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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.

Cystic fibrosis (CF) is an inherited recessive disease that affects mucocillary clearance in the lung, allowing it to be colonised with bacteria such as Staphylococcus aureus. To survive in the CF lung S. aureus adapts both phenotypically and genotypically, through various mechanisms. In this study, multiple specimens were collected from the participants and were processed routinely and were additionally cultured in chromogenic media. Multiplex PCR assays were employed to detect methicillin resistance and selected virulence and quaternary ammonium compound (qac) genes. Genetic relatedness of the S. aureus was determined using agr, SCCmec and spa typing as well as pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Thirty-three S. aureus isolates were isolated, of which 51% (17/33) were methicillin resistant S. aureus (MRSA). The virulence and qac genes were more prevalent in MRSA than the methicillin sensitive S. aureus (MSSA) isolates. The PFGE analysis showed nine distinct pulsotypes while MLST showed eight sequence types. All the STs detected in this study, except for ST508 have been previously isolated from CF patients according to the literature. This study showed a genetically diverse S. aureus population with a high prevalence of virulence genes among the MRSA isolates from the CF clinic.

We detected Chlamydia trachomatis biovar L2 in vaginal swab specimens of 7 women with vaginal discharge in South Africa. Whole-genome sequencing directly from clinical specimens identified a closely related cluster of strains. The clinical role of this infection in the context of syndromic management should be clarified.

OBJECTIVE: To evaluate the performance of three different guidelines for the management of vaginal discharge syndrome (VDS) for women living in a rural setting in South Africa.METHODS: We conducted a secondary analysis of data from a cross-sectional study in Mopani District, South Africa. The 2015 and 2008 guidelines of the South African Department of Health (DoH) and the most recent WHO guidelines were evaluated for adequate treatment of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis infection.RESULTS: Of the 489 women included in this analysis, 35% presented with VDS according to the DoH and 30% per WHO definition of VDS. 56% of the women with VDS would be treated adequately for these STI when using the 2015 DoH guideline, whereas 76% (p=0.01) and 64% (p=0.35) would receive adequate treatment with the 2008 DoH and WHO guidelines respectively. Of the symptomatic women who tested negative for all four STI, STI treatment would have been indicated for 36% as per 2015 DoH guideline vs. 69% (pCONCLUSION: A considerable proportion of symptomatic women infected with these common curable STI would receive adequate treatment when using a syndromic management approach, and significant differences exist between the three guidelines. Many symptomatic women without these STI receive broad-spectrum antibiotics, so new approaches are needed to improve syndromic STI control. This article is protected by copyright. All rights reserved.

Background The burden of catheter-related infections (CRIs) in developing countries is severe. In South Africa, a standardised surveillance definition does not exist and the collection of catheter days is challenging. The aim of the study was to provide baseline data on the prevalence of CRIs and to describe the epidemiology of CRI events within a tertiary academic hospital. Methods Surveillance was laboratory-based and conducted for a six month period. A microbiologically confirmed CRBSI (MC-CRBSI) event was defined as the isolation of the same microorganism from the catheter and concomitant blood cultures (BCs), within 48 h of catheter removal, which were not related to an infection at another site. Results A total of 508 catheters, removed from 332 patients, were processed by the laboratory, of which only 50% (253/508 removed from 143/332 patients) of the catheters were accompanied by BCs within 48 h. Sixty-five episodes of MC-CRBSI in 57 patients were detected, involving 71 catheters and 195 microbial isolates. The institutional prevalence rate was 3.7 episodes per 1 000 admissions and 5.8 episodes per 10 000 in-patient days. Catheter day data was collected in only six wards of the hospital. The pooled laboratory incidence was 10.1 MC-CRBSI episodes per 1 000 catheter days, whereas the hospital-based central line-associated bloodstream infection (CLABSI) rate was pooled at 5.7 episodes per 1 000 catheter days. The majority of patients had an underlying gastro-intestinal condition (33%; 19/56) with a non-tunnelled, triple-lumen central venous catheter, placed in the subclavian vein (38%; 27/71). The most predominant pathogen was methicillin-resistant Staphylococcus epidermidis (28%; 55/195), followed by extensively-drug resistant Acinetobacter baumannii (18%; 35/195). Conclusions Catheter-related infection prevention and control efforts require urgent attention, not only to keep patients safe from preventable harm, but to prevent the spread of multidrug resistant microorganisms.

Objectives: Pregnant women are especially at risk of developing complications when infected with reproductive tract infections (RTIs). The objective of this study was to determine the prevalence of bacterial vaginosis (BV) and genital mycoplasmas in pregnant women and investigate the associations between BV, genital mycoplasmas, HIV infection, age and gestational age. Design: Cross-sectional study with descriptive and analytical components. Setting: Antenatal clinic of a tertiary academic hospital in South Africa. Participants: 220 pregnant women older than 18 were included in the study and provided self-collected vaginal swabs. Primary and secondary outcomes: BV and genital mycoplasma colonisation and/or infection in women of differing age, gestational period and HIV status. Results: The prevalence of BV was 17.7% (39/220) (95% CI 12.9 to 23.4), intermediate vaginal flora (IVF) 15% (33/220) (95% CