Search

Abstract Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Methods Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Results Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. Conclusions It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

Introduction: Adolescent girls and young women (AGYW) account for two-thirds of new HIV infections in Africa. African AGYW have had high uptake of oral HIV pre-exposure prophylaxis (PrEP) but low adherence, which might be improved by point-of-care adherence monitoring with tailored counselling., Methods: From August 2022 to July 2023, we conducted a PrEP demonstration project with sexually active AGYW ages 16-30 years from 20 sites in South Africa, Eswatini, Kenya, Malawi, Uganda and Zambia. Participants were offered oral tenofovir-based PrEP at enrolment and followed up at 1, 3 and 6 months. PrEP adherence was assessed by a point-of-care qualitative lateral flow urine tenofovir (TFV) assay indicating PrEP use in the prior 4 days, which accompanied real-time adherence counselling that incorporated urine TFV results when testing was available (70.8% of month 1, 35.3% of month 3 and 83.9% of month 6 visits). We estimated overall adherence, correcting for missing test results, and analysed the association of having received urine TFV results at month 1 or 3 with subsequent urine TFV test positivity, using modified Poisson regression., Results: Of the 3087 AGYW enrolled, the median age was 24 years (interquartile range 21-27), 75.7% were from South Africa, 2878 (93.2%) initiated PrEP at enrolment and 107 (3.5%) after enrolment. Visit retention was 92.0-96.2% for months 1, 3 and 6, and 2518 (90.1%) exited the study with a PrEP refill. Adherence, based on the point-of-care urine tenofovir test positivity rate, was estimated as 72%, 71% and 65% at months 1, 3 and 6, respectively. Women who received one prior urine TFV test had a 42% higher likelihood of a subsequent positive urine TFV test (adjusted odds ratio, OR = 1.42, 95% confidence interval, CI 1.27-1.60), and those having received two prior tests had a 67% higher likelihood (adjusted OR = 1.67; 95% CI 1.41-1.98). Observed HIV incidence was 1.38/100 person-years (95% CI 0.97-2.08)., Conclusions: Oral PrEP uptake, recent adherence and persistence were high in a multisite cohort of young African women over 6 months of follow-up. The use of a novel point-of-care tenofovir assay with tailored real-time adherence counselling was associated with increased adherence to PrEP at subsequent visits, warranting further study., Clinical Trials Registration: clinicaltrials.gov NCT05746065., (© 2024 The Author(s). Journal of the International AIDS Society published by John Wiley & Sons Ltd on behalf of International AIDS Society.)

Background: Globally, there is suboptimal coverage of antiretroviral treatment to treat and prevent HIV. It is crucial for individuals to know their partner's HIV status so they may use all appropriate and available prevention tools. For sexual minority men in South Africa, a population known to face intersecting forms of marginalization including a disparate burden of HIV incidence, there are challenges to status sharing., Objective: We explore perspectives of healthcare workers (HCW) with expertise providing services to sexual minority men to identify strategies to support HIV status sharing., Methods: As part of a larger study designed to improve HIV-related health outcomes for sexual minority men, we conducted one focus group discussion (participant n  = 4) and two in-depth-interviews with HCW. We used thematic analysis to synthesize qualitative themes and identify corresponding implications for interventions., Results: HCW each had 5-23 years of experience. We identified three implementation considerations to support sharing of HIV status: (1) ensuring partner support for sharing status while circumventing risk of personal harms, (2) facilitating concordant couple-based peer support and belonging, and (3) leveraging the strengths of mass media as educational tools., Conclusion: HCW highlighted that sharing that one is living with HIV is a sensitive and potentially dangerous process that can be managed by involving both partners in the process. This process may be supported by incorporating HIV status sharing narratives in popular media.

Sexually transmitted infections (STIs) are widespread worldwide and negatively affect sexual and reproductive health. Gaps in evidence and in available tools have long hindered STI programmes and policies, particularly in resource-limited settings. In 2022, WHO initiated a research prioritisation process to identify the most important STI research areas to address the global public health need. Using an adapted Child Health and Nutrition Research Initiative methodology including two global stakeholder surveys, the process identified 40 priority STI research needs. The top priorities centred on developing and implementing affordable, feasible, rapid point-of-care STI diagnostic tests and new treatments, especially for gonorrhoea, chlamydia, and syphilis; designing new multipurpose prevention technologies and vaccines for STIs; and collecting improved STI epidemiologic data on both infection and disease outcomes. The priorities also included innovative programmatic approaches, such as new STI communication and partner management strategies. An additional six research areas related to mpox (formerly known as monkeypox) reflect the need for STI-related research during disease outbreaks where sexual transmission can have a key role. These STI research priorities provide a call to action for focus, investment, and innovation to address existing roadblocks in STI prevention, control, and management to advance sexual and reproductive health and wellbeing for all., Competing Interests: Declaration of interests SLG received support from the Bill & Melinda Gates Foundation paid to WHO for work on therapeutic human papillomavirus vaccines and on COVID-19 vaccines and pregnancy, and the Gates Foundation travel support to meetings on maternal immunisation and women's health innovations. LHB received royalties for book editing on Sexually Transmitted Infections in HIV-infected Adults and Special Populations. JDK received grants and support from the US National Institutes of Health (NIH), US Centers for Disease Control and Prevention, and Open Philanthropy; royalties and licences from UpToDate and McGraw-Hill; one-time consulting fees from Visby Medical, Diagnostics Direct, and Biofire; payment or honoraria from AIDS Healthcare Foundation; and payment for expert testimony from Gray Robinson. He is currently President of the non-profit organisation Herpes Cure Advocacy. JJO received grant support paid to his institution from the Australian National Health and Medical Research Council (NHMRC) and US NIH; and honoraria for presentations or other speaking events and support for attending meetings from Gilead Sciences. He is currently Board Director for the Australian Society for HIV, Hepatitis and Sexual Health Medicine and for Health Equity Matters and is a World Executive Committee member for the International Union against Sexually Transmitted Infections (IUSTI). RPHP received grants from NIH, Global AMR Innovation Fund–Foundation for Innovative New Diagnostics, Open Philanthropy, Global Antibiotic Research and Development Program–South African Medical Research Council, and the Swiss National Science Foundation. KLS received grants paid to her institute from the Australian NHMRC (numbers 1182443, 2017383, and 2002182). She has also received airfare and conference registration support from the International Pathogenic Neisseria Conference and the IUSTI World Congress. PJW received support from the UK Medical Research Council and National Institute for Health and Care Research, salary from the UK Health Security Agency and Imperial College London, and consulting fees from Pfizer and the National Institute for Public Health and the Environment. BVDP received consulting fees as an advisory board member for Abbot Rapid Diagnostics and Detect, consulting fees from Preventx, and speaking honoraria from Roche. She is President of the International Society for STD Research. NB received a consultancy contract from WHO for assistance with this project and had a contract with the Daffodil Centre on cervical cancer elimination. All other authors report no competing interests., (This is an Open Access article published under the CC BY 3.0 IGO license which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In any use of this article, there should be no suggestion that WHO endorses any specific organisation, products or services. The use of the WHO logo is not permitted. This notice should be preserved along with the article's original URL.)

