our understanding of TPA's genetic diversity, delineate heterogeneous evolutionary trajectories across key vaccine-relevant loci, and underscore the importance of geographically representative genomic analyses to inform syphilis vaccine design and for antimicrobial resistance monitoring. Significance Statement:Despite increasing syphilis rates worldwide, genomic data from its causative agent Treponema pallidum subsp. pallidum have largely originated from a small number of high-income countries. This study significantly expands our understanding of TPA genomic diversity by sampling across underrepresented low- and middle-income countries (LMICs) in Africa, Asia and South America. We analyze 1,707 genomes, including 298 newly sequenced from 11 LIMCs, and identify novel subpopulations, lineage-specific variation in outer membrane proteins, and geographic differences in antimicrobial resistance markers. These results illustrate how sampling from understudied regions reveals previously unappreciated, geographically structured diversity, improving our understanding of TPA population structure and informing the development of globally relevant vaccines, treatment strategies, and diagnostic tools.

Background: Lymphoma is one of the most common cancers affecting young adults in Sub-Saharan Africa, yet survival outcomes lag far behind those in high-resource settings. A significant contributor to these disparities is treatment abandonment, driven by limited access to essential palliative care support and lack of symptom management medications. This study aimed to assess the feasibility and early uptake of a Symptom Toolkit intervention to support symptom recognition and self-management. Methods: We designed and implemented a novel, low-cost, culturally appropriate Symptom Toolkit into an oncology clinic in Malawi. The toolkit included nurse-delivered patient education and take-home essential therapies targeting high-burden symptoms, including pain, nausea and vomiting, insomnia, gastritis, mucositis, and constipation, with pictorial labels and a journal to record use. Included therapies were selected based on local clinical guidelines and availability. At follow-up visits, a palliative care nurse completed survey assessments and distributed new Symptom Toolkits, noting both symptom occurrence and rates of medication use. Results: A total of 65 patients with lymphoma (median age 39) participated, including individuals with acute lymphoblastic leukemia, Burkitt lymphoma, diffuse large B-cell lymphoma, and Hodgkin’s lymphoma. Across the 602 toolkit reports completed, use of symptom-directed medications increased over time, indicating improved uptake and engagement with the intervention. Conclusions: This pilot intervention demonstrates the feasibility of a nurse-delivered Symptom Toolkit as a means to enhance symptom recognition and self-management in a low-resource oncology setting. Further evaluation of the Toolkit in future studies will assess its impact on symptom burden and quality of life.

Background The prevalence of chancroid, which is caused by Haemophilus ducreyi, has declined globally. However, H. ducreyi remains a cause of genital ulcer disease in some sub-Saharan African countries and causes non-genital cutaneous ulcers in tropical settings. Genomic data on H. ducreyi are exceedingly scarce, limiting understanding of transmission dynamics, lineage structure, and antimicrobial resistance (AMR). We examined H. ducreyi circulating in Malawi among genital ulcer disease participants using target-enrichment-based whole-genome sequencing (WGS). Methods We performed culture-free WGS, using a custom SureSelect Target-Enrichment RNA probe panel, of H. ducreyi from PCR-positive samples (n = 118, from 118 chancroid episodes) collected in Malawi (2020–2022). Eighty-seven H. ducreyi genomes were generated and analysed alongside 55 publicly available genomes. Phylogenomic reconstruction, recombination, genomic and pan-genome analysis, and genome-wide association studies characterised population structure, clinical associations, and AMR determinants. Findings All Malawian genomes were assigned as class I and formed an extremely clonal lineage, with a mean pairwise distance of 2.6 SNPs and lack of recombination, consistent with recent ongoing transmission. All Malawian genomes carried plasmid-associated AMR determinants including blaTEM-1, tet(B), tet(32), and sul2, indicating multidrug resistance to previously used antibiotics. No determinants associated with resistance to fluoroquinolones or macrolides were identified. Interpretation A clonal expansion of one H. ducreyi strain is driving contemporary chancroid transmission in Malawi, highlighting the continued public health relevance of this pathogen. No AMR determinants associated with resistance to fluoroquinolones or azithromycin were detected, supporting continued use of recommended first-line therapies while highlighting the importance of continued AMR surveillance. Continued genomic H. ducreyi surveillance is essential to monitor transmission, support early detection, and timely detection of emerging AMR. Funding ÖUH, US NIH, Gates Foundation

