Comparison of an in-house real-time duplex PCR assay with commercial HOLOGIC® APTIMA assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in urine and extra-genital specimens

Abstract Background Extra-genital Neisseria gonorrhoeae and Chlamydia trachomatis infections are mostly asymptomatic, and important reservoir sites of infection as they often go undetected and may be more difficult to eradicate with recommended therapeutic regimens. Commercial nucleic acid amplification tests (NAATs) have not received regulatory approval for the detection of N. gonorrhoeae and C. trachomatis in extra-genital specimens. The HOLOGIC® APTIMA Combo2 assay for N. gonorrhoeae and C. trachomatis has performed well in evaluations using extra-genital specimens. Methods We assessed the performance of an in-house real-time duplex PCR assay for the detection of N. gonorrhoeae and C. trachomatis in urine and extra-genital specimens using the HOLOGIC® APTIMA assays as gold standard comparators. Urine, oropharyngeal and ano-rectal specimens were collected from each of 200 men-who-have-sex-with-men (MSM) between December 2011 and July 2012. Results For N. gonorrhoeae detection, the in-house PCR assay showed 98.5–100% correlation agreement with the APTIMA assays, depending on specimen type. Sensitivity for N. gonorrhoeae detection was 82.4% for ano-rectal specimens, 83.3% for oropharyngeal specimens, and 85.7% for urine; and specificity was 100% with all specimen types. The positive predictive value (PPV) for N. gonorrhoeae detection was 100% and the negative predictive value (NPV) varied with sample type, ranging from 98.5–99.5%. For C. trachomatis detection, correlation between the assays was 100% for all specimen types. The sensitivity, specificity, PPV and NPV of the in-house PCR assay was 100% for C. trachomatis detection, irrespective of specimen type. Conclusion The in-house duplex real-time PCR assay showed acceptable performance characteristics in comparison with the APTIMA® assays for the detection of extra-genital N. gonorrhoeae and C. trachomatis

Prevalence and Antimicrobial Resistance of Mycoplasma genitalium Infection Among Women Living With Human Immunodeficiency Virus in South Africa: A Prospective Cohort Study.

This prospective cohort study of 622 women living with human immunodeficiency virus (HIV) from Johannesburg (2012) detected Mycoplasma genitalium in 7.4% (95% confidence interval [CI]: 5.5-9.7, 46/622), with detection more likely with lower CD4 counts(adjusted odds ratio [AOR] 1.02 per 10 cells/μL decrease, 95% CI: 1.00-1.03) and higher plasma HIV-1 RNA (AOR 1.15 per log copies/mL increase, 95% CI: 1.03-1.27). No mutations for macrolide/quinolone resistance was detected

Southern African HIV Clinicians Society 2022 guideline for the management of sexually transmitted infections : moving towards best practice

Sexually transmitted infections (STIs) are among the most common acute conditions worldwide with sub-Saharan Africa ranking among the regions with the highest burdens globally. Adolescent girls and young women (AGYW), people living with HIV (PLHIV), pregnant women, and key and vulnerable populations are disproportionally affected by STIs. The social determinants of health, gender inequality, and STI-associated stigma and discrimination (at both the community and facility level) are important contributors to the sustained high burden of infection.http://www.sajhivmed.org.za/index.php/hivmeddm2022Medical Microbiolog

Clinical Characteristics of Mycoplasma genitalium and the Usefulness of Syndromic Management Among Women Living With Human Immunodeficiency Virus.

We report the clinical symptoms and examination findings of Mycoplasma genitalium (MG) in women living with human immunodeficiency virus in South Africa. If we relied on syndromic management alone to treat MG, only 15 of 46 MG-infected women would have received. appropriate treatment: sensitivity of 32.6% (95% confidence interval, 19.5-48.0) and specificity of 67.4% (95% confidence interval, 63.4-71.2)

Prevalence and trends of staphylococcus aureus bacteraemia in hospitalized patients in South Africa, 2010 to 2012: laboratory-based surveillance mapping of antimicrobial resistance and molecular epidemiology.