Background: Identifying factors associated with vaccine uptake among health care workers (HCWs) remains crucial to generating evidence aimed at guiding national COVID-19 vaccination and future infectious disease outbreak strategies. This study aimed to elucidate these factors, focusing on the interplay between socio-demographic, health, knowledge, beliefs and attitudinal indicators., Methods: This was a cross-sectional online survey administered to HCWs across South Africa between August and October 2022. Bivariate and Multivariate logistic regressions identified associations between COVID-19 vaccine uptake and demographics, occupational characteristics, general knowledge of and attitudes towards vaccination, perceived COVID-19 risk and perceived importance of COVID-19 vaccine attributes., Results: Analysis revealed high vaccine uptake rates among the sample of 5564 HCWs, with 87.6% of the sample vaccinated at the time of the study. Demographic measures significantly associated with vaccine uptake were age (P-value = 0.001), race (P-value = 0.021), religion (P-value = 0.004), and having a chronic illness (P-value <0.001). Belief and attitude measures significantly associated with vaccine uptake included: need for vaccines (P-value <0.001), perceived risk of infection (P-value = 0.001), perceived patient risk (P-value <0.001), and perceived vaccine knowledge (P-value <0.001). Multivariate analysis revealed that HCWs who listed their religion as African Spirituality (OR = 0.4; 95% CI = 0.2-0.7; P-value = 0.002) and had any occupation other than nurse or doctor (OR = 0.6; 95% CI = 0.4-0.8; P-value <0.001), were less likely to vaccinate, while HCWs who had a chronic condition (OR = 1.5; 95% CI = 1.2-2.0; P-value <0.001) were more likely to have been vaccinated., Conclusion: This study provides useful insights into the factors associated with and possibly driving COVID-19 vaccine uptake among HCWs in South Africa. These results add to a limited body of knowledge on contextual dynamics associated with vaccination programmes in Africa., Competing Interests: Declaration of competing interest Douglas Wassenaar was the Chair of the UKZN BREC (IRB) that approved this study. This conflict was declared to BREC, and this application was managed independently by a BREC Deputy-Chair. The other authors declare no conflicts of interest., (Copyright © 2024. Published by Elsevier Ltd.)

Background: Syndromic treatment is the standard of care for vaginal discharge syndrome (VDS) in resource-constrained settings. However, the outcomes of VDS treatment have not been well documented. This study aimed to determine the incidence, risk factors, and microbial etiology of treatment failure in women with VDS., Methods: This prospective cohort study of women with VDS was conducted between September 2021 and March 2022 at Katutura Intermediate Hospital in Windhoek, Namibia. Microbiological analyses of sexually transmitted infections (STIs; Chlamydia trachomatis , Neisseria gonorrhoeae , Trichomonas vaginalis , Mycoplasma genitalium ), bacterial vaginosis, and vulvovaginal candidiasis (VVC) were performed. Treatment outcomes were assessed at 7 and 30 days after treatment, followed by microbial investigation in case of treatment failure., Results: One hundred nine women were enrolled, and 94 (86%) completed the follow-up. At baseline, 58 of 109 women (53%) were diagnosed with STI, 47 of 109 (43%) with bacterial vaginosis, and 45 of 109 (41%) with VVC. Candida albicans (33 of 45; 73%) was the main pathogen in VVC, with fluconazole resistance detected in 8 of 33 isolates (24%); 10 of 12 (80%) of non- albicans Candida species showed resistance. The incidence of treatment failure was 3.6 per 100 person-years at 7 days and 1.0 per 100 person-years at 30 days of follow-up; 17 of 94 women (18%) had recurrent VDS, and 12 of 94 women (13%) had persistent VDS. Vulvovaginal candidiasis (odds ratio, 4.3; 95% confidence interval, 1.7-11; P = 0.002) at baseline was associated with treatment failure., Conclusions: Treatment failure after syndromic management of VDS is common in resource-constrained settings. Access to diagnostic testing, including fungal culture and susceptibility testing, is recommended to improve outcomes., Competing Interests: Conflict of Interest and Sources of Funding: The authors declare that they have no competing interests. This study was supported by a University of Pretoria Doctoral Commonwealth Scholarship awarded to Cara Mia Dunaiski under the supervision of Prof. Remco P.H. Peters., (Copyright © 2024 American Sexually Transmitted Diseases Association. All rights reserved.)

Syphilis, 'the great imitator', caused by Treponema pallidum infection, remains a complex and multifaceted disease with a rich history of clinical diversity. This guideline aims to be a comprehensive guide for healthcare workers in Southern Africa, offering practical insights into the epidemiology, pathogenesis, clinical manifestations, diagnostic testing, therapeutic principles, and public health responses to syphilis. Although the syphilis burden has declined over the years, recent data indicate a troubling resurgence, particularly among pregnant women and neonates. This guideline highlights the diagnostic challenges posed by syphilis, stemming from the absence of a single high-sensitivity and -specificity test. While treatment with penicillin remains the cornerstone of treatment, alternative regimens may be used for specific scenarios. We highlight the importance of thorough patient follow-up and management of sex partners to ensure optimal care of syphilis cases. In the context of public health, we emphasise the need for concerted efforts to combat the increasing burden of syphilis, especially within high-risk populations, including people living with HIV., Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this article., (© 2024. The Authors.)

Antimicrobial resistance alongside other challenges in tuberculosis (TB) therapeutics have stirred renewed interest in host-directed interventions, including the role of antibodies as adjunct therapeutic agents. This study assessed the binding efficacy of two novel IgG1 opsonic monoclonal antibodies (MABs; GG9 & JG7) at 5, 10, and 25 µg/mL to live cultures of Mycobacterium tuberculosis, M. avium , M. bovis , M. fortuitum , M. intracellulare , and M. smegmatis American Type Culture Collection laboratory reference strains, as well as clinical susceptible, multi-drug resistant, and extensively drug resistant M. tuberculosis strains using indirect enzyme-linked immunosorbent assays. These three MAB concentrations were selected from a range of concentrations used in previous optimization (binding and functional) assays. Both MABs bound to all mycobacterial species and sub-types tested, albeit to varying degrees. Statistically significant differences in MAB binding activity were observed when comparing the highest and lowest MAB concentrations (p < 0.05) for both MABs GG9 and JG7, irrespective of the M. tuberculosis resistance profile. Binding affinity increased with an increase in MAB concentration, and optimal binding was observed at 25 µg/mL. JG7 showed better binding activity than GG9. Both MABs also bound to five MOTT species, albeit at varied levels. This non-selective binding to different mycobacterial species suggests a potential role for GG9 and JG7 as adjunctive agents in anti-TB chemotherapy with the aim to enhance bacterial killing., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Background: A rapid and affordable point-of-care test is a priority for Neisseria gonorrhoeae control. WHO and Foundation for Innovative New Diagnostics (FIND) have a target product profile for a non-molecular N gonorrhoeae rapid point-of-care test that requires a clinical sensitivity of greater than 80% and a specificity over 95% to be considered useful in syndromic management; test turnaround time should be 30 min or under, and the test should cost less than US$3. A novel lateral flow assay (LFA) was developed to achieve that profile., Methods: In this cross-sectional study we evaluated the performance of the novel N gonorrhoeae lateral flow assay (NG-LFA) at the primary health-care level in South Africa. Male patients with urethral discharge syndrome and female patients with vaginal discharge syndrome were recruited from five primary health-care facilities in the Buffalo City Metropolitan Municipality health district of South Africa. First-void urine specimens and nurse-collected vaginal swabs were tested in-facility with the NG-LFA and Xpert CT/NG PCR assay. N gonorrhoeae multi-antigen sequence typing (NG-MAST) was performed on all LFA positive specimens., Findings: Between March 7, and Sept 19, 2022, we enrolled 200 male patients with urethral discharge and 200 female patients with vaginal discharge. The median age of male patients was 24 years (IQR 21-31 years), and the median age of female patients was 25 years (IQR 21-32 years). In addition, 23 male patients and 12 female patients who presented at the facility with a partner notification slip were enrolled of whom one (4%) and five (42%) were symptomatic, respectively. NG-LFA and Xpert results were available for all participants. In urine specimens, NG-LFA sensitivity was 96·1% (Wilson 95% CI 91·2-98·3; 123 LFA-positive among 128 PCR-positive specimens) and 91·7% in vaginal swab specimens (78·2-97·1; 33 LFA-positive among 36 PCR-positive). The specificity was 97·2% in urine specimens (90·4-99·2; 70 LFA-negative among 72 PCR-negative) and 96·3% in vaginal specimens (92·2-98·3; 158 LFA-negative among 164 PCR-negative). In 156 LFA-positive specimens, NG-MAST showed 93 different sequence types., Interpretation: The novel NG-LFA had excellent clinical sensitivity and specificity in symptomatic male and female patients. The test met the optimal requirement for sensitivity and the minimal requirement for specificity specified in the target product profile. NG-LFA could provide an important tool to optimise clinical management and reduce excess antibiotic use in settings without direct access to laboratory testing., Funding: Global Antimicrobial Resistance Innovation Fund (GAMRIF) via FIND and National Institutes of Health., Competing Interests: Declaration of interests The Foundation for Professional Development (RPHP, MMM and LdV) received institutional funding from FIND for this work. LM is employed as a consultant by FIND. All other authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Candida glabrata is the most common non-albicans Candida species that causes vulvovaginal candidiasis (VVC). Given the intrinsically low susceptibility of C. glabrata to azole drugs, investigations into C. glabrata prevalence, fungal susceptibility profile, and molecular epidemiology are necessary to optimise the treatment of VVC. This molecular epidemiological study was conducted to determine antifungal drug profile, single nucleotide polymorphisms (SNPs) associated with phenotypic antifungal resistance and epidemic diversity of C. glabrata isolates from women with VVC in Namibia. Candida glabrata isolates were identified using phenotypic and molecular methods. Antifungal susceptibility of strains was determined for fluconazole, itraconazole, amphotericin B, and anidulafungin. Whole genome sequencing was used to determine SNPs in antifungal resistance genes and sequence type (ST) allocation. Among C. glabrata isolates, all (20/20; 100%) exhibited phenotypic resistance to the azole class antifungal drug, (fluconazole), and phenotypic susceptibility to the polyene class (amphotericin B), and the echinocandins (anidulafungin). Non-synonymous SNPs were identified in antifungal resistance genes of all fluconazole-resistant C. glabrata isolates including ERG6 (15%), ERG7 (15%), CgCDR1 (25%), CgPDR1 (60%), SNQ2 (10%), FKS1 (5.0%), FKS2 (5.0%), CgFPS1 (5.0%), and MSH2 (15%). ST15 (n = 8/20, 40%) was predominant. This study provides important insight into phenotypic and genotypic antifungal resistance across C. glabrata isolates from women with VVC in Namibia. In this study, azole resistance is determined by an extensive range of SNPs, while the observed polyene and echinocandin resistance-associated SNPs despite phenotypic susceptibility require further investigation., (© The Author(s) 2024. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