Background:Chancroid, a sexually transmitted infection (STI) caused by Haemophilus ducreyi resulting in genital ulcer disease (GUD), is now considered rare in many parts of the world. However, chancroid has remained highly prevalent in Malawi since the 1990s. Methods:We combined data from two recent studies conducted in Malawi (2019-2022, 2021) that screened and enrolled patients ≥ 18 years of age presenting to a STI clinic with GUD. Polymerase chain reaction (PCR) was conducted for H. ducreyi and other STIs from ulcer swabs. We evaluated demographic, sexual and clinical characteristics of participants with positive H. ducreyi PCRs to describe the epidemiology of chancroid using descriptive statistics. Results:Among 618 participants with GUD, 137 (22%) tested positive for H. ducreyi by PCR. Of these, most were male 85 (63%), the median age was 27 years (interquartile range [IQR]: 23, 33) and 19 (17%) had HIV co-infection. About a third (n=42, 31%) were co-infected with other STIs. Among 15 (11%) enrolled participants with additional clinical data, most reported one sexual partner in the past month (median = 1 [IQR: 1, 1). However, a history of prior transactional sex was reported by 5/15 (33%). The clinical presentation of the ulcers varied and over half presented with multiple ulcers (53%). Most ulcers (89%) were associated with pain, but few (20%) had associated inguinal lymphadenopathy. Conclusions:This review confirmed the high prevalence and persistence of chancroid in Malawi. However, additional investigations are needed to further characterize the epidemiology of chancroid and determine the reasons for its persistence in Malawi.

BACKGROUND:As syphilis rates have increased globally, chancroid has dramatically declined as a cause of genital ulcer disease (GUD). METHODS:We recruited patients aged ≥18 years presenting to a sexually transmitted infection clinic with GUD from Lilongwe, Malawi, from November 2019 through April 2022. Lesion exudates were tested by darkfield microscopy (DFM) and polymerase chain reaction (PCR) for Treponema pallidum (TP) and by PCR for Haemophilus ducreyi (HD), herpes simplex virus, and Chlamydia trachomatis. We evaluated the sensitivity and specificity of DFM relative to TP PCR, the distribution of GUD etiologies by PCR, and the performance of our HD PCR relative to Allplex Genital Ulcer assay (Seegene Inc) using the Cohen's kappa statistic. RESULTS:We enrolled 568 participants; the median age was 27 years (interquartile range: 23, 34), 61% (345/564) were men, and 13% (60/464) had human immunodeficiency virus (HIV) or were newly diagnosed with HIV. DFM identified TP in 55 (10%) participants, with a sensitivity and specificity of 12% and 94%, respectively. PCR identified TP in 367 (65%), HD in 128 (23%), herpes simplex virus in 98 (17%), and Chlamydia trachomatis in 36 (6%) of participants with only 1/36 (2.8%) with serovar L1, L2, or L3 consistent with lymphogranuloma venereum; no etiology was identified in 48 (8%). External validation confirmed the high HD prevalence (Cohen's kappa 0.78, 89% agreement). CONCLUSIONS:Syphilis and chancroid are common etiologies of GUD in Malawi. Our findings underscore the value of highly sensitive molecular diagnostic methods to periodically assess GUD causes among patients with sexually transmitted infections in countries using syndromic management.

Among patients with primary syphilis, sensitivity of the toluidine red unheated serum test was 55% (6/11) compared with darkfield microscopy and 60% (9/15) compared with Treponema pallidum polymerase chain reaction. Sensitivity of rapid plasma reagin was 78% (38/49) and 93% (43/46), respectively. Treponema pallidum particle agglutination had a sensitivity of 95% (41/43) compared with darkfield microscopy and 96% (43/45) compared with polymerase chain reaction.