CAPRISA, 2015.Abstract available in pdf

National sentinel site surveillance for antimicrobial resistance in Klebsiella pneumoniae isolates in South Africa, 2010-2012

Please cite as follows: Perovic, O. et al. 2014. National sentinel site surveillance for antimicrobial resistance in Klebsiella pneumoniae isolates in South Africa, 2010-2012. South African Medical Journal, 104(8):563-568, doi:10.7196/SAMJ.7617.The original publication is available at http://www.samj.org.zaBackground. The increasing rates of antimicrobial resistance observed in the nosocomial pathogen Klebsiella pneumoniae are of major public health concern worldwide. Objectives. To describe the antibiotic susceptibility profiles of K. pneumoniae isolates from bacteraemic patients submitted by sentinel laboratories in five regions of South Africa from mid-2010 to mid-2012. Molecular methods were used to detect the most commonly found extended-spectrum beta-lactamase (ESBL) and carbapenemase resistance genes. Methods. Thirteen academic centres serving the public healthcare sector in Gauteng, KwaZulu-Natal, Free State, Limpopo and Western Cape provinces submitted K. pneumoniae isolates from patients with bloodstream infections. Vitek 2 and MicroScan instruments were used for organism identification and susceptibility testing. Multiplex polymerase chain reactions (PCRs) were used to detect blaCTX-M, blaSHV and blaTEM genes in a proportion of the ESBL isolates. All isolates exhibiting reduced susceptibility to carbapenems were PCR tested for blaKPC and blaNDM-1 resistance genes. Results. Overall, 68.3% of the 2 774 isolates were ESBL-positive, showing resistance to cefotaxime, ceftazidime and cefepime. Furthermore, 46.5% of all isolates were resistant to ciprofloxacin and 33.1% to piperacillin-tazobactam. The major ESBL genes were abundantly present in the sample analysed. Most isolates (95.5%) were susceptible to the carbapenems tested, and no isolates were positive for blaKPC or blaNDM-1. There was a trend towards a decrease in susceptibility to most antibiotics. Conclusion. The high proportion of ESBL-producing K. pneumoniae isolates observed, and the prevalence of ESBL genes, are of great concern. Our findings represent a baseline for further surveillance in SA, and can be used for policy and treatment decisions.http://www.samj.org.za/index.php/samj/article/view/7617Publisher's versio

National sentinel site surveillance for antimicrobial resistance in Klebsiella pneumoniae isolates in South Africa, 2010 - 2012

Background. The increasing rates of antimicrobial resistance observed in the nosocomial pathogen Klebsiella pneumoniae are of major public health concern worldwide.Objectives. To describe the antibiotic susceptibility profiles of K. pneumoniae isolates from bacteraemic patients submitted by sentinel laboratories in five regions of South Africa from mid-2010 to mid-2012. Molecular methods were used to detect the most commonly found extended-spectrum beta-lactamase (ESBL) and carbapenemase resistance genes.Methods. Thirteen academic centres serving the public healthcare sector in Gauteng, KwaZulu-Natal, Free State, Limpopo and Western Cape provinces submitted K. pneumoniae isolates from patients with bloodstream infections. Vitek 2 and MicroScan instruments were used for organism identification and susceptibility testing. Multiplex polymerase chain reactions (PCRs) were used to detect blaCTX-M, blaSHV and blaTEM genes in a proportion of the ESBL isolates. All isolates exhibiting reduced susceptibility to carbapenems were PCR tested for blaKPC and blaNDM-1 resistance genes.Results. Overall, 68.3% of the 2 774 isolates were ESBL-positive, showing resistance to cefotaxime, ceftazidime and cefepime. Furthermore, 46.5% of all isolates were resistant to ciprofloxacin and 33.1% to piperacillin-tazobactam. The major ESBL genes were abundantly present in the sample analysed. Most isolates (95.5%) were susceptible to the carbapenems tested, and no isolates were positive for blaKPC or blaNDM-1. There was a trend towards a decrease in susceptibility to most antibiotics.Conclusion. The high proportion of ESBL-producing K. pneumoniae isolates observed, and the prevalence of ESBL genes, are of great concern. Our findings represent a baseline for further surveillance in SA, and can be used for policy and treatment decisions

