Mycoplasma hominis increases the risk for Ureaplasma parvum infection in Human immunodeficiency virus infected pregnant women.

INTRODUCTION: Mycoplasma hominis and Ureaplasma parvum have been recently linked to sexually transmitted diseases and other conditions. There are a limited number of studies conducted on South African pregnant women that have assessed the prevalence and risk factors for genital mycoplasmas. METHODOLOGY: This study included 264 HIV infected pregnant women attending the King Edward VIII antenatal clinic in eThekwini, South Africa. DNA was extracted using the PureLink Microbiome kit and pathogens were detected using the TaqMan Real-time PCR assays. The statistical data analysis was conducted in a freely available Statistical Computing Environment, R software, version 3.6.3 using the RStudio platform. RESULTS: The prevalence of M. hominis and U. parvum, was 215/264 (81.4%), and 203/264 (76.9%), respectively. In the M. hominis positive group, a significantly (p = 0.004) higher proportion, 80.5% tested positive for U. parvum infection when compared to 61.2% among the M. hominis negative. Of the U. parvum positive women, a significantly (p = 0.004) higher proportion of women (85.2%) tested positive for M. hominis when compared to 68.9% among the U. parvum negative. In the unadjusted and adjusted analysis, being M. hominis positive increased the risk for U. parvum by approximately 3 times more (p = 0.014) and 4-fold (p = 0.008), respectively. CONCLUSIONS: This study showed a significant link between M. hominis and U. parvum infection. To date, there are a limited number of studies that have investigated M. hominisbeing a risk factor for U. parvum infection. Therefore, the data presented in the current study now fills in this gap in the literature.

Excretory-secretory products from adult helminth Nippostrongylus brasiliensis have in vitro bactericidal activity.

Introduction. Intestinal helminths and microbiota share the same anatomical niche during infection and are likely to interact either directly or indirectly. Whether intestinal helminths employ bactericidal strategies that influence their microbial environment is not completely understood.Hypothesis. In the present study, the hypothesis that the adult hookworm Nippostrongylus brasiliensis produces molecules that impair bacterial growth in vitro, is tested.Aim. To investigate the in vitro bactericidal activity of Nippostrongylus brasiliensis against commensal and pathogenic bacteria.Methodology. The bactericidal effect of somatic extract and excretory-secretory products of adult Nippostrongylus brasiliensis on Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella pneumoniae) bacteria was assessed using growth assays. Minimum inhibitory concentration and minimum bactericidal concentration assays were performed using excretory-secretory products released from the pathogen.Results. Broad-spectrum in vitro bactericidal activity in excretory-secretory products, but not somatic extract of adult Nippostrongylus brasiliensis was detected. The bactericidal activity of excretory-secretory products was concentration-dependent, maintained after heat treatment, and preserved after repeated freezing and thawing.Conclusion. The results of this study demonstrate that helminths such as Nippostrongylus brasiliensis release molecules via their excretory-secretory pathway that have broad-spectrum bactericidal activity. The mechanisms responsible for this bactericidal activity remain to be determined and further studies aimed at isolating and identifying active bactericidal molecules are needed.

Cytokine Gene Expression Profiles during HIV and Helminth Coinfection in Underprivileged Peri-Urban South African Adults.