Background: South Africa maintains an integrated health system where syndromic management of sexually transmitted infections (STI) is the standard of care. An estimated 2 million cases of Neisseria gonorrhoeae (N. gonorrhoeae) occur in South Africa every year. Point-of-care diagnostic tests (POCT) may address existing STI control limitations such as overtreatment and missed cases. Subsequently, a rapid lateral flow assay with fluorescence-based detection (NG-LFA) with a prototype reader was developed for N. gonorrhoeae detection showing excellent performance and high usability; however, a better understanding is needed for device implementation and integration into clinics., Methods: A qualitative, time-series assessment using 66 in-depth interviews was conducted among 25 trained healthcare workers involved in the implementation of the NG-LFA. Findings were informed by the Normalization Process Theory (NPT) as per relevant contextual (strategic intentions, adaptive execution, and negotiation capacity) and procedural constructs (coherence, cognitive participation, collective action, reflexive monitoring) to examine device implementation within primary healthcare levels. Interviews were audio-recorded, transcribed, and then analyzed using a thematic approach guided by NPT to interpret results., Results: Overall, healthcare workers agreed that STI POCT could guide better STI clinical decision-making, with consideration for clinic integration such as space constraints, patient flow, and workload. Perceived NG-LFA benefits included enhanced patient receptivity and STI knowledge. Further, healthcare workers reflected on the suitability of the NG-LFA given current limitations with integrated primary care. Recommendations included sufficient STI education, and appropriate departments for first points of entry for STI screening., Conclusions: The collective action and participation by healthcare workers in the implementation of the NG-LFA revealed adaptive execution within the current facility environment including team compositions, facility-staff receptivity, and STI management experiences. User experiences support future clinic service integration, highlighting the importance of further assessing patient-provider communication for STI care, organizational readiness, and identification of relevant departments for STI screening., (© 2024. The Author(s).)

Introduction: Preterm birth complications are the most common cause of death in children under 5 years. The presence of multiple microorganisms and genital tract inflammation could be the common mechanism driving early onset of labour. South Africa has high levels of preterm birth, genital tract infections and HIV infection among pregnant women. We plan to investigate associations between the presence of multiple lower genital tract microorganisms in pregnancy and gestational age at birth., Methods and Analysis: This cohort study enrols around 600 pregnant women at one public healthcare facility in East London, South Africa. Eligible women are ≥18 years and at <27 weeks of gestation, confirmed by ultrasound. At enrolment and 30-34 weeks of pregnancy, participants receive on-site tests for Chlamydia trachomatis and Neisseria gonorrhoeae , with treatment if test results are positive. At these visits, additional vaginal specimens are taken for: PCR detection and quantification of Trichomonas vaginalis , Candida spp., Mycoplasma genitalium, M. hominis , Ureaplasma urealyticum and U. parvum ; microscopy and Nugent scoring; and for 16S ribosomal RNA gene sequencing and quantification. Pregnancy outcomes are collected from a postnatal visit and birth registers. The primary outcome is gestational age at birth. Statistical analyses will explore associations between specific microorganisms and gestational age at birth. To explore the association with the quantity of microorganisms, we will construct an index of microorganism load and use mixed-effects regression models and classification and regression tree analysis to examine which combinations of microorganisms contribute to earlier gestational age at birth., Ethics and Dissemination: This protocol has approvals from the University of Cape Town Research Ethics Committee and the Canton of Bern Ethics Committee. Results from this study will be uploaded to preprint servers, submitted to open access peer-reviewed journals and presented at regional and international conferences., Trial Registration Number: NCT06131749; Pre-results., Competing Interests: Competing interests: CAM has received research grant funding to her institution by Gilead, Abbott Molecular, Visby and Lupin Pharmaceuticals. She is a consultant to BioNTech, Cepheid and BioFire Diagnostics. She has received honoraria for educational presentations and review activities from Scynexis, Visby, Abbott, Elsevier, UpToDate and DynaMed Plus., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)

Background: There is a paucity of Neisseria gonorrhoeae antimicrobial resistance data from resource-constrained settings because of the lack of diagnostic testing and limited scale of surveillance programs. This study aimed to determine the antimicrobial resistance profile of N. gonorrhoeae in the rural Eastern Cape province of South Africa., Methods: Specimens for N. gonorrhoeae culture were obtained from men with urethral discharge and women with vaginal discharge attending primary health care facilities. Direct inoculation of the agar plates was performed followed by culture and drug susceptibility testing using the Etest at the laboratory. Whole-genome sequencing of the isolates was performed to identify resistance-determining variants., Results: One hundred N. gonorrhoeae isolates were obtained. Most strains were nonsusceptible to ciprofloxacin (76%), tetracycline (75%), and penicillin G (72%). The gyrA S91F mutation was present in 68 of 72 ciprofloxacin-resistant isolates (94%), with concurrent parC mutations in 47 of 68 (69%); gyrA I250M was the only mutation in 4 other resistant strains. One azithromycin-resistant isolate was identified with a minimal inhibitory concentration (MIC) of 8.0 mg/L and the 23S rDNA gene mutation C2597T. The median MIC of cefixime was 0.016 mg/L (range, 0.016-0.064 mg/L), and that of ceftriaxone was 0.016 mg/L (range, 0.016 mg/L). Whole-genome sequencing showed 58 sequence types as revealed in N. gonorrhoeae sequence typing for antimicrobial resistance and 70 sequence types in N. gonorrhoeae multiantigen sequence typing., Conclusions: This study confirmed high rates of N. gonorrhoeae antimicrobial resistance to ciprofloxacin, penicillin G, and tetracycline in our setting. The MICs of cephalosporins are reassuring for ceftriaxone use in syndromic treatment regimens, but the identification of azithromycin resistance warrants further attention., Competing Interests: Conflict of Interest and Sources of Funding: None of the authors declare a conflict of interest. This study was funded by the South African Medical Research Council through a grant awarded to the Global Antibiotic Research and Development Partnership (GARDP) under the project “Evaluating antimicrobial resistance of Neisseria gonorrhoeae infection in population groups at high risk of STI acquisition” (SAMRC project code 96150)., (Copyright © 2023 American Sexually Transmitted Diseases Association. All rights reserved.)