Standardised protocol for a prospective cross-sectional multicentre clinic-based evaluation of two dual point-of-care tests for the screening of HIV and syphilis in men who have sex with men, sex workers and pregnant women

Introduction Dual point-of-care tests (POCTs) for detecting antibodies to HIV and syphilis have been developed for use with venous whole blood, serum/plasma or finger-prick capillary whole blood. Several tests are commercially available showing encouraging performance compared with ‘gold-standard’ reference tests in laboratory-based studies. However, data on their performance in the field are limited. This prospective cross-sectional study will conduct a clinic-based evaluation to assess the performance characteristics and acceptability to end-users of two dual HIV/syphilis POCTs for the screening of HIV and syphilis among men who have sex with men (MSM), sex workers (SWs) and pregnant women (PW). This master protocol outlines the overall research approach that will be used in seven countries. Method and analysis MSM, SWs and PW presenting at clinic evaluation sites in high, low and middle-income countries will be enrolled. The (WHO preapproved) POCTs to be evaluated are SD Bioline HIV/Syphilis Duo (Abbott) and Dual Path Platform HIV-Syphilis Assay (Chembio). Finger-prick blood will be collected to perform POCTs and compared with laboratory results (venepuncture blood). Procedures will be carried out by trained healthcare staff and tests performed according to the manufacturers’ directions. Sample size was calculated based on local prevalence of HIV and syphilis. The sensitivity, specificity, positive and negative predictive values for each POCT will be calculated. The study is ongoing with recruitment expected to be completed in all countries by mid to late 2021. Ethics and dissemination This core protocol was independently peer reviewed and approved by the Research Project Review Panel (RP2) of the WHO Department of Sexual and Reproductive Health and Research and by the WHO Ethics Review Committee (ERC). The protocol has been adapted to individual countries and approved by RP2, ERC and institutional review boards at each site. Results will be disseminated through peer-reviewed journals and relevant conferences

Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.

Funder: Queensland GovernmentSyphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides

Invasive disease caused by Streptococcus pneumoniane resistant to penicillin and third-generation cephalosporins

Resistance to penicillin G and third-generation cephalosporins among Streptococcus pneum oniae is an emerging and increasing microbial threat. Over a AVi year study period, w e identified 4 0 patients with either intermediate (26/40, 65%) or high-level (14/40, 35%) resistance to third-generation cephalosporins (i.e., ceftriaxone and cefotaxime). Fifteen subjects were adults (mean age 47 years) and 25 were children (mean age 26.5 months). Study isolates were recovered from the follow ing body sites: blood (25 isolates); CSF (5); sputum (5); tracheal aspirates (4); eye socket swabs (4); bronchial washings (1); and ascitic fluid (1). Sites o f primary pneumococcal infection were: pneumonia (26 cases); meningitis (5); skin and soft tissue (post-enucleation for retinoblastoma)(4 ); primary bacteremia (4); and primary peritonitis (1). Sixty-three percent o f infections were community-acquired and 37% were nosocom ial in origin. Thirty-three percent and 29% of subjects with community-acquired and nosocomial infection,respectively, had been hospitalized within the three months prior to pneumococcal infection. Overall, one third o f patients had. received prior antibiotic therapy. HTV/AIDS was the m ost common underlying condition for both adults and children. Overall mortal!uy was 10.5% (4/38 patients), all were fem ale adults with poor prognostic features including severe underlying illness, advanced age, nosocomial pneumococcal infection, and multilobar pneumonia. O f the three patients with both clinical and m icrobiological evidence of meningitis, two received appropriate combination therapy and recovered; one patient receiving ceftriaxone alone died. All study isolates were contained within .'if current 23-polyvalent vaccine, and 84% o f patients were vaccine candidates. More accurate survcillanr. ■ ' cephalosporin resistance among pneumococci is needed including routine screening o f clinically sig iu f "a«t isolates. M odification of current empiric treatment guidelines for suspected pneumococcal meningitis may be necessary based upon local, regional, and national prevalences o f cephalosporin resistance