BACKGROUND: Intestinal helminth parasites are potent stimulators of T helper type 2 (Th2) and regulatory Th3 anti-inflammatory immune responses, while human immunodeficiency virus (HIV) infections are activators of predominantly T helper type 1(Th1) pro-inflammatory responses. Studies investigating the immune profiles of individuals coinfected with helminths and HIV are scarce. Although it is well known that helminths cause a type 2 immune response during the chronic stage of infection that is characterised by Th2 cell differentiation, eosinophil recruitment, and alternative macrophage activation, the immune mechanisms that regulate tissue damage at the time of parasite invasion are poorly understood. AIM: The aim of the study was to determine the cytokine gene expression profiles during HIV and helminth coinfection in underprivileged South African adults living in a peri-urban area with poor sanitary conditions and a lack of clean water supply. METHOD: Study participants (n = 164) were subdivided into uninfected controls, HIV-infected, helminth-infected, and HIV and helminth-coinfected groups. The Kato-Katz and Mini Parasep techniques and Ascaris lumbricoides-specific Immunoglobulin E (IgE) and Immunoglobulin G4 (IgG4) levels were used to detect helminth infections. Participants' HIV status was determined using two HIV1/2 antibody test kits. RNA was isolated from white blood cells for cytokine (Th1-, Th2-, and Th17-related) and transcription factor gene expression profiling using real-time PCR. RESULTS: Multivariate regression data were adjusted for age, gender, BMI, antiretroviral treatment (ART), and nutritional supplement intake. The HIV and helminth-coinfected group had significantly higher tumour necrosis factor alpha (TNF-α) (adjusted ß = 0.53, p = 0.036), interleukin 2 (IL-2) (adjusted ß = 6.48, p = 0.008), and interleukin 17 (IL-17) (adjusted ß = 1.16, p = 0.001) levels and lower GATA binding protein 3 (GATA3) levels (adjusted ß = -0.77, p = 0.018) compared to the uninfected controls. No statistical significance was noted for Th2-related cytokines. CONCLUSION: The coinfected group had higher proinflammatory Th1- and Th17-related cytokine gene expression profiles compared to the uninfected controls. The findings suggest that pro-inflammatory responses are elevated during coinfection, which supports the hypothesis that helminths have a deleterious effect on HIV immune responses.

Cytokine Responses during Mycobacterium tuberculosis H37Rv and Ascaris lumbricoides Costimulation Using Human THP-1 and Jurkat Cells, and a Pilot Human Tuberculosis and Helminth Coinfection Study.

BACKGROUND: Helminth infections are widespread in tuberculosis-endemic areas and are associated with an increased risk of active tuberculosis. In contrast to the pro-inflammatory Th1 responses elicited by Mycobacterium tuberculosis (Mtb) infection, helminth infections induce anti-inflammatory Th2/Treg responses. A robust Th2 response has been linked to reduced tuberculosis protection. Several studies show the effect of helminth infection on BCG vaccination and TB, but the mechanisms remain unclear. AIM: To determine the cytokine response profiles during tuberculosis and intestinal helminth coinfection. METHODS: For the in vitro study, lymphocytic Jurkat and monocytic THP-1 cell lines were stimulated with Mtb H37Rv and Ascaris lumbricoides (A. lumbricoides) excretory-secretory protein extracts for 24 and 48 h. The pilot human ex vivo study consisted of participants infected with Mtb, helminths, or coinfected with both Mtb and helminths. Thereafter, the gene transcription levels of IFN-γ, TNF-α, granzyme B, perforin, IL-2, IL-17, NFATC2, Eomesodermin, IL-4, IL-5, IL-10, TGF-ß and FoxP3 in the unstimulated/uninfected controls, singly stimulated/infected and costimulated/coinfected groups were determined using RT-qPCR. RESULTS: TB-stimulated Jurkat cells had significantly higher levels of IFN-γ, TNF-α, granzyme B, and perforin compared to unstimulated controls, LPS- and A. lumbricoides-stimulated cells, and A. lumbricoides plus TB-costimulated cells (p < 0.0001). IL-2, IL-17, Eomes, and NFATC2 levels were also higher in TB-stimulated Jurkat cells (p < 0.0001). Jurkat and THP-1 cells singly stimulated with TB had lower IL-5 and IL-4 levels compared to those singly stimulated with A. lumbricoides and those costimulated with TB plus A. lumbricoides (p < 0.0001). A. lumbricoides-singly stimulated cells had higher IL-4 levels compared to TB plus A. lumbricoides-costimulated Jurkat and THP-1 cells (p < 0.0001). TGF-ß levels were also lower in TB-singly stimulated cells compared to TB plus A. lumbricoides-costimulated cells (p < 0.0001). IL-10 levels were lower in TB-stimulated Jurkat and THP-1 cells compared to TB plus A. lumbricoides-costimulated cells (p < 0.0001). Similar results were noted for the human ex vivo study, albeit with a smaller sample size. CONCLUSIONS: Data suggest that helminths induce a predominant Th2/Treg response which may downregulate critical Th1 responses that are crucial for tuberculosis protection.

Consequences of rpoB mutations missed by the GenoType MTBDRplus assay in a programmatic setting in South Africa.

Background: Rifampicin resistance missed by commercial rapid molecular assays but detected by phenotypic assays may lead to discordant susceptibility results and affect patient management. Objective: This study was conducted to evaluate the causes of rifampicin resistance missed by the GenoType MTBDRplus and its impact on the programmatic management of tuberculosis in KwaZulu-Natal, South Africa. Methods: We analysed routine tuberculosis programme data from January 2014 to December 2014 on isolates showing rifampicin susceptibility on the GenoType MTBDRplus assay but resistance on the phenotypic agar proportion method. Whole-genome sequencing was performed on a subset of these isolates. Results: Out of 505 patients with isoniazid mono-resistant tuberculosis on the MTBDRplus, 145 (28.7%) isolates showed both isoniazid and rifampicin resistance on the phenotypic assay. The mean time from MTBDRplus results to initiation of drug-resistant tuberculosis therapy was 93.7 days. 65.7% of the patients had received previous tuberculosis treatment. The most common mutations detected in the 36 sequenced isolates were I491F (16; 44.4%) and L452P (12; 33.3%). Among the 36 isolates, resistance to other anti-tuberculosis drugs was 69.4% for pyrazinamide, 83.3% for ethambutol, 69.4% for streptomycin, and 50% for ethionamide. Conclusion: Missed rifampicin resistance was mostly due to the I491F mutation located outside the MTBDRplus detection area and the L452P mutation, which was not included in the initial version 2 of the MTBDRplus. This led to substantial delays in the initiation of appropriate therapy. The previous tuberculosis treatment history and the high level of resistance to other anti-tuberculosis drugs suggest an accumulation of resistance.

Demographic profile of HIV and helminth-coinfected adults in KwaZulu-Natal, South Africa.

Background: Helminth and HIV infections are endemic among poor populations. Studies investigating the socio-demographic and economic risk factors associated with dual HIV and helminth coinfection are scarce. Objectives: This study aimed to describe risk factors associated with HIV and helminth coinfections among peri-urban South African adults residing in poorly developed areas with high poverty levels, lack of sanitation and a clean water supply. Method: Adult participants (n = 414) were recruited from clinics in the south of Durban, KwaZulu-Natal, South Africa. Participants' demographic, socio-economic, sanitation and household information, anthropometric measurements and HIV status were collected. Stool samples were donated for coproscopy to detect helminths using the Kato-Katz and Mini Parasep techniques. Blood was collected to confirm participants' HIV status and to determine Ascaris lumbricoides-specific immunoglobulin E (IgE) and immunoglobulin G4 (IgG4) levels to improve microscopy sensitivity. Results: Overall coinfection was 15%, and single helminth and HIV prevalence were 33% and 52%, respectively. Ascaris lumbricoides was predominant (18%). Univariate analysis of variance (ANOVA) showed that coinfection was 11.9% and 19.8%, respectively, among the 18-34 years and 35-59 years age groups (p = 0.0006), 16.4% and 19.9%, respectively, for the no income and < R1000.00 groups (p = 0.0358) and 22.8% and 17.1%, respectively, for the pit or public toilets and toilets not connected to sewage groups (p = 0.0007). Conclusion: Findings suggest that the dual infection with HIV and helminth infections among adults residing in under-resourced areas with poor sanitary conditions is frequent. Older age, poor toilet use and low income are associated with coinfection. More attention is required to break the cycle of coinfections and possible disease interactions. Contribution: The study highlights the importance of determining and treating helminth infections among adult population during HIV and helminth coinfection and the influence of poor sanitation and socioeconomic status on disease transmission.

Aetiology of genital ulcer disease and associated factors among Mthatha public clinic attendees.

Background: Genital ulcer disease (GUD) is a sexually transmitted disease characterised by ulcerating lesions. Despite the introduction of sexually transmitted infections (STIs) syndromic management approach into primary healthcare in South Africa (SA) in 1995, the prevalence of STIs in South Africa remains high. Objectives: The study investigated the aetiology of GUD and factors influencing it among public community health centre (CHC) attendees in the Eastern Cape, South Africa. Method: A total of 105 participants were recruited among individuals presenting with GUD from three CHCs located in the Eastern Cape Province, South Africa. Blood and genital ulcer samples were collected from consented participants. Blood samples with suitable sera were tested for human immunodeficiency virus (HIV) and syphilis. Herpes simplex virus types 1/2 (HSV-1/2), Chlamydia trachomatis, Treponema pallidum, Haemophilus ducreyi and Klebsiella granulomatis were detected in nucleic acid extracted from genital ulcer specimens. Results: Out of the 98 samples with suitable sera, 55.1% and 8.2% were HIV and syphilis seropositive, respectively. Ulcerating STI pathogens were detected in 31.4% of the study participants. Herpes simplex virus type 2 was the most detected pathogen (16.2%) followed by Chlamydia trachomatis (10.5%), HSV-1 (8.6%), Haemophilus ducreyi (8.6%) and Treponema pallidum (6.7%). Multiple pathogens were detected in 13.3% of participants. Detected multiple ulcerating pathogens were common among HIV-positives (p = 0.016). Conclusion: Molecular methods for diagnosing pathogens have the potential to improve the management of GUD. Data generated from this study would contribute to the limited data on GUD in the Eastern Cape Province. Further research with a larger sample size is recommended. Contribution: Data generated would contribute to the limited data on GUD in the Eastern Cape province, South Africa.

Anaemia and Nutritional Status during HIV and Helminth Coinfection among Adults in South Africa.

Sub-Saharan Africa is burdened with helminthiasis and HIV/AIDS, and there is a significant overlap between these infections. However, little is known about the extent of anaemia and malnutrition in HIV/AIDS and helminth coinfected adults. The study investigated the anaemia profiles and nutritional status of HIV and helminth coinfected adult South Africans. Stool samples were collected from participants (N = 414) for parasite detection using the Kato−Katz and Mini Parasep® SF techniques. Blood was collected to determine participants' HIV status, micro- and macronutrients, haematological parameters, and Ascaris lumbricoides-specific IgE and IgG4 levels. Thereafter, participants were stratified into single infection (HIV or helminths), coinfection, and uninfected controls (no HIV and helminth) groups. The majority (74.9%) of participants had CD4 counts of >500 cells/µL, indicating no significant immunosupression. The coinfected group had an overall anaemia prevalence of 16.9%, which was lower than that of the HIV-infected group (44.6%) and higher than helminth infected group (15.4%). Overall helminth prevalence was 33%, with Ascaris lumbricoides being the most prevalent. The coinfected group also had lower vitamin A (p = 0.0107), calcium (p = 0.0002), and albumin (p < 0.0001) levels compared to HIV/helminth uninfected controls. Unexpectedly, the coinfected group had the highest serum iron levels, followed by the helminth-infected and control groups, both of which had similar iron levels, and finally, the HIV-infected group, which had the lowest iron levels (p = 0.04). Coinfected adults may be prone to micronutrient deficiency and anaemia. Further research and intervention programmes are required in this neglected field.

Immunological Interactions between Intestinal Helminth Infections and Tuberculosis.

Helminth infections are among the neglected tropical diseases affecting billions of people globally, predominantly in developing countries. Helminths' effects are augmented by coincident tuberculosis disease, which infects a third of the world's population. The role of helminth infections on the pathogenesis and pathology of active tuberculosis (T.B.) remains controversial. Parasite-induced suppression of the efficacy of Bacille Calmette-Guerin (BCG) has been widely reported in helminth-endemic areas worldwide. T.B. immune response is predominantly proinflammatory T-helper type 1 (Th1)-dependent. On the other hand, helminth infections induce an opposing anti-inflammatory Th2 and Th3 immune-regulatory response. This review summarizes the literature focusing on host immune response profiles during single-helminth, T.B. and dual infections. It also aims to necessitate investigations into the complexity of immunity in helminth/T.B. coinfected patients since the research data are limited and contradictory. Helminths overlap geographically with T.B., particularly in Sub-Saharan Africa. Each disease elicits a response which may skew the immune responses. However, these effects are helminth species-dependent, where some parasites have no impact on the immune responses to concurrent T.B. The implications for the complex immunological interactions that occur during coinfection are highlighted to inform government treatment policies and encourage the development of high-efficacy T.B. vaccines in areas where helminths are prevalent.

Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis.

Introduction: Treatment of gonorrhoea infection is limited by the increasing prevalence of multidrug-resistant strains. Cost-effective molecular diagnostic tests can guide effective antimicrobial stewardship. The aim of this study was to correlate mRNA expression levels in Neisseria gonorrhoeae antibiotic target genes and efflux pump genes to antibiotic resistance in our population. Methods: This study investigated the expression profile of antibiotic resistance-associated genes (penA, ponA, pilQ, mtrR, mtrA, mtrF, gyrA, parC, parE, rpsJ, 16S rRNA, and 23S rRNA) and efflux pump genes (macAB, norM, and mtrCDE), by quantitative real-time PCR, in clinical isolates from KwaZulu-Natal, South Africa. Whole-genome sequencing was used to determine the presence or absence of mutations. Results: N. gonorrhoeae isolates, from female and male patients presenting for care at clinics in KwaZulu-Natal, South Africa, were analysed. As determined by binomial regression and ROC analysis, the most significant (p ≤ 0.05) markers for resistance prediction in this population, and their cutoff values, were determined to be mtrC (p = 0.024; cutoff <0.089), gyrA (p = 0.027; cutoff <0.0518), parE (p = 0.036; cutoff <0.0033), rpsJ (p = 0.047; cutoff <0.0012), and 23S rRNA (p = 0.042; cutoff >7.754). Conclusion: Antimicrobial stewardship includes exploring options to conserve currently available drugs for gonorrhoea treatment. There is the potential to predict an isolate as either susceptible or nonsusceptible based on the mRNA expression level of specific candidate markers, to inform patient management. This real-time qPCR approach, with few targets, can be further investigated for use as a potentially cost-effective diagnostic tool to detect resistance.

Pyrazinamide resistance in rifampicin discordant tuberculosis.

INTRODUCTION: Mycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported. MATERIALS AND METHODS: We evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid. RESULTS: Pyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates. CONCLUSION: Given the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.

Detection of metronidazole resistance in Trichomonas vaginalis using uncultured vaginal swabs.

Trichomonas vaginalis (T. vaginalis) is the most prevalent sexually transmitted infection (STI) globally. Metronidazole is the drug of choice for treating T. vaginalis infections although metronidazole-resistant T. vaginalis has been reported in clinical isolates. The purpose of this study was to determine the presence of mutations in nitroreductase genes associated with metronidazole resistance in vaginal swabs testing positive for T. vaginalis. This study included 385 human immunodeficiency virus (HIV)-positive pregnant women. Vaginal swabs were collected from consenting pregnant women and used for the detection of T. vaginalis using the TaqMan assay. From the vaginal swabs, nitroreductase genes ntr4 and ntr6 containing mutations associated with metronidazole resistance were amplified using a quantitative polymerase chain reaction (PCR) assay. To validate the PCR assay, T. vaginalis cultured isolates with known metronidazole resistance profiles were used as controls in the mutation detection assays. The prevalence of T. vaginalis in the study population was 12.2% (47/385). Mutations associated with resistance to metronidazole were detected in more than 40% of the samples tested, i.e. 21/47 (45%) and 24/47 (51%) for ntr4 and ntr6, respectively. A total of 19 samples (40%) carried mutations for both ntr4 and ntr6 genes associated with metronidazole resistance. The validation assays showed a positive correlation between phenotypic and genotypic resistance profiles. This study found a high prevalence of mutations associated with metronidazole resistance. This is concerning since metronidazole is currently used in the syndromic management of STIs in South Africa. Molecular-based assays for monitoring metronidazole resistance profiles using nitroreductase genes may serve as a feasible method for antimicrobial surveillance studies for T. vaginalis.

High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens.