This study aimed examin the factors associated with the uptake and non-acceptance of COVID-19 vaccine booster doses among healthcare workers (HCWs) in South Africa. We used a mixed-methods design with data from a web-based self-administered survey followed by semi-structured in-depth interviews (IDIs) with selected participants. Of the 6235 HCWs included in our analysis who had fully vaccinated, 3470 (56%) had taken their booster dose with a further 17% intending to get the booster. HCWs aged 35 to 49 years (OR = 1.30 [95% CI: 1.15-1.46]), and those aged 50 years or older (OR = 2.66 [95% CI: 2.32-3.05]) were more likely to get the booster dose. Females were less likely to have received the booster dose (OR = 0.88 [95% CI: 0.79-0.98]) with doctors more likely (OR = 1.58 [95% CI: 1.35-1.84]) than Nurses to have received the booster dose. HCWs in direct contact with patients (OR = 1.17 [95% CI: 1.00-1.38]) and who had previously received a flu vaccine (OR = 1.99 [95% CI: 1.56-2.55]) were more likely to have received the booster dose. Four themes emerged from the qualitative data analysis: (1) Vaccination as routine practice among HCWs; (2) Emergence of new COVID-19 variants necessitating vaccine boosters; (3) Fear of potential side-effects; and (4) Limited value of COVID-19 vaccine boosters. Some HCWs broadly accepted the value of vaccination, and believed that boosters were necessary to effectively combat emergent new virus strains, which contrasted with peers who believed that boosters offered little defence against virus mutations. Fear prohibited some HCWs from getting the booster, with some having experienced adverse side effects from their initial vaccination, whilst others were concerned about future complications. Waning booster uptake rates could be arrested through invigorated communication strategies, while effective evidence-based training can potentially create positive normative vaccination practices amongst HCWs., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 George et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Therapeutic options for Neisseria gonorrhoeae are limited due to emerging global resistance. New agents and treatment options to treat patients with susceptible and multi-extensively drug-resistant N. gonorrhoeae is a high priority. This study used an in vitro approach to explore the antimicrobial potential, as well as synergistic effects of Medicine for Malaria Venture (MMV) Pathogen Box compounds against ATCC and clinical N. gonorrhoeae strains. Microbroth dilution assay was used to determine pathogen-specific minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the Pathogen Box compounds against susceptible and resistant N. gonorrhoeae strains, with modification, by adding PrestoBlue HS Cell Viability Reagent. A checkerboard assay was used to determine synergy between the active compounds and in conjunction with ceftriaxone. Time-kill kinetics was performed to determine if the compounds were either bactericidal or bacteriostatic. The Pathogen Box compounds: MMV676501, MMV002817, MMV688327, MMV688508, MMV024937, MMV687798 (levofloxacin), MMV021013, and MMV688978 (auranofin) showed potent activity against resistant strains of N. gonorrhoeae at an MIC and MBC of ≤10 µM. Besides the eight compounds, MMV676388 and MMV272144 were active against susceptible N. gonorrhoeae strains, also at MIC and MBC of ≤10 µM. All the compounds were bactericidal and were either synergistic or additive with fractional inhibitory concentration index ranging between 0.40 and 1.8. The study identified novel Pathogen Box compounds with potent activity against N. gonorrhoeae strains and has the potential to be further investigated as primary or adjunctive therapy to treat gonococcal infections., Competing Interests: The authors declare no conflict of interest.

South Africa has a large burden of bacterial sexually transmitted infections (STIs) with high rates among men who have sex with men (MSM). Randomised controlled trials have recently demonstrated high effectiveness of doxycycline post-exposure prophylaxis (PEP) for prevention of bacterial STIs in MSM, with 70% - 85% reductions in Chlamydia trachomatis infection and syphilis, and approximately 50% reduction in Neisseria gonorrhoeae infection. Doxycycline PEP was not demonstrated to be effective in reducing C. trachomatis and N. gonorrhoeae infection among Kenyan cisgender women. Although no worrisome trends in antimicrobial resistance (AMR) were observed in the trials, important concerns remain about doxycycline PEP and AMR development in STIs, other pathogens, commensals, and the microbiome. Tetracycline resistance in N. gonorrhoeae is already widespread in South Africa, but emergence of AMR in other STIs would be concerning. Larger sample sizes of doxycycline PEP users with longer follow-up time are needed to understand the impact that doxycycline PEP may have on AMR at individual and population level. In this opinion article, we weigh the benefits of doxycycline PEP for prevention of bacterial STIs against the existing AMR concerns and data gaps in the South African context. Based on the current evidence, we conclude that it would be reasonable to offer doxycycline PEP to high-risk MSM on a case-by-case basis, provided that it is offered by experienced sexual health clinicians in settings that have access to diagnostic STI testing and ongoing AMR surveillance., Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this article., (© 2023. The Authors.)

In South Africa, HIV prevalence for gay, bisexual, and men who have sex with men (GBMSM) is as high as 49.5%, yet only 25.7% are taking treatment, resulting in transmission risk between partners and the need for dyadic interventions for men in relationships. Through our preliminary research, we identified the evidence-based intervention Healthy Relationships (HR)-an HIV risk assessment and status disclosure intervention for those in relationships-to be tailored into videoconference format for partnered HIV-positive GBMSM in South Africa. The HR adaptation, called SOAR (Speaking Out & Allying Relationships), applied a human-centered design approach. In-depth interviews were conducted with HIV-positive GBMSM ( N = 15) to refine intervention preferences with results used to establish a beta SOAR. A trained interventionist conducted SOAR functionality ( n = 6) and usability ( n = 7) tests with separate invited groups composed of the original participants interviewed. Field logs, focus group discussions, and a study-specific preference survey were administered. Thematic analysis and descriptive statistics were completed with a convergent analytical approach used to understand usability. Overall experience of GBMSM in SOAR was good (69%) or excellent (31%). More than half of the participants (61%) rated using videoconferencing for SOAR as good, with 38% rating it as fair. All participants stated that SOAR was understandable and satisfactory with willingness to recommend it to other GBMSM. This adaptation approach was effective, and the resultant SOAR intervention has the potential to improve individual coping and HIV communication skills with partners to engage with biomedical prevention and in turn support GBMSM couples.

Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this article.