Background Understanding the burden of incident sexually transmitted infections (STIs) among persons in Eastern and Southern Africa after initiating HIV pre-exposure prophylaxis (PrEP) is critical to allocate scarce STI testing and HIV prevention resources. Methods Participants were recruited from an STI clinic in Lilongwe, Malawi (March-December 2022). Eligibility reflected oral PrEP eligibility per contemporary guidelines, limited to persons seeking STI services. We enrolled three groups: “index participants” who initiated PrEP, “PrEP-eligible decliners” who declined PrEP, and PrEP-initiating “referred partners” referred by index participants. Surveys and PrEP use assessments were conducted at baseline, 1, 3, and 6 months; Chlamydia trachomatis, Neisseria gonorrhoeae, and syphilis testing done at baseline, 3, and 6 months. A subset of participants completed in-depth interviews that were thematically analyzed. Results We enrolled 238 participants (174 index, 37 PrEP-eligible decliners, 27 referred partners); most were male (58%), median age 27 (IQR 22, 31). Forty-seven incident STIs were identified during 89.3 person years (py) of follow-up (52.6/100py). Men had a higher incidence versus women (55.8/100py versus 48.6/100py). Index participants had the highest STI incidence (61.3/100py), compared to PrEP-eligible decliners (26.4/100py) and referred partners (27.1/100py). Most incident infections were asymptomatic. Nearly all 27 interviewed participants described an STI as related to perceived HIV risk and need for PrEP. Conclusions Incident, asymptomatic STIs in the six months following PrEP initiation were common. STI testing contextualizes perceived HIV risk and may encourage PrEP persistence. Integrating bacterial STI testing within PrEP care may reduce transmission via expedient treatment and should be considered alongside PrEP program expansion.

BackgroundPreexposure prophylaxis (PrEP) remains one of the most efficacious interventions for preventing HIV, but its effectiveness is often limited by poor persistence. Although regional efforts have primarily focused on young women and men who have sex with men, heterosexual men in East and Southern Africa represent a crucial group to engage and retain in PrEP care—both to improve health outcomes for men and to interrupt HIV transmission chains. Men seeking sexually transmitted infection (STI) services are particularly vulnerable to HIV acquisition, yet only a few interventions have tested strategies for engaging and retaining these men in PrEP services. Systems navigation, which addresses barriers to health care access and enhances comfort in clinical settings, may offer a promising approach to improving persistent PrEP use among heterosexual men. ObjectiveThis study will assess the effect of a peer-delivered systems navigator–facilitated HIV prevention package on PrEP persistence at 26 weeks among heterosexual men seeking STI clinical services in Lilongwe, Malawi. It will also evaluate the acceptability of the intervention and barriers to implementation among key stakeholders. Insights will inform the feasibility of a future randomized controlled trial. MethodsIn this single-site pilot type I effectiveness-implementation hybrid randomized controlled trial, 200 heterosexual men seeking STI services and initiated on PrEP in Lilongwe, Malawi, will be randomized (1:2) to standard-of-care PrEP services or systems navigator–assisted PrEP care (intervention). Participants will be followed every 13 weeks for at least 26 and up to 52 weeks. PrEP use and engagement in care will be assessed through medical record review and intraerythrocytic tenofovir diphosphate measurement, using objective biomedical analyses via dried blood spot. Primary effectiveness and implementation outcomes include 26-week PrEP persistence (adapted to accommodate daily oral, event-driven oral, or injectable PrEP) and acceptability, respectively. Additional implementation outcomes include feasibility and cost. Exploratory objectives characterize preferences for PrEP modalities, perceived and experienced stigma, and the influence of gender norms on PrEP persistence. All clinical services, including the provision of PrEP and PrEP safety monitoring, are being conducted by the Malawi Ministry of Health. ResultsHPTN (HIV Prevention Trials Network) 112 was funded in November 2023. Study recruitment began in April 2024 and closed in November 2024. As of February 3, 2025, the study has enrolled 199 participants, with follow-up expected through June 2025. No interim analyses were planned; data analysis for primary end points is expected in the summer of 2025. ConclusionsImproving PrEP use outcomes among heterosexual men in East and Southern Africa is critical to interrupting HIV transmission. This study offers unique insights into a low-resource, potentially scalable intervention, focusing on a group of men at particularly high risk of HIV acquisition—those with recent STIs. The hybrid RCT design addresses clinically relevant effectiveness questions and explores key determinants that will inform future multisite implementation trials. Trial RegistrationClinicalTrials.gov NCT06200545; https://clinicaltrials.gov/study/NCT06200545 International Registered Report Identifier (IRRID)DERR1-10.2196/72981

