Extragenital Sexually Transmitted Infections Among High-Risk Men Who Have Sex With Men in Johannesburg, South Africa.

BACKGROUND: In South Africa, extragenital etiological sexually transmitted infection (STI) screening among men who have sex with men (MSM) is not routinely available. We aimed to determine the prevalence of STI pathogens at rectal and pharyngeal sites, syphilis seroprevalence, and associated risk factors among a selection of high-risk MSM without symptomatic urethritis attending a men's health clinic in Johannesburg, South Africa. METHODS: A cross-sectional study was conducted in 2022. Enrolled clients self-reported demographic, sexual behavioral risks, and clinical information. Client or clinician-collected rectal and pharyngeal swabs were tested for Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, and Trichomonas vaginalis. C. trachomatis-positive rectal samples were reflex tested for lymphogranuloma venereum. Blood specimens were screened for syphilis. Univariate and multivariate regression models were used to determine factors independently associated with the presence of an extragenital STI or syphilis. RESULTS: Among the 97 participants (median age, 29 years), 24.7% had an extragenital STI and 9.4% had high nontreponemal antibody titers (rapid plasma reagin ≥1:16). Rectal STIs were detected in 26.4% participants: N. gonorrhoeae (14.3%), C. trachomatis (9.9%), and M. genitalium (5.5%). Pharyngeal STIs were less prevalent (4.1%). Overall, the prevalence of any STI was 41%. Sex under the influence of drugs (adjusted odds ratio, 4.94; 95% confidence interval, 1.56-15.69) and engaging in condomless receptive anal intercourse with a casual partner (adjusted odds ratio, 8.36; 95% confidence interval, 1.73-40.28) were independent risk factors for having an extragenital STI. CONCLUSIONS: The high burden of extragenital STIs and active syphilis in asymptomatic MSM underscores the importance of routine etiological screening in this key population, as the syndromic approach would not enable detection or treatment of these infections.

Medical Male Circumcision and Associations Among Sexually Transmitted Infections Service Attendees.

Medical male circumcision (MMC) is a proven intervention for preventing HIV acquisition among males. We describe the circumcision status, eligibility for MMC referral and associations with HIV positivity among symptomatic males attending sexually transmitted infections (STI) services. This study was a secondary analysis of cross-sectional data collected during sentinel surveillance for STI aetiologies. In the sentinel surveillance conducted at primary care facilities located in six South African provinces, an anonymous questionnaire was administered followed by collection of appropriate genital and blood specimens for laboratory testing including HIV, rapid plasma reagin (RPR) and HSV-2 serological testing. During analysis, multivariable logistic regression was used to determine association between prevalent HIV infection and male circumcision among males who were HSV-2 AND/OR RPR serology positive and among those who were negative. A total of 847 males were included the analysis, among whom the median age was 28 years (IQR 24-32 years) with 26.3% aged < 25 years. Of these, 166 (19.6%) were medically circumcised, 350 (41.4%) traditionally circumcised while 324 (39%) were not circumcised. The yield of assessment for MMC referral was 27.7%. Overall HIV positivity was 23.1%. Compared to no circumcision, MMC had a statistically insignificant 62% lower odds of being HIV positive -among males who were HSV-2 and RPR negative- adjusted odds ratio [aOR] 0.38 [95% confidence interval (CI) 0.12-1.18], p = 0.094. Among those HSV-2 AND/OR RPR positive, MMC had a statistically insignificant 26% lower odds of being HIV positive- aOR 0.74 (95% CI 0.41-1.36), p = 0.334. In both groups HIV positivity increased with age but was positively associated with condom use at last sexual encounter [aOR 3.41 (95% CI 1.43-8.15)] and previous treatment for an STI syndrome [aOR 3.81 (95% CI 1.60-9.05)] among those HSV-2 and RPR negative. High HIV positivity and high yield of eligibility for VMMC referral among males attending STI services points to the need for better integration of HIV prevention and treatment with STI care.

Knowledge of HIV status and antiretroviral therapy use among sexually transmitted infections service attendees and the case for improving the integration of services in South Africa: A cross sectional study.