Accurate and user-friendly rapid point-of-care diagnostic tests (POCT) are needed to optimize treatment of Neisseria gonorrhoeae, especially in low-resource settings where syndromic management is the standard of care for sexually transmitted infections. This study aimed to assess the acceptability and usability of a novel lateral flow assay and portable reader for the point-of-care detection of N. gonorrhoeae infection (NG-LFA). This mixed-methods study was conducted as part of a diagnostic performance and usability evaluation of a prototype NG-LFA for detection of N. gonorrhoeae in symptomatic men and women at primary healthcare facilities in the Buffalo City Metro, South Africa. The Standardized System Usability Scale (SUS) was administered, and in-depth interviews were conducted among healthcare professionals (HCPs) and fieldworkers (FWs) at pre-implementation, initial use and 3- and 6-month study implementation to assess user expectations, practical experience, and future implementation considerations for the NG-LFA. Data collection and analysis was guided by the Health Technology Adoption Framework, including new health technology attributes, learnability, satisfaction, and suitability. The framework was adapted to include perceived durability. A total of 21 HCPs and FWs were trained on the NG-LFA use. SUS scores showed good to excellent acceptability ranging from 78.8-90.6 mean scores between HCPs and FWs across study time points. All transcripts were coded using Dedoose and qualitative findings were organized by learnability, satisfaction, suitability, and durability domains. Usability themes are described for each time point. Initial insecurity dissipated and specimen processing dexterity with novel POCT technology was perfected over time especially amongst FWs through practical learning and easy-to-use instructions (learnability). Participants experienced both positive and negative test results, yielding perceived accuracy and minimal testing challenges overall (satisfaction). By 3- and 6-month use, both HCPs and FWs found the NG-LFA convenient to use in primary health care facilities often faced with space constraints and outlined perceived benefits for patients (suitability and durability). Findings show that the NG-LFA device is acceptable and usable even amongst paraprofessionals. High SUS scores and qualitative findings demonstrate high learnability, ease-of-use and suitability that provide valuable information for first-step scale-up requirements at primary healthcare level. Minor prototype adjustments would enhance robustness and durability aspects., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 de Vos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Competing Interests: Potential conflicts of interest . The authors (R. P. H. P. and J. D. K.) received a donation of STI GeneXpert tests from Cepheid (California). C. A. M. declares grants or contracts from the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R21AI167754-01 and R01AI146065-01A1), the Centers for Disease Control and Prevention/US Department of Health and Human Services/the National Center for HIV, Viral Hepatitis, STD, and TB Prevention (NU62PS924587), Gilead (GS-US-528-9023), Abbott (protocol E239479959-21-007), and Lupin (for an investigator-initiated trial). C. A. M. also reports consulting fees from Abbott, Visby, and Cepheid; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing, or educational events from Visby, Scynexis, and Cepheid (paid to the author); participation on scientific advisory boards for BioNTech, Abbott, and Scynexis (payment to the author); service as a scientific reviewer for DynaMed (payment to the author); and a US patent currently pending (no. 63/355,887). All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Objectives: Globally, there have been significant changes in utilisation of STI testing and treatment services during the period of the COVID-19 pandemic. The impact of COVID-19 in countries that use syndromic STI management is not documented. This study used routine STI surveillance data to evaluate the impact of COVID-19 on utilisation of STI syndromic management services during the first wave of the COVID-19 epidemic in South Africa., Methods: We conducted a time-trend analysis of male urethritis syndrome (MUS) cases reported through routine national STI surveillance in South Africa and COVID-19 data available through the national dashboard. We defined three time periods (prelockdown, lockdown and postlockdown) based on COVID-19 response levels. Trends in MUS reporting was compared between these time periods at national and provincial level and with the number of positive COVID-19 tests in a district., Results: An overall reduction of 27% in the national number of MUS cases reported (monthly average from 27 117 to 20 107) occurred between the pre-COVID-19 and COVID-19 lockdown periods (p<0.001), with a range of 18%-39% between the nine provinces. Postlockdown, case numbers returned almost to the prelockdown level (26 304; -3.0%). No significant difference was found in number of MUS cases between the prelockdown and postlockdown periods. A weak correlation (R 2 =0,21) was identified between the change in number of MUS reported and COVID-19 positive tests in a district., Conclusions: A strong reduction in reported MUS cases for syndromic management was observed during the first wave of the COVID-19 epidemic and lockdown across all provinces in South Africa. This is likely the result of various healthcare system and service delivery factors associated with lockdown measures. The observed return of MUS cases reported to prelockdown measures is reassuring., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)

In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5 / mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible ( fbiD : del555GCT) or rifampicin mono-resistant ( fbiA : 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678 , glpK , nuoG , and uvrD1 . Genes with variants in the bedaquiline resistant mutants included atpE , fadE28 , truA , mmpL5 , glnH , and pks8 , while clofazimine-resistant mutants displayed ppsD , fbiA , fbiD , mutT3 , fadE18 , Rv0988 , and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.

Competing Interests: Potential conflicts of interest. All authors: No reported conflicts.

Background: Vulvovaginal yeast infections in pregnancy are common and can cause extensive inflammation, which could contribute to adverse pregnancy outcomes. Symptomatic yeast infections are likely to cause more inflammation than asymptomatic. The objective of this study was to investigate associations between symptomatic and asymptomatic vulvovaginal yeast infections in pregnancy and perinatal outcomes., Methods: We did a systematic review and searched eight databases until 01 July 2022. We included studies reporting on pregnant women with and without laboratory confirmed vulvovaginal yeast infection and preterm birth or eight other perinatal outcomes. We used random effects meta-analysis to calculate summary odds ratios (OR), 95% confidence intervals (CI) and prediction intervals for the association between yeast infection and outcomes. We described findings from studies with multivariable analyses. We assessed the risk of bias using published tools., Results: We screened 3909 references and included 57 studies. Only 22/57 studies reported information about participant vulvovaginal symptoms. Preterm birth was an outcome in 35/57 studies (49,161 women). In 32/35 studies with available data, the summary OR from univariable analyses was 1.01 (95% CI 0.84-1.21, I 2 60%, prediction interval 0.45-2.23). In analyses stratified by symptom status, we found ORs of 1.44 (95% CI 0.92-2.26) in two studies with ≥ 50% symptomatic participants, 0.84 (95% CI 0.45-1.58) in seven studies with < 50% symptomatic participants, and 1.12 (95% CI 0.94-1.35) in four studies with asymptomatic participants. In three studies with multivariable analysis, adjusted ORs were greater than one but CIs were compatible with there being no association. We did not find associations between vulvovaginal yeast infection and any secondary outcome. Most studies were at high risk of bias in at least one domain and only three studies controlled for confounding., Conclusions: We did not find strong statistical evidence of an increased risk for preterm birth or eight other adverse perinatal outcomes, in pregnant women with either symptomatic or asymptomatic vulvovaginal yeast infection. The available evidence is insufficient to make recommendations about testing and treatment of vulvovaginal yeast infection in pregnancy. Future studies should assess vulvovaginal symptoms, yeast organism loads, concomitant vaginal or cervical infections, and microbiota using state-of-the-art diagnostics., Systematic Review Registration: PROSPERO CRD42020197564., (© 2023. The Author(s).)

Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this research article.

This study aims to assess the potential association of MBL2 gene single nucleotide polymorphisms (SNPs) to Chlamydia trachomatis infection. We analysed a selected sample of 492 DNA and serum specimens from Dutch Caucasian women. Women were categorized into four groups of infection status based on the results of DNA and antibody tests for C. trachomatis: Ct-DNA+/IgG+, Ct-DNA+/IgG−, Ct-DNA−/IgG+, and Ct-DNA−/IgG−. We compared six MBL2 SNPs (−619G > C (H/L), −290G > C (Y/X), −66C > T (P/Q), +154C > T (A/D), +161A > G (A/B), and +170A > G (A/C)) and their respective haplotypes in relation to these different subgroups. The −619C (L) allele was less present within the Ct-DNA−/IgG+ group compared with the Ct-DNA−/IgG− group (OR = 0.49; 95% CI: 0.28−0.83), while the +170G (C) allele was observed more in the Ct-DNA+/IgG+ group as compared with the Ct-DNA−/IgG− group (OR = 2.4; 95% CI: 1.1−5.4). The HYA/HYA haplotype was more often present in the Ct-DNA−/IgG− group compared with the Ct-DNA+/IgG+ group (OR = 0.37; 95% CI: 0.16−0.87). The +170G (C) allele was associated with increased IgG production (p = 0.048) in C. trachomatis PCR-positive women. This study shows associations for MBL in immune reactions to C. trachomatis. We showed clear associations between MBL2 genotypes, haplotypes, and individuals’ stages of C. trachomatis DNA and IgG positivity.

Background: Vaginal discharge syndrome (VDS) is a common condition. Clinical management targets sexually transmitted infections (STIs) and bacterial vaginosis (BV); there is limited focus on Candida infection as cause of VDS. Lack of Candida treatment coverage and, if present, antifungal resistance may result in VDS treatment failure. This study aimed to determine the prevalence of Candida infection, antifungal resistance, and coinfections in Namibian women with VDS., Methods: A cross-sectional study was performed using 253 vaginal swabs from women with VDS in Namibia. Demographic data was collected, and phenotypic and molecular detection of Candida species was performed followed by fluconazole susceptibility testing of Candida isolates. BV was diagnosed using Nugent score microscopy; molecular detection of Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis was performed., Results: Candida species was detected in 110/253 women (43%). Ninety women (36%) had Candida albicans and 24 (9.5%) had non-albicans Candida species. The non-albicans species detected were 19 (17%) Candida glabrata, 4.0 (3.5%) Candida krusei, and 1.0 (0.9%) Candida parapsilosis. Candida albicans were more frequently isolated in younger (p = 0.004) and pregnant women (p = 0.04) compared to non-albicans Candida species. Almost all (98%) Candida albicans isolates were susceptible to fluconazole while all non-albicans Candida species were fluconazole resistant. STIs were diagnosed in 92 women (36%): 30 (12%) with C. trachomatis, 11 (4.3%) N. gonorrhoeae, and 70 (28%) T. vaginalis; 98 (39%) women had BV. Candida infection alone was diagnosed in 30 women (12%), combined with STIs in 42 women (17%) and was concurrent with BV in 38 women (15%). Candida infection was more often detected in swabs from women without C. trachomatis detected (6.4% vs. 16%; OR 0.30; 95% CI 0.10-0.77, p = 0.006)., Conclusions: The high prevalence of Candida infection, especially those due to non-albicans Candida species that are resistant to fluconazole, is a great concern in our setting and may lead to poor treatment outcomes. Access to microbiological testing for Candida species in the context of syndromic management is warranted., (© 2022. The Author(s).)