HIV transmission during early HIV infection impedes efforts to end HIV as a public health threat, as diagnosis typically occurs after this period of elevated transmission risk. To guide diagnosis and prevention strategies, we evaluated the geospatial and phylogenetic clustering of acute and recent HIV infection in Lilongwe, Malawi. We identified people with acute (pre-seroconversion) HIV infection (AHI) and a random sample of people with post-acute HIV infection who presented to a sexually transmitted infections (STI) clinic in Lilongwe, Malawi between 2015 and 2019. We evaluated infection recency in people with post-acute HIV using a LAg-Avidity assay. We mapped the household locations of people with AHI and identified geospatial clusters using a flexible scan statistic. We constructed consensus sequences from deep sequencing reads to identify phylogenetic clusters through genetic distance thresholds and maximum likelihood trees. We identified 141 people with AHI, 30 people with recent HIV, and 652 people with chronic (non-recent) HIV. We identified four geospatial clusters that contained the residences of 30% of clinic attendees with AHI, despite comprising just 0.8% of the populated land area and 3.5% of the population. We also identified fourteen distinct two-person phylogenetic clusters. Ten of the fourteen were male-female pairs, nine of which were clinic referral pairs. The remaining four were same-sex pairs who had not referred each other to the clinic and may have been missing network intermediaries. Three of the fourteen phylogenetic pairs consisted of only acute/recent members, and zero phylogenetic linkages were located within geospatial clusters. AHI detection programs anchored in STI clinic populations and their neighborhoods could facilitate identification of early HIV infection, enabling treatment initiation and transmission prevention efforts during this most infectious period. Future studies of intervention packages and deployment approaches can help inform the optimal design and implementation of AHI-focused strategies for reducing HIV incidence.

BACKGROUND:Understanding the burden of incident sexually transmitted infections (STIs) among persons in Eastern and Southern Africa after initiating HIV preexposure prophylaxis (PrEP) is critical to allocate scarce STI testing and HIV prevention resources. METHODS:Participants were recruited from an STI clinic in Lilongwe, Malawi (March-December 2022). Eligibility reflected oral PrEP eligibility per contemporary guidelines, limited to persons seeking STI services. We enrolled 3 groups: "index participants" who initiated PrEP, "PrEP-eligible decliners" who declined PrEP, and PrEP-initiating "referred partners" referred by index participants. Surveys and PrEP use assessments were conducted at baseline and at 1, 3, and 6 months; Chlamydia trachomatis, Neisseria gonorrhoeae, and syphilis testing done at baseline and at 3 and 6 months. A subset of participants completed in-depth interviews that were thematically analyzed. RESULTS:We enrolled 238 participants (174 index, 37 PrEP-eligible decliners, 27 referred partners); most were male (58%), and the median age was 27 years (interquartile range, 22-31 years). Forty-seven incident STIs were identified during 89.3 person-years (py) of follow-up (52.6/100 py). Men had a higher incidence versus women (55.8/100 py vs. 48.6/100 py). Index participants had the highest STI incidence (61.3/100 py), compared with PrEP-eligible decliners (26.4/100 py) and referred partners (27.1/100 py). Most incident infections were asymptomatic. Nearly all 27 interviewed participants described an STI as related to perceived HIV risk and need for PrEP. CONCLUSIONS:Incident, asymptomatic STIs in the 6 months after PrEP initiation were common. Testing of STI contextualizes perceived HIV risk and may encourage PrEP persistence. Integrating bacterial STI testing within PrEP care may reduce transmission via expedient treatment and should be considered alongside PrEP program expansion.Clinical Trial Number: NCT05307991 ( https://clinicaltrials.gov/ct2/show/NCT05307991 ).