We describe knowledge of human immunodeficiency virus (HIV) status, correct report of HIV status and antiretroviral therapy (ART) use among sexually transmitted infection (STI) service attendees in South Africa.An anonymous questionnaire was administered and serological HIV testing done. Proportions of attendees reporting knowledge of HIV status and HIV status consistent with laboratory results and ART use (among HIV positives) were determined as were factors associated with knowledge and inconsistent report of HIV status.Of 1054 attendees, 288 (27.3%) were HIV positive and 830 (78.8%) self-reported knowledge of HIV status. Not knowing one's HIV status was associated with male gender [adjusted Odds Ratio (aOR) 2.66 (95% confidence interval (CI) 1.70-4.18] medical circumcision [aOR 0.48 (95% CI 0.24-0.95)] and site [Gauteng Province (GP)-aOR 6.20 (95% CI 3.51-10.95), Eastern Cape (EC)-aOR 17.29 (95% CI 10.08- 29.66) versus Free State (FS)/Western Cape (WC) sites]. Of 219 HIV positive attendees with knowledge of HIV status, 136 (62.1%) self-reported being HIV positive, of whom 80 (58.8%) reported taking ARVs in the preceding 3 days. Inconsistent report of status was associated with males [aOR 2.26 (95%CI 1.05-4.87)], prior STI treatment [aOR 0.33 (95% CI 0.16-0.69)], recent HIV testing (6months) [aOR 3.20 (95% CI 1.62-6.36)] and site [GP-aOR 6.89 (95% 3.21-14.82), EC-aOR 5.08 (95% CI 2.15-11.64) versus FS/WC sites]. Knowledge of HIV status was lower than targeted. HIV testing and linkage to care services are essential in STI-related care and validation of self-reported indicators in this population maybe necessary.

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.

Field evaluation of Standard Diagnostics' Bioline HIV/Syphilis Duo test among female sex workers in Johannesburg, South Africa.

BACKGROUND: Point-of-care tests provide immediate results with the opportunity for same-day interventions with improved public health outcomes. A dual HIV/syphilis test enables early treatment of both diseases. METHODS: We conducted a field evaluation of the Standard Diagnostics' SD Bioline HIV/Syphilis Duo test (SD Bioline) among female sex workers. SD Bioline was conducted on finger-prick blood according to manufacturer's instructions and compared with (i) Genscreen HIV1/2 (third generation) and Vironostika Ag/Ab (fourth generation) assays for HIV, and (ii) Treponema pallidum particle agglutination (TPPA) and rapid plasma reagin (RPR) assays for syphilis. A negative TPPA test was considered negative, a TPPA-confirmed RPR titre ≤1:4 as past infection and a TPPA-confirmed RPR titre ≥1:8 as active syphilis. Sensitivity, specificity, positive and negative predictive values were calculated. RESULTS: Of 263 women recruited, 14 (5.3%) declined an HIV test. Among the remaining 249 women, 187 (75.1%) were HIV positive, 51 (20.5%) had syphilis antibodies with seven (2.8%) active infections. For HIV, the sensitivity and specificity were 98.9% (95% CI 95.8% to 99.8%) and 100% (95% CI 92.7% to 100%). For syphilis, the sensitivity and specificity were 66.7% (95% CI 52.0% to 78.9%) and 98.0% (95% CI 94.5% to 99.3%). Sera with high TPPA titres were more likely to test positive. CONCLUSIONS: In field conditions, while the SD Bioline test has high sensitivity and specificity for HIV and high specificity for syphilis, the test has lower sensitivity for syphilis than reported from laboratory evaluations. As the dual test detects only two thirds of syphilis cases, it should only be used in areas with weak screening programmes.

Trends and associations of Trichomonas vaginalis infection in men and women with genital discharge syndromes in Johannesburg, South Africa.