BACKGROUND: Antimicrobial resistance is limiting treatment options for Neisseria gonorrhoeae infections. To aid or replace culture and the syndromic management approach, molecular assays are required for antimicrobial susceptibility testing to guide appropriate and rapid treatment. OBJECTIVE: We aimed to detect single-nucleotide polymorphisms and plasmids associated with antimicrobial resistance from N. gonorrhoeae isolates from a clinic population in South Africa, using real-time PCR as a rapid test for AMR detection. METHODS: N. gonorrhoeae isolates, from female and male patients presenting for care at a sexually transmitted infections clinic in Durban, South Africa, were analysed using phenotypic and genotypic methods for identification and antibiotic susceptibility testing (AST). Real-time PCR and high-resolution melting analysis were used to detect porA pseudogene (species-specific marker) and resistance-associated targets. Whole-genome sequencing was used as the gold standard for the presence of point mutations. RESULTS: The real-time porA pseudogene assay identified all N. gonorrhoeae-positive isolates and specimens. Concordance between molecular detection (real-time PCR and HRM) and resistance phenotype was ≥92% for bla TEM (HLR penicillin), rpsJ_V57M (tetracycline), tetM (tetracycline), and gyrA_S91F (ciprofloxacin). Resistance determinants 16SrRNA_C1192U (spectinomycin), mtrR_G45D (azithromycin), and penA_D545S, penA_mosaic (cefixime/ceftriaxone) correlated with the WHO control isolates. CONCLUSIONS: Eight resistance-associated targets correlated with phenotypic culture results. The porA pseudogene reliably detected N. gonorrhoeae. Larger cohorts are required to validate the utility of these targets as a convenient culture-free diagnostic tool, to guide STI management in a South African population.

The challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in low-middle income countries and possible cost-effective measures in resource-limited settings.

Diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains a challenge around the world, especially in low-middle-income countries (LMICs) with poor socio-economic backgrounds. From the beginning of the pandemic in December 2019 to August 2021, a total of approximately 3.4 billion tests were performed globally. The majority of these tests were restricted to high income countries. Reagents for diagnostic testing became a premium, LMICs either cannot afford or find manufacturers unwilling to supply them with expensive analytical reagents and equipment. From March to December 2020 obtaining testing kits for SARS-CoV-2 testing was a challenge. As the number of SARS-CoV-2 infection cases increases globally, large-scale testing still remains a challenge in LMICs. The aim of this review paper is to compare the total number and frequencies of SARS-CoV-2 testing in LMICs and high-income countries (HICs) using publicly available data from Worldometer COVID-19, as well as discussing possible interventions and cost-effective measures to increase testing capability in LMICs. In summary, HICs conducted more SARS-CoV-2 testing (USA: 192%, Australia: 146%, Switzerland: 124% and Canada: 113%) compared to middle-income countries (MICs) (Vietnam: 43%, South Africa: 29%, Brazil: 27% and Venezuela: 12%) and low-income countries (LICs) (Bangladesh: 6%, Uganda: 4% and Nigeria: 1%). Some of the cost-effective solutions to counteract the aforementioned problems includes using saliva instead of oropharyngeal or nasopharyngeal swabs, sample pooling, and testing high-priority groups to increase the number of mass testing in LMICs.

Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study.

We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the blaOXA-181, blaOXA-48, blaOXA-484, blaNDM-1, and blaGES-5 genes. Multiple species/clones carried blaOXA-48 and blaNDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most ß-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.

'Mycoplasma hominis does not share common risk factors with other genital pathogens': Findings from a South African pregnant cohort.

BACKGROUND: The role of Mycoplasma hominis (M. hominis) as a genital tract pathogen was still debatable. This study identified the risk factors associated with the prevalence of M. hominis in South African pregnant women. METHODS: This was a cross-sectional analysis of n = 221 prenatal patients attending a Durban hospital during November 2017 to April 2018. M. hominis was detected from urine samples using the quantitative polymerase chain reaction. The population characteristics were described using frequencies stratified by the infection status of M. hominis. In addition, a univariate analysis was used to assess the relationship between each risk factor and infection status. The analysis further considered logistic regression to assess the influence of these risk factors univariately and in the presence of other factors. The coinfection rate between M. hominis and bacterial vaginosis (BV), Trichomonas vaginalis (T. vaginalis), Mycoplasma genitalium (M. genitalium) and Candida species was also determined. All the tests were conducted at 5% level of significance. RESULTS: The prevalence of M. hominis in this study population was 48% (106/221). In the univariate analysis, factors significantly associated with M. hominis positivity included having past abnormal vaginal discharge (p = 0.037), having current abnormal vaginal discharge (p = 0.010) and a borderline significance (p = 0.052), which were noted for previous pre-term delivery. However, none of these factors were sustained in the multivariate analysis. There was a statistically significant association between M. hominis and BV positivity (p < 0.001). Similarly, M. hominis and M. genitalium positivity was significant (p = 0.006). CONCLUSION: This study showed that M. hominis does not share common risk factors with known genital tract pathogens in a population of pregnant women and therefore cannot be considered a genital tract pathogen.