RATIONALE:Organizational characteristics, including structures, culture, and climate, are important determinants of intervention scale-up success. Little is known about which characteristics are most important for HIV intervention scale-up success in low and middle-income countries (LMICs), and how they influence implementation in these contexts. AIMS AND OBJECTIVES:We sought to examine the relationship between organizational characteristics and scale-up success within an implementation trial testing strategies to scale up Systems Navigation and Psychosocial Counselling (SNaP) for people who inject drugs (PWID) with HIV in Vietnam. METHODS:This study was conducted in 42 HIV testing clinics in Vietnam. Informed by the Exploration, Preparation, Implementation, and Sustainment Framework, we assessed the association between five organizational characteristics and SNaP scale-up success: (1) implementation leadership; (2) staff workload; (3) percent PWID; (4) implementation climate; and (5) organizational readiness. We conducted a mixed methods study including surveys at baseline and endline with clinic staff and PWID participants in all clinics and interviews with clinic staff (n = 48) in six high and six low-performing clinics. To develop a context-driven scale-up success index for our outcome measure, we undertook a modified Delphi process with 14 experts in HIV, PWID, and implementation science. We assessed the relationship between our organizational characteristics and scale-up success using thematic and multiple linear regression analyses and explored the convergence of results. RESULTS AND CONCLUSION:Greater implementation leadership (ß = 12.20, p = 0.004), high staff workload (ß = 4.71, p = 0.008), and lower implementation climate scores (ß = -6.23, p = 0.046) were significantly associated with scale-up success. Qualitatively, participants described the importance of implementation leadership, particularly during COVID-19, and, to a lesser extent, implementation climate and organizational readiness for scale-up success. Some also described how more time spent on SNaP delivery improved fidelity but exacerbated workload. These findings demonstrate that prioritizing implementation leadership-focused strategies for the scale-up of HIV interventions like SNaP could improve implementation outcomes.

Objective: Systems Navigation and Psychosocial counseling (SNaP) is an evidence-based intervention that was clinically proven to improve HIV-related health outcomes among people who inject drugs living with HIV in a study in Indonesia, Ukraine, and one province in Vietnam. However, whether or not the SNaP intervention is effective when it is scaled up to different regions in Vietnam. This study was conducted in 2 provinces (Hanoi and Thai Nguyen) to explore key determinants for scaling up the SNaP intervention in Vietnam. Methods: Data were collected via 4 focus group discussions (FGDs) with leaders of provincial and site health departments. FGDs were transcribed, translated into English, and coded using Dedoose software to categorize determinants based on five domains of the Consolidated Framework for Implementation Research (CFIR). Results: The SNaP intervention's alignment with the country’s current health regulations (outer setting) was most highlighted as the key facilitator for scaling up, followed by the willingness of healthcare leaders and providers to incorporate SNaP into their clinical practices, which was due to the intervention’s strong evidence base and quality (intervention characteristics). The most prevalent barrier was clinics’ limited resources, specifically, time, personnel, and financial support (inner setting). Conclusions: The reported determinants provided practical implications to inform the development of relevant implementation strategies to scale up the SNaP intervention across Vietnam.

BACKGROUND:Pre-exposure prophylaxis (PrEP) prevents HIV acquisition but strategies are needed to improve uptake among high-risk groups. Assisted partner notification (aPN), proven for HIV case-finding, may expand PrEP services to sexual partners of sexually transmitted infection (STI) patients. While passive (index-led) partner notification for STI treatment receipt is standard, offering an assisted strategy may increase linkage to PrEP for HIV vulnerable partners who may otherwise be missed. This study explored the feasibility and outcomes of integrating aPN into PrEP programs at an STI clinic in Malawi. METHODS:Between March 2022 and January 2023, this prospective cohort study enrolled men and women presenting for STI services who were initiating PrEP (index PrEP user) and their referred sexual partners. Using World Health Organization-recommended aPN methods, recent (within last 6 months) sexual partners named by index participants were traced via phone or in-person. We assessed demographic characteristics of index participants and referred partners, tracing outcomes, and PrEP initiation among partners. RESULTS:174 index PrEP user participants were enrolled, most were male (109/174; 63%) with median age of 27 years (IQR 22, 32). The 174 index participants were asked to provide contact information for their partners, 69 of whom did. These 69 participants named 101 sexual partners (57% female). Partners were named as primary partners (53%), casual partners (41%), or sex workers (6%). Tracing efforts were employed for 52 partners with phone tracing yielding a 57% contact success and physical tracing yielding a 10% contact success. 58 partners (including those not traced) presented at the clinic for screening. Most presenting partners were female (39/58; 67%) and the median age was 28 years (IQR 23, 31). Among the presenting partners, 34/58 were eligible for PrEP, and 31/34 (91%) initiated PrEP. 20 of 55 named partners who agreed to testing were HIV positive, with 20% of these newly diagnosed during PrEP screening. CONCLUSIONS:aPN, including passive notification, effectively identifies and links at-risk partners of persons initiating PrEP to HIV prevention services, achieving high rates of PrEP uptake among eligible presenting partners, though less than half of index PrEP users named partners for tracing. Notably, phone tracing was more effective than physical tracing, but phone number availability was limited. This study highlights the potential of aPN in expanding PrEP access and strengthening HIV prevention efforts among persons seeking STI services. TRIAL REGISTRATION:This trial is registered on 5 October, 2023 at ClinicalTrials.gov NCT05307991 .