Background: Sexually transmitted infections (STIs) during pregnancy are associated with adverse birth outcomes, including preterm birth, low birth weight, perinatal death, and congenital infections such as increased mother-to-child HIV transmission. Prevalence of STIs among pregnant women in South Africa remains high, with most women being asymptomatic for their infection(s). Unfortunately, most STIs remain undetected and untreated due to standard practice syndromic management in accordance with World Health Organization (WHO) guidelines. Although lab-based and point-of-care molecular tests are available, optimal screening strategies during pregnancy, their health impact, and cost-effectiveness are unknown., Methods: We will implement a 3-arm (1:1:1) type-1 hybrid effectiveness-implementation randomized-controlled trial (RCT). We will enroll 2500 pregnant women attending their first antenatal care (ANC) visit for their current pregnancy at participating health facilities in Buffalo City Metro District, Eastern Cape Province, South Africa. Participants allocated to arms 1 and 2 (intervention) will receive GeneXpert® point-of-care diagnostic testing for Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis, with same-day treatment for detected infection(s). Arm 1 will additionally receive a test-of-cure 3 weeks post-treatment, while Arm 2 will receive a repeat test at 30-34 weeks' gestation. Those allocated to Arm 3 will receive syndromic management (standard-of-care). The RE-AIM framework will be used to guide collection of implementation indicators to inform potential future scale up. Primary outcome measures include (1) frequency of adverse birth outcomes among study arms, defined by a composite measure of low birth weight and pre-term delivery, and (2) change in STI prevalence between baseline and birth outcome among intervention arms and compared to standard-of-care. Estimates and comparative costs of the different screening strategies relative to standard-of-care and the costs of managing adverse birth outcomes will be calculated. Cost-effectiveness will be assessed per STI and disability-adjusted life year averted., Discussion: This trial is the first RCT designed to identify optimal, cost-effective screening strategies that decrease the burden of STIs during pregnancy and reduce adverse birth outcomes. Demonstrating the impact of diagnostic screening and treatment, compared to syndromic management, on birth outcomes will provide critical evidence to inform changes to WHO guidelines for syndromic management of STIs during pregnancy., Trial Registration: ClinicalTrials.gov NCT04446611 . Registered on 25 June 2020., (© 2022. The Author(s).)

Background: Gay, bisexual, and other men who have sex with men (GBMSM) living with HIV have low antiretroviral treatment adherence in South Africa due to limited skills in managing disclosure and prevention behaviors with sexual and romantic partners. As a result, there is a high HIV transmission risk within HIV-discordant partnerships, but an existing intervention may address these outcomes, if adapted effectively. Healthy Relationships (HR) is a behavioral intervention that was originally delivered in groups and in person over 5 sessions to develop coping skills for managing HIV-related stress and sexually risky situations, enhance decision-making skills for HIV disclosure to partners, and establish and maintain safer sex practices with partners. HR effectively improves prevention behaviors but has yet to be tailored to a non-US context., Objective: We aim to adapt HR into a new culturally grounded intervention entitled Speaking Out & Allying Relationships for GBMSM and then assess its feasibility in Eastern Cape, South Africa., Methods: The study will have 2 aims. For aim 1-adaptation-we will use a human-centered design approach. Initial intervention tailoring will involve integrating Undetectable=Untransmittable and pre-exposure prophylaxis education, developing intervention content for a videoconference format, and designing role-plays and movies for skill building based on preliminary data. Afterward, interviews and surveys will be administered to GBMSM to assess intervention preferences, and a focus group will be conducted with health care providers and information technology experts to assess the intervention's design. Finally, a usability test will be performed to determine functionality and content understanding. Participants will be GBMSM living with HIV (n=15) who are in a relationship and health care providers and information technology (n=7) experts working in HIV care and programming with this population. For aim 2, we will examine the feasibility of the adapted intervention by using a pilot randomized control design. There will be 60 individuals per arm. Feasibility surveys and interviews will be conducted with the intervention arm, and behavioral and biomedical assessments for relationship and treatment adherence outcomes will be collected for both arms. All participants will be GBMSM living with HIV who are in a relationship with an HIV-negative or unknown status partner., Results: Intervention adaptation began in August 2021. Initial tailoring and the refining of GBMSM intervention preferences were completed in December 2021. Usability and feasibility assessments are due to be completed by March 2022 and February 2024, respectively., Conclusions: GBMSM need efficacious interventions that tackle partnership dynamics, HIV prevention, and treatment outcomes for antiretroviral treatment adherence and viral suppression in South Africa. Harnessing everyday technology use for social networking (eg, videoconferences), Undetectable=Untransmittable education, and pre-exposure prophylaxis to update an existing intervention for South African GBMSM has the potential to strengthen relationship communication about HIV treatment and prevention and, in turn, improve outcomes., International Registered Report Identifier (irrid): DERR1-10.2196/36845., (©Joseph Daniels, Remco P H Peters, Andrew Medina-Marino, Cikizwa Bongo, Rob Stephenson. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 16.05.2022.)

Background: Sexually transmitted infections (STIs) during pregnancy may increase the risk of adverse pregnancy outcomes. STI syndromic management is standard of care in South Africa but has its limitations. We evaluated the impact of diagnosing and treating curable STIs during pregnancy on adverse pregnancy and birth outcomes., Methods: We combined data from two prospective studies of pregnant women attending public sector antenatal care (ANC) clinics in Tshwane District and Cape Town, South Africa. Pregnant women were enrolled, tested and treated for STIs. We evaluated the association between any STI at the first ANC visit and a composite adverse pregnancy outcome (miscarriage, stillbirth, preterm birth, early neonatal death, or low birthweight) using modified Poisson regression models, stratifying by HIV infection and adjusting for maternal characteristics., Results: Among 619 women, 61% (n = 380) were from Tshwane District and 39% (n = 239) from Cape Town; 79% (n = 486) were women living with HIV. The prevalence of any STI was 37% (n = 228); C. trachomatis, 26% (n = 158), T. vaginalis, 18% (n = 120) and N. gonorrhoeae, 6% (n = 40). There were 93% (n = 574) singleton live births, 5% (n = 29) miscarriages and 2% (n = 16) stillbirths. Among the live births, there were 1% (n = 3) neonatal deaths, 7% (n = 35) low birthweight in full-term babies and 10% (n = 62) preterm delivery. There were 24% (n = 146) for the composite adverse pregnancy outcome. Overall, any STI diagnosis and treatment at first ANC visit was not associated with adverse outcomes in women living with HIV (adjusted relative risk (aRR); 1.43, 95% CI: 0.95-2.16) or women without HIV (aRR; 2.11, 95% CI: 0.89-5.01). However, C. trachomatis (aRR; 1.57, 95% CI: 1.04-2.39) and N. gonorrhoeae (aRR; 1.69, 95% CI: 1.09-3.08), were each independently associated with the composite adverse outcome in women living with HIV., Conclusion: Treated STIs at the first ANC visit were not associated with adverse pregnancy outcome overall. In women living with HIV, C. trachomatis or N. gonorrhoeae at first ANC were each independently associated with adverse pregnancy outcome. Our results highlights complex interactions between the timing of STI detection and treatment, HIV infection and pregnancy outcomes, which warrants further investigation., (© 2022. The Author(s).)