Lack of resistance to macrolides in Mycoplasma genitalium detected in South African pregnant women.

BACKGROUND: Azithromycin regimens have been considered first-line treatment for Mycoplasma genitalium (M. genitalium), a sexually transmitted infection (STI) associated with adverse pregnancy outcomes. However, recent years have seen rapid emergence of macrolide resistance in M. genitalium as a result of widespread administration of azithromycin. Currently, there are limited data on macrolide resistance in pregnant women from KwaZulu-Natal (KZN), South Africa. This study investigated the prevalence of M. genitalium and emerging patterns of macrolide resistance in pregnant women from KZN. METHODS: This was a sub-study of a larger study which involved laboratory-based detection of STIs in pregnant women. In the main study, pregnant women provided urine samples for detection of STIs. For this study, deoxyribose nucleic acid (DNA) extracted from stored urine was used to determine emerging macrolide resistance by amplification of the 23S ribosomal ribonucleic acid (rRNA) gene of M. genitalium by polymerase chain reaction (PCR) and sequencing of amplicons to identify mutations associated with resistance. The Allplex™ MG & AziR assay was used as a confirmatory assay. RESULTS: The prevalence of M. genitalium in pregnant women was 5.9% (13 out of 221). Sequencing of PCR amplicons did not reveal the presence of the A2059G and A2058G mutations associated with macrolide resistance. These findings were confirmed by the Allplex™ MG & AziR assay. CONCLUSION: Despite the lack of resistance to macrolides in this study population, continued antimicrobial resistance surveillance for M. genitalium in pregnant women is important because azithromycin is now part of the South African national STI syndromic management guidelines for vaginal discharge syndrome.

Antimicrobial Resistance Mechanisms, Multilocus Sequence Typing, and NG-STAR Sequence Types of Diverse Neisseria gonorrhoeae Isolates in KwaZulu-Natal, South Africa.

Antimicrobial resistance (AMR) is a major challenge to managing infectious diseases. Africa has the highest incidence of gonorrhoea, but there is a lack of comprehensive data from sparse surveillance programs. This study investigated the molecular epidemiology and AMR profiles of Neisseria gonorrhoeae isolates in KwaZulu-Natal province (KZN), South Africa. Repository isolates from patients attending public health care clinics for sexually transmitted infection (STI) care were used for phenotypic and genotypic analysis. An Etest was performed to determine antimicrobial susceptibility. Whole-genome sequencing (WGS) was used to determine epidemiology and to predict susceptibility by detecting resistance-associated genes and mutations. Among the 61 isolates, multiple sequence types were identified. Six isolates were novel, as determined by multilocus sequence typing. N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) determined 48 sequence types, of which 35 isolates had novel antimicrobial profiles. Two novel penA alleles and eight novel mtrR alleles were identified. Point mutations were detected in gyrA, parC, mtrR, penA, ponA, and porB1. This study revealed a high prevalence of AMR (penicillin 67%, tetracycline 89%, and ciprofloxacin 52%). However, spectinomycin, cefixime, ceftriaxone, and azithromycin remained 100% effective. This study is one of the first to comprehensively describe the epidemiology and AMR of N. gonorrhoeae in KZN, South Africa and Africa, using WGS. KZN has a wide strain diversity and most of these sequence types have been detected in multiple countries; however, more than half of our isolates have novel antimicrobial profiles. Continued surveillance is crucial to monitor the emergence of resistance to cefixime, ceftriaxone, and azithromycin.

Recent Semen Exposure Impacts the Cytokine Response and Bacterial Vaginosis in Women.