OBJECTIVES: To better understand the epidemiology of Trichomonas vaginalis infection, we investigated the association between T vaginalis and demographic, clinical, microbiological and behavioural characteristics of patients presenting with genital discharges to a primary healthcare clinic in Johannesburg, South Africa. METHODS: During six annual surveys (2007-2012), 1218 cases of male urethral discharge syndrome and 1232 cases of vaginal discharge syndrome were consecutively recruited. Diagnostic methods included nucleic acid amplification (Neisseria gonorrhoeae, Chlamydia trachomatis, T vaginalis and Mycoplasma genitalium), microscopy (bacterial vaginosis and Candida) and serology (Treponema pallidum, herpes simplex virus type 2 (HSV-2) and HIV). Logistic regression analyses and χ2 tests were used to identify predictors of T vaginalis infection. RESULTS: The prevalence of T vaginalis decreased from 2007 to 2012 (men from 13.4% to 4.8%; women from 33.8 to 23.1%). Overall, 74 (6.1%) men and 291 (23.6%) women were T vaginalis positive, with the highest prevalence in those aged ≥40 years (men 13.6%; women 30.9%). T vaginalis infection occurred more often in pregnant women (adjusted OR (aOR) 2.67; 95% CI 1.29 to 5.54) and in women with serological evidence of T pallidum (aOR 1.63; 95% CI 1.08 to 2.45) or HSV-2 infections (aOR 1.75; 95% CI 1.16 to 2.64). T vaginalis infection occurred less often in men with coexistent gonorrhoea (aOR 0.35; 95% CI 0.21 to 0.57) and in women with either bacterial vaginosis (aOR 0.60; 95% CI 0.44 to 0.82) or Candida morphotypes (OR 0.61; 95% CI 0.43 to 0.86). CONCLUSIONS: Although the prevalence of T vaginalis infection has decreased over time, it remains an important cause of genital discharge in South Africa, particularly in older patients and pregnant women.

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.

The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C. trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C. trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C. trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA in conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern.

Prevalence and associations of genital ulcer and urethral pathogens in men presenting with genital ulcer syndrome to primary health care clinics in South Africa.

BACKGROUND: This study aimed to determine the prevalence of genital ulcer and urethral pathogens, as well as their association with clinical features, in men with genital ulcer disease (GUD) enrolled in a clinical trial. METHODS: Clinical data were collected by questionnaire. Ulcer swabs were tested for herpes simplex viruses (HSV-1/2), Treponema pallidum, Haemophilus ducreyi, and Chlamydia trachomatis L1-L3. First-pass urine was tested for urethral pathogens, namely Neisseria gonorrhoeae, C. trachomatis, Trichomonas vaginalis, and Mycoplasma genitalium. Pathogens were detected by real-time molecular assays. Blood was tested for HIV, HSV-2, and syphilis-associated antibodies. Pathogens and clinical associations were investigated using the χ test. RESULTS: A total of 615 men with GUD were recruited. Herpes simplex virus (HSV-1, 4.2%; HSV-2, 98.2%) and bacterial pathogens were detected in 451 (73.6%) and 48 (7.8%) of genital ulcers, respectively. Human immunodeficiency virus, HSV-2, and treponemal antibodies were detected in 387 (62.9%), 434 (70.6%), and 141 (23.0%) men, respectively, whereas 54 men (8.8%) were rapid plasmin reagin (RPR) seropositive. A total of 223 urethral infections were diagnosed in 188 men (30.6%), including 69 (11.2%) M. genitalium, 64 (10.4%) T. vaginalis, 60 (9.8%) C. trachomatis, and 30 (4.9%) N. gonorrhoeae infections. Dysuria was reported by 170 men (27.6%), and 69 men (11.5%) had urethral discharge on examination. Urethral pathogens were detected in 102/409 (24.9%) men without these clinical features. CONCLUSIONS: Herpes accounted for most GUD cases and urethral pathogen coinfections were common. Erythromycin, dispensed to treat infrequent chancroid and lymphogranuloma venereum cases, provided additional treatment of some asymptomatic urethral pathogens. Additional antibiotics would be required to treat asymptomatic trichomoniasis and gonorrhea.

Urethritis/cervicitis pathogen prevalence and associated risk factors among asymptomatic HIV-infected patients in South Africa.