Background: Reports have emerged globally of antimicrobial resistance (AMR) in Neisseria gonorrhoeae and Mycoplasma genitalium infections. In South Africa (SA), there are substantial differences between private and public healthcare with regard to antimicrobial drug prescribing practice, which could affect AMR patterns of private and public healthcare patients., Objectives: To perform a pilot study to determine the frequency of AMR of N. gonorrhoeae and M. genitalium in patients accessing SA's private healthcare sector., Methods: In this cross-sectional study, N. gonorrhoeae-positive cultures and M. genitalium DNA samples were collected from a private healthcare reference laboratory from August 2018 to August 2019. In N. gonorrhoeae-positive cultures, antimicrobial susceptibility testing was performed, followed by N. gonorrhoeae multiantigen sequence typing (NG-MAST) to determine genetic relatedness of the isolates. To determine macrolide and fluoroquinolone resistance rates, M. genitalium-positive samples were analysed by sequencing the 23S rRNA, gyrA and parC genes., Results: Twenty-one N. gonorrhoeae- and 27 M. genitalium-positive specimens were included in this analysis. High rates of resistance were detected among gonococcal isolates, with 90% resistance to tetracycline, 86% to penicillin and 62% to ciprofloxacin, but no resistance to azithromycin, cefixime and ceftriaxone. NG-MAST revealed genetically diverse isolates with 83% novel NG-MAST sequence types. Macrolide and fluoroquinolone resistance-associated mutations were detected in 18.5% (n=5/27) and 7.4% (n=2/27) of M. genitalium strains, respectively., Conclusions: We observed high frequencies of ciprofloxacin, penicillin and tetracycline resistance in N. gonorrhoeae and macrolide resistance-associated mutations in M. genitalium in private healthcare sector patients in SA. This finding highlights the need to use diagnostics for sexually transmitted infections and to include the private healthcare sector in antimicrobial surveillance and stewardship programmes.

Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings., (© 2021. The Author(s).)

Background: The vaginal microbiota (VMB) are the set of microorganisms residing in the human vagina. During pregnancy, their composition is Lactobacillus-dominant in most Caucasian women. Previous studies suggest that the VMB of women with African ancestry is more likely to be non-Lactobacillus dominant (dysbiotic) compared to other populations, and possibly relate to the high incidence of pregnancy complications, such as preterm birth. This work reviewed the literature on VMB composition in pregnant women from sub-Saharan Africa., Methods: A search was conducted in PubMed and Embase databases following PRISMA guidelines. Observational and intervention studies analysing VMB communities from sub-Saharan African pregnant women using molecular techniques were included., Results: Ten studies performed in seven sub-Saharan African countries were identified. They independently showed that Lactobacillus-dominant VMB (particularly L. iners or L. crispatus) or VMB containing Lactobacilli are the most prevalent, followed by a more diverse anaerobe-dominant VMB, in the studied populations. The majority of pregnant women with a sexually-transmitted infection had a Lactobacillus-dominant VMB, but with a significantly higher presence of anaerobic species., Conclusion: In agreement with studies performed in other populations, Lactobacillus species are the most prevalent VMB species during pregnancy in sub-Saharan African women. The frequency of diverse anaerobe-dominant VMB is high in these populations. In Africa, studies on VMB in pregnancy are scant, heterogeneous in methodology, and knowledge remains limited. More insights on VMB composition and their possible sequalae among these populations is needed., (© 2021. The Author(s).)

Objective: STIs during pregnancy increase adverse pregnancy and birth outcomes and may increase HIV risk. STI syndromic management is standard of care in South Africa. Our study evaluated the prevalence and incidence of STIs in pregnant women and the associated risk factors., Methods: We combined data from two prospective observational studies of pregnant women enrolled while attending their first antenatal clinic (ANC) visit in Tshwane District and Cape Town. Women ≥18 years were tested at first ANC visit and at their first postpartum visit for Chlamydia trachomatis , Neisseria gonorrhoeae and Trichomonas vaginalis using Xpert assays (Cepheid, USA). We evaluated the prevalence and incidence of STI and the associated risk factors using multivariable regression models., Results: We enrolled 669 pregnant women, 64% (n=427) from Tshwane District and 36% (n=242) from Cape Town; 80% (n=534) were women living with HIV (WLHIV) and 20% (n=135) without HIV. At enrolment, 37% (n=250) were diagnosed with at least one STI, of which 76% (n=190) were asymptomatic. STI prevalence was 40% (n=213) in WLHIV and 27% (n=37) in women without HIV (p=0.01). Baseline STI infection was associated with younger age (OR=0.95 per year, 95% CI 0.92 to 0.98), higher gestational age (adjusted OR (aOR)=1.03 per week, 95% CI 1.00 to 1.05), single relationship status (aOR=1.53, 95% CI 1.09 to 2.15) and HIV status (aOR=1.86, 95% CI 1.17 to 2.95). Of 419 participants with no STI at baseline, 21 had an incident STI during follow-up, with a mean follow-up time of 140 days. The incidence rate of STI during pregnancy and early post partum was 15 infections per 100 women-years (95% CI 9 to 23). Younger age was associated with STI incidence., Conclusion: Our study shows high prevalence and incidence of STIs in pregnancy, especially in WLHIV, demonstrating the need for STI screening in ANC to prevent adverse pregnancy and birth outcomes. Most STI cases were asymptomatic and would have gone untreated with syndromic management. Aetiological STI screening is urgently needed to reduce the burden of STIs in pregnancy., Competing Interests: Competing interests: The authors received a donation of STI Xpert assays from Cepheid (California, USA)., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: HIV incidence among South African adolescent girls and young women (AGYW) remains high, but could be reduced by highly effective pre-exposure prophylaxis (PrEP). Unfortunately, AGYW report significant barriers to clinic-based sexual and reproductive health services. Even when AGYW access PrEP as an HIV prevention method, poor prevention-effective use was a serious barrier to achieving its optimal HIV prevention benefits. Determining the acceptability and feasibility of community-based platforms to increase AGYW's access to PrEP, and evaluating behavioural interventions to improve prevention-effective use of PrEP are needed., Methods: We propose a mixed-methods study among AGYW aged 16-25 years in Eastern Cape Province, South Africa. In the first component, a cross-sectional study will assess the acceptability and feasibility of leveraging community-based HIV counselling and testing (CBCT) platforms to refer HIV-negative, at-risk AGYW to non-clinic-based, same-day PrEP initiation services. In the second component, we will enrol 480 AGYW initiating PrEP via our CBCT platforms into a three-armed (1:1:1) randomized control trial (RCT) that will evaluate the effectiveness of adherence support interventions to improve the prevention-effective use of PrEP. Adherence will be measured over 24 months via tenofovir-diphosphate blood concentration levels. Qualitative investigations will explore participant, staff, and community experiences associated with community-based PrEP services, adherence support activities, study implementation, and community awareness. Costs and scalability of service platforms and interventions will be evaluated., Discussion: This will be the first study to assess the acceptability and feasibility of leveraging CBCT platforms to identify and refer at-risk AGYW to community-based, same-day PrEP initiation services. It will also provide quantitative and qualitative results to inform adherence support activities and services that promote the prevention-effective use of PrEP among AGYW. By applying principles of implementation science, behavioural science, and health economics research, we aim to inform strategies to improve access to and prevention-effective use of PrEP by AGYW., Trial Registration: ClinicalTrials.gov NCT03977181 . Registered on 6 June 2019-retrospectively registered., (© 2021. The Author(s).)

Provision of high-quality care and ensuring retention of children on antiretroviral therapy (ART) are essential to reduce human immunodeficiency virus (HIV)-associated morbidity and mortality. Virological non-suppression (≥1000 viral copies/ml) is an indication of suboptimal HIV care and support. This retrospective cohort study included ART-naïve children who initiated first-line ART between July 2015 and August 2017 in Johannesburg and rural Mopani district. Of 2739 children started on ART, 29.5% (807/2739) were lost to care at the point of analysis in August 2018. Among retained children, overall virological non-suppression was 30.2% (469/1554). Virological non-suppression was associated with higher loss to care 30.3% (229/755) compared with suppressed children (9.7%, 136/1399, P < 0.001). Receiving treatment in Mopani was associated with virological non-suppression in children under 5 years (adjusted odds ratio (aOR) 1.7 (95% confidence interval (CI) 1.1-2.4), 5-9 years (aOR 1.8 (1.1-3.0)) and 10-14 years (aOR 1.9 (1.2-2.8)). Virological non-suppression was associated with lower CD4 count in children 5-9 years (aOR 2.1 (1.1-4.1)) and 10-14 years (aOR 2.1 (1.2-3.8)). Additional factors included a shorter time on ART (<5 years aOR 1.8-3.7 (1.3-8.2)), and male gender (5-9 years, aOR1.5 (1.01-2.3)), and receiving cotrimoxazole prophylaxis (10-14 years aOR 2.0 (1.2-3.6)). In conclusion, virological non-suppression is a factor of subsequent programme loss in both regions, and factors affecting the quality of care need to be addressed to achieve the third UNAIDS 90 in paediatric HIV.