The integration of HIV pre-exposure prophylaxis (PrEP) into STI services can improve PrEP uptake among a population at elevated risk of acquiring HIV. The effectiveness of PrEP relies on ongoing coverage during periods of HIV risk, however, and little is known about longitudinal PrEP use among people accessing PrEP through STI clinics in sub-Saharan Africa. In this study, we analyzed routine records data from people who newly initiated PrEP at an STI clinic in Lilongwe, Malawi in March-December 2022. We assessed PrEP persistence among clients who received Malawi's standard-of-care PrEP services (n = 662) and reweighted the data to reflect the baseline distribution of age, sex, and PrEP indication among the full study population (n = 835). We used weighted generalized estimating equations to estimate the proportion of clients expected to persist on PrEP if all clients had received Malawi's standard-of-care services. We also assessed predictors of persistence and described re-engagement in PrEP among clients who did not persist. We estimated that, had all clients received standard-of-care services, 17% (95% CI: 14%, 20%), 7% (95% CI: 6%, 10%), and 4% (95% CI: 3%, 5%) would have persisted on PrEP at 1, 3, and 6 months, respectively, and that 8% (95% CI: 5%, 11%) of those who did not persist on PrEP at 1 month would have re-engaged in PrEP services by 12 months. Persistence varied by age and PrEP indication. Our findings indicate very low PrEP persistence in this population and suggest opportunities to support ongoing PrEP use in settings with integrated PrEP/STI services.

BACKGROUND:The global resurgence of syphilis necessitates vaccine development. METHODS:We collected ulcer exudates and blood from 17 participants with primary syphilis (PS) and skin biopsies and blood from 51 patients with secondary syphilis (SS) in Guangzhou, China, for Treponema pallidum subsp pallidum (TPA) quantitative polymerase chain reaction, whole genome sequencing (WGS), and isolation of TPA in rabbits. RESULTS:TPA DNA was detected in 15 of 17 ulcer exudates and 3 of 17 blood PS specimens. TPA DNA was detected in 50 of 51 SS skin biopsies and 27 of 51 blood specimens. TPA was isolated from 47 rabbits with success rates of 71% (12/17) and 69% (35/51), respectively, from ulcer exudates and SS bloods. We obtained paired genomic sequences from 24 clinical samples and corresponding rabbit isolates. Six SS14- and 2 Nichols-clade genome pairs contained rare discordances. Forty-one of the 51 unique TPA genomes clustered within SS14 subgroups largely from East Asia, while 10 fell into Nichols C and E subgroups. CONCLUSIONS:Our TPA detection rate was high from PS ulcer exudates and SS skin biopsies and over 50% from SS blood, with TPA isolation in more than two-thirds of samples. Our results support the use of WGS from rabbit isolates to inform vaccine development.