BACKGROUND: To determine sexually transmitted infection (STI) prevalence, and patient characteristics associated with detection of urethritis/cervicitis pathogens, among HIV-infected individuals offered voluntary STI screening at a South African HIV treatment center. METHODS: Individuals, asymptomatic for genital discharge, were screened for Neisseria gonorrhoeae (NG), Chlamydia trachomatis, Trichomonas vaginalis (TV), Mycoplasma genitalium (MG) infections (real-time polymerase chain reaction assay), for syphilis and herpes simplex type 2 (serologically), and for bacterial vaginosis and Candida (microscopy, women only). Patients' most recent CD4 and viral load results were recorded. Demographic, clinical, and behavioral data were collected by nurse-administered questionnaire. RESULTS: Compared with men (n = 551), women (n = 558) were younger (mean age, 35.0 vs. 37.9 years; P < 0.001), reported more STIs in the past year (65.5% vs. 56.5%; P = 0.002), had more urethritis/cervicitis pathogens detected (21.3% vs.16.4%, P = 0.035), and were less aware of their partner's HIV status (53.1% vs. 62.3%; P = 0.007). The overall prevalence of individual urethritis/cervicitis pathogens was TV (7.6%), MG (6.1%), NG (5.4%), and C. trachomatis (2.1%). Multivariate analysis highlighted 4 significant factors associated with the detection of specific urethritis/cervicitis pathogens, namely female gender (TV, adjusted odds ratio [aOR] 2.53, 95% confidence interval [CI]: 1.47-4.37), having a regular sexual partner in the past 3 months (NG, aOR 2.26, 95% CI: 1.01-5.08), suboptimal condom use with regular partners (TV, aOR 2.07, 95% CI: 1.25-3.42), and a history of genital warts in the past year (NG, 2.25, 95% CI: 1.26-4.03). CONCLUSIONS: Asymptomatic urethritis/cervicitis pathogens were highly prevalent in this population. Few urethritis/cervicitis pathogen-associated patient characteristics were identified, emphasizing the need for affordable STI diagnostics to screen HIV-infected patients.

Etiology and STI/HIV coinfections among patients with urethral and vaginal discharge syndromes in South Africa.

BACKGROUND: This study was undertaken to establish the etiology of the male urethral discharge (MUDS) and vaginal discharge (VDS) syndromes, to determine the prevalence of other sexually transmitted infections (STI) and human immunodeficiency virus (HIV) coinfections, and to examine associations between STIs and HIV serostatus among STI patients in South Africa. METHODS: A total of 507 MUDS and 300 VDS patients were recruited in Cape Town (CPT) and Johannesburg (JHB). A multiplex polymerase chain reaction assay detected Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, and Mycoplasma genitalium infections. Bacterial vaginosis and candidiasis were detected by microscopy. Sera were screened for syphilis, HSV-2, and HIV antibodies. RESULTS: Etiological diagnoses were made for 92% of MUDS patients and 85% of VDS patients. Gonorrhoea accounted for 85% (CPT) and 71% (JHB) of MUDS presentations. Chlamydia was the second most frequently detected MUDS pathogen (CPT, 13%; JHB, 24%). Among VDS patients, bacterial vaginosis was the most common cause (CPT, 46%; JHB, 36%) and trichomoniasis the most frequently detected STI pathogen (CPT, 19%; JHB, 34%). Few patients (4%) had serological evidence of syphilis. The HSV-2 and HIV seroprevalence were higher in Johannesburg compared to Cape Town and among women compared to men. HIV infection was statistically significantly associated with HSV-2 seropositivity at both sites and with the presence of N. gonorrhoeae and absence of C. trachomatis in Cape Town MUDS patients. CONCLUSIONS: Gonorrhoea and bacterial vaginosis were confirmed as the most frequent causes of MUDS and VDS. The high HIV seroprevalence in STI patients emphasizes the need to address HIV testing among this population.

Early detection of human immunodeficiency virus type 1-specific B-lymphocyte-derived antibodies in a high-risk population.

Diagnosis of acute human immunodeficiency virus (HIV) infection, a key driver of the HIV epidemic, remains a public health challenge. The PlasmAcute technology offers an opportunity to detect early anti-HIV antibody responses. B lymphocytes (B cells) were isolated from the blood of seronegative miners in South Africa by using the PlasmAcute method. B-cell lysates and paired sera were tested for anti-HIV-1 antibodies by two different enzyme-linked immunosorbent assays; immunoreactivity was confirmed by Western blotting. All volunteers were tested for HIV type 1 (HIV-1) viral load, p24 antigen, and CD4 count. Sera from HIV-seronegative men who had positive viral loads and were positive for p24 antigen were retested for anti-HIV antibodies after immune complex dissociation. Anti-HIV antibodies were detected in lysates from 16/259 subjects without immunoreactivity in paired sera. Four subjects, one of whom had a positive viral load initially, subsequently seroconverted. Six subjects showed transient anti-HIV-1 antibodies in the lysates and tested negative for all markers at the follow-up. Five subjects without follow-up data initially had lysate-positive/serum-negative samples, and these cases were classified as inconclusive. One subject had lysate antibodies and a detectable viral load but was seronegative at follow-up. In conclusion, lysate-derived anti-HIV-1 B-cell antibodies can be detected prior to seroconversion and earlier than or contemporary with HIV-1 RNA detection.