Background: The presence of semen in the vagina from unprotected sex may influence the immune and microbial environment of the female genital tract. Inflammatory cytokine concentrations and BV-associated bacteria in female genital secretions may influence HIV risk, although the effect of recent sexual intercourse on incident BV and the cytokine milieu of cervicovaginal secretions has rarely been measured in previous studies. Here, we investigated the extent to which partner semen impacts the cytokine response and incident BV. Methods: At baseline, we assessed the recency of semen exposure in menstrual cup supernatants by quantifying prostate specific antigen (PSA) levels using ELISA in 248 HIV-uninfected women at high risk for HIV infection. Luminex was used to measure 48 cytokines in menstrual cup supernatants and vaginal swabs to diagnose BV by Nugent score. Point-of-care screening for Chlamydia trachomatis and Neisseria gonorrhoeae was conducted using GeneXpert while OSOM was used for Trichomonas vaginalis detection. Multivariable models, adjusted for age, sexually transmitted infections, BV, current contraception use and condom use, were used to assess the impact of semen exposure on biomarkers of inflammation and BV. Results: Presence of PSA, indicating recent semen exposure within 48 hours prior to sampling, was observed in menstrual cup supernatants of 17% (43/248) of women. Of these women, 70% (30/43) had self-reported condom use at their last sex act and 84% (36/43) had BV (Nugent score >7). PSA presence was significantly associated with prevalent BV (Relative Risk (RR), 2.609; 95% Confidence Interval (CI), 1.104 - 6.165; p = 0.029). Furthermore, women with detectable PSA had high median concentrations of macrophage inflammatory protein- beta (MIP-1α, p=0.047) and low median concentration of the stem cell growth factor beta (SCGF-ß, p=0.038) compared to those without PSA. Conclusion: A degree of discordance between self-reports of consistent condom use and PSA positivity was observed. There was also evidence of a relationship between recent semen exposure, BV prevalence and altered cytokine concentrations. These findings suggest that PSA, as a semen biomarker, should be taken into consideration when investigating biological markers in the female genital tract and self-reported condom use in studies on reproductive and sexual health.

Transient association between semen exposure and biomarkers of genital inflammation in South African women at risk of HIV infection.

INTRODUCTION: Semen induces mucosal changes in the female reproductive tract to improve pregnancy outcomes. Since semen-induced alterations are likely short-lived and genital inflammation is linked to HIV acquisition in women, we investigated the contribution of recent semen exposure on biomarkers of genital inflammation in women at high HIV risk and the persistence of these associations. METHODS: We assessed stored genital specimens from 152 HIV-negative KwaZulu-Natal women who participated in the CAPRISA 008 trial between November 2012 and October 2014. During the two-year study period, 651 vaginal specimens were collected biannually (mean five samples per woman). Cervicovaginal lavage (CVL) was screened for prostate-specific antigen (PSA) by ELISA, whereas Y-chromosome DNA (YcDNA) detection and quantification were conducted by RT-PCR, representing semen exposure within 48 hours (PSA+YcDNA+) and semen exposure within three to fifteen days (PSA-YcDNA+). Soluble protein concentrations were measured in CVLs by multiplexed ELISA. T-cell frequencies were assessed in cytobrushes by flow-cytometry, and vulvovaginal swabs were used to detect common vaginal microbes by PCR. Linear mixed models adjusting for factors associated with genital inflammation and HIV risk were used to assess the impact of semen exposure on biomarkers of inflammation over multiple visits. RESULTS: Here, 19% (125/651) of CVLs were PSA+YcDNA+, 14% (93/651) were PSA-YcDNA+ and 67% (433/651) were PSA-YcDNA-. Semen exposure was associated with how often women saw their partners, the frequency of vaginal sex in the past month, HSV-2 antibody detection, current gonorrhoea infection and Nugent Score. Both PSA detection (PSA+YcDNA+) and higher cervicovaginal YcDNA concentrations predicted increases in several cytokines, barrier-related proteins (MMP-2, TIMP-1 and TIMP-4) and activated CD4+CCR5+HLA-DR+ T cells (ß = 0.050; CI 0.001 to 0.098; p = 0.046) and CD4+HLA-DR+ T cells (ß = 0.177; CI 0.016 to 0.339; p = 0.032) respectively. PSA detection was specifically associated with raised pro-inflammatory cytokines (including IL-6, TNF-α, IP-10 and RANTES), and with the detection of BVAB2 (OR = 1.755; CI 1.116 to 2.760; p = 0.015), P. bivia (OR = 1.886; CI 1.102 to 3.228; p = 0.021) and Gardnerella vaginalis (OR = 1.815; CI 1.093 to 3.015; p = 0.021). CONCLUSIONS: More recent semen exposure was associated with raised levels of inflammatory biomarkers and the detection of BV-associated microbes, which declined by three to fifteen days of post-exposure. Although transient, semen-induced alterations may have implications for HIV susceptibility in women.