BACKGROUND:The increase in syphilis rates worldwide necessitates development of a vaccine with global efficacy. We aimed to explore Treponema pallidum subspecies pallidum (TPA) molecular epidemiology essential for vaccine research by analysing clinical data and specimens from early syphilis patients using whole-genome sequencing (WGS) and publicly available WGS data. METHODS:In this multicentre, cross-sectional, molecular epidemiology study, we enrolled patients with primary, secondary, or early latent syphilis from clinics in China, Colombia, Malawi, and the USA between Nov 28, 2019, and May 27, 2022. Participants aged 18 years or older with laboratory confirmation of syphilis by direct detection methods or serological testing, or both, were included. Patients were excluded from enrolment if they were unwilling or unable to give informed consent, did not understand the study purpose or nature of their participation, or received antibiotics active against syphilis in the past 30 days. TPA detection and WGS were conducted on lesion swabs, skin biopsies, skin scrapings, whole blood, or rabbit-passaged isolates. We compared our WGS data to publicly available genomes and analysed TPA populations to identify mutations associated with lineage and geography. FINDINGS:We screened 2802 patients and enrolled 233 participants, of whom 77 (33%) had primary syphilis, 154 (66%) had secondary syphilis, and two (1%) had early latent syphilis. The median age of participants was 28 years (IQR 22-35); 154 (66%) participants were cisgender men, 77 (33%) were cisgender women, and two (1%) were transgender women. Of the cisgender men, 66 (43%) identified as gay, bisexual, or other sexuality. Among all participants, 56 (24%) had HIV co-infection. WGS data from 113 participants showed a predominance of SS14-lineage strains with geographical clustering. Phylogenomic analyses confirmed that Nichols-lineage strains were more genetically diverse than SS14-lineage strains and clustered into more distinct subclades. Differences in single nucleotide variants (SNVs) were evident by TPA lineage and geography. Mapping of highly differentiated SNVs to three-dimensional protein models showed population-specific substitutions, some in outer membrane proteins (OMPs) of interest. INTERPRETATION:Our study substantiates the global diversity of TPA strains. Additional analyses to explore TPA OMP variability within strains is vital for vaccine development and understanding syphilis pathogenesis on a population level. FUNDING:US National Institutes of Health National Institute for Allergy and Infectious Disease, the Bill & Melinda Gates Foundation, Connecticut Children's, and the Czech Republic National Institute of Virology and Bacteriology.

In Vietnam and other global settings, men who have sex with men (MSM) have become the population at greatest risk of HIV infection. Although HIV pre-exposure prophylaxis (PrEP) has been implemented as a prevention strategy, PrEP outcomes may be affected by low persistence and adherence among MSM with unhealthy alcohol use. MSM have a high prevalence of unhealthy alcohol use in Vietnam, which may affect PrEP outcomes. Design: We will conduct a two-arm hybrid type 1 effectiveness-implementation randomized controlled trial of a brief alcohol intervention (BAI) compared to the standard of care (SOC) at the Sexual Health Promotion (SHP) clinic Hanoi, Vietnam. Participants: Sexually active MSM (n=564) who are newly initiating PrEP or re-initiating PrEP and have unhealthy alcohol use will be recruited and randomized 1:1 to the SOC or BAI arm. A subgroup of participants (n=20) in each arm will be selected for longitudinal qualitative interviews; an additional subset (n=48) in the BAI arm will complete brief quantitative and qualitative interviews after completion of the BAI to assess the acceptability of the intervention. Additional implementation outcomes will be assessed through interviews with clinic staff and stakeholders (n=35). Intervention: Study participants in both arms will receive standard care for PrEP clients. In the BAI arm, each participant will receive two face-to-face intervention sessions and two brief booster phone sessions, based on cognitive behavioral therapy and delivered in motivational interviewing informed style, to address their unhealthy alcohol use. Outcomes: Effectiveness (PrEP and alcohol use) and cost-effectiveness outcomes will be compared between the two arms. Intervention implementation outcomes (acceptability, feasibility, adoption) will be assessed among MSM participants, clinic staff, and stakeholders. This proposed trial will assess an alcohol intervention for MSM with unhealthy alcohol use who initiate or re-initiate PrEP, while simultaneously preparing for subsequent implementation. The study will measure the effectiveness of the BAI for increasing PrEP persistence through reducing unhealthy alcohol use in a setting where excessive alcohol consumption is a normative behavior. If effective, implementation-focused results will inform future scale-up of the BAI in similar settings. NCT06094634 on clinicaltrials.gov. Registered 16 October 2023.