Objectives: Macrolide resistance in Mycoplasma genitalium is emerging globally. There is paucity of data from sub-Saharan Africa where syndromic management is used to treat sexually transmitted infections (STIs). We conducted a molecular epidemiological study to determine the prevalence of azithromycin resistance and epidemic diversity of M. genitalium infections in South Africa., Methods: We analysed 90 M. genitalium -positive specimens that had been collected consecutively from men and women (50% symptomatic) from geographically diverse communities across the northern part of South Africa between 2015 and 2019. Melting curve analysis followed by targeted sequencing of the 23S rRNA gene was performed to detect azithromycin resistance. Molecular typing was done through single nucleotide polymorphism (SNP) analysis of the MG191 gene and short tandem repeats (STR) assessment of the MG309 gene. An overview of all published M. genitalium sequence types was generated and novel sequence types identified in this study were allocated numbers accordingly., Results: Azithromycin resistance was detected in 1/90 M. genitalium -positive specimens (1.1%; 95% CI 0% to 3.3%) as conferred by A2071G mutation; this strain also harboured a C234T mutation in the parC gene with wild type gyrA gene. SNP typing and STR assessment was successful in 38/90 specimens (42%) and showed a genetically diverse epidemic, without geographic clustering, with eight novel sequence types identified., Conclusion: This is the first study that determines resistance in M. genitalium infection since introduction of azithromycin in the syndromic management regimen for STIs in South Africa in 2015. Despite a well-established epidemic, azithromycin-resistant M. genitalium infection is still uncommon in the public healthcare sector. However, it has the potential to undermine the effectiveness of syndromic management. Introduction of molecular diagnostics and continuous surveillance are warranted for early detection emergence of resistance., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. No commercial re-use. See rights and permissions. Published by BMJ.)

Abstract: We conducted an observational study of lymphogranuloma venereum (LGV) biovar Chlamydia trachomatis infection in HIV-infected women in South Africa. The LGV biovar was detected in vaginal specimens of 17 (20%) of 85 women with C. trachomatis infection; 29% were symptomatic. All cases were negative for the LGV biovar after single-dose azithromycin., Competing Interests: Conflict of Interest and Sources of Funding: The authors do not report any conflict of interest. This work was supported by The Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health, award R21HD084274 to A.M.M. and J.D.K., and the President’s Emergency Plan for AIDS Relief through the US Agency of the Cooperative Agreement AID 674-A-12-00017 to the Foundation for Professional Development., (Copyright © 2020 American Sexually Transmitted Diseases Association. All rights reserved.)

Background: Previous studies have described the association between dysbiosis of the vaginal microbiota (VMB) and related dysbiotic conditions, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), and various adverse pregnancy outcomes. There is limited overview of this association from countries in sub-Saharan Africa (SSA), which bear a disproportionally high burden of both vaginal dysbiotic conditions and adverse pregnancy outcomes. This systematic review assesses the evidence on the association between VMB dysbiosis, BV, and AV, and late adverse pregnancy outcomes in women living in SSA. Methods: The Preferred Reporting Items for Systematic Review and Meta-Analysis Statement (PRISMA) guidelines were followed. Three databases [PubMed, Embase (Ovid), and Cochrane] were used to retrieve observational and intervention studies conducted in SSA that associated VMB dysbiosis, BV, or AV and preterm birth/labor/delivery, preterm rupture of membranes (PROM), low birthweight, small for gestational age, intrauterine growth restriction, intrauterine infection, intrauterine (fetal) death, stillbirth, perinatal death, or perinatal mortality. Results: Twelve studies out of 693 search records from five SSA countries were included. One study identified a positive association between VMB dysbiosis and low birthweight. Despite considerable differences in study design and outcome reporting, studies reported an association between BV and preterm birth (7/9), low birthweight (2/6), PROM (2/4), intrauterine infections (1/1), and small for gestational age (1/1). None of the retrieved studies found an association between BV and pregnancy loss (5/5) or intrauterine growth retardation (1/1). At least two studies support the association between BV and PROM, low birthweight, and preterm birth in Nigerian pregnant women. No reports were identified investigating the association between AV and late adverse pregnancy outcomes in SSA. Conclusion: Two of the included studies from SSA support the association between BV and PROM. The remaining studies show discrepancies in supporting an association between BV and preterm birth or low birthweight. None of the studies found an association between BV and pregnancy loss. As for the role of VMB dysbiosis, BV, and AV during pregnancy among SSA women, additional research is needed. These results provide useful evidence for prevention efforts to decrease vaginal dysbiosis and its contribution to adverse pregnancy outcomes in SSA., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Juliana, Suiters, Al-Nasiry, Morré, Peters and Ambrosino.)

Neisseria gonorrhoeae antimicrobial drug resistance has emerged worldwide; however, the situation in sub-Saharan Africa is not well documented. We investigated the molecular epidemiology and occurrence of antimicrobial resistance in Neisseria gonorrhoeae infections in two core transmission groups of men in Johannesburg, South Africa. We recruited men who have sex with men (MSM) presenting with urethral discharge and men with recurrent episodes of urethral discharge. Molecular testing and culture for N. gonorrhoeae were performed, followed by antimicrobial susceptibility testing. Whole-genome sequencing (WGS) was used to identify resistance-conferring mutations and to determine the genetic relatedness of the isolates. In all, 51 men were recruited; 42 (82%) had N. gonorrhoeae infections. Most gonococcal isolates were resistant to ciprofloxacin (78%) and tetracycline (74%); 33% were penicillin resistant. All gonococcal isolates were susceptible to cephalosporins and spectinomycin. Azithromycin resistance was observed in 4 (15%) isolates (epidemiological cutoff), all with mutations in the mtrR promoter region. Most of the isolates (19/27) harbored the gonococcal genetic island, which is associated with antimicrobial resistance. WGS revealed a diverse epidemic with mostly novel NG-STAR (70%) and NG-MAST (70%) sequence types. Thus, we demonstrate a high prevalence of antimicrobial resistance in Neisseria gonorrhoeae strains obtained from high-risk men in South Africa. The introduction of diagnostics and scale-up of surveillance are warranted to prevent the emergence of multidrug-resistant infections., (Copyright © 2020 American Society for Microbiology.)

Syphilis and HIV infection may coexist in the same individual. Ocular syphilis and/or neurosyphilis may develop at any stage of coinfection, with a stronger association between ocular and neurosyphilis in individuals living with HIV, than in HIV-uninfected individuals. The diagnosis of ocular syphilis in HIV-infected and -uninfected patients remains with some controversy due to unspecific clinical manifestations and limited diagnostic tests. Penicillin is the mainstay of treatment of ocular syphilis, but alternative options are warranted. This review describes the epidemiology, pathophysiology, and clinical manifestations, as well as the diagnostic and therapeutic challenges posed by ocular syphilis against the background of HIV coinfection.

Purpose : Overview of the evolving epidemiology of human immunodeficiency virus (HIV)-related ocular disease over time. Method : Narrative review. Results : HIV enhances susceptibility to opportunistic eye infections, has direct pathogenic effects, and places patients at risk of immune recovery inflammatory syndromes in previously infected eyes after starting highly-active antiretroviral therapy (HAART). Widespread availability of HAART has resulted in a decrease of infectious ocular conditions such as cytomegalovirus retinitis, toxoplasmic retinitis, squamous cell carcinoma of the conjunctiva, and microvascular retinopathy. However, large coexisting burdens of tuberculosis, herpesvirus infection and syphilis (among others) continue to contribute to the burden of ocular disease, especially in low-resource settings. Growing risks of cataract, retinopathy and retinal nerve fiber thinning can affect patients with chronic HIV on HAART; thought due to chronic inflammation and immune activation. Conclusion : The changing epidemic of ocular disease in HIV-infected patients warrants close monitoring and identification of interventions that can help reduce the imminent burden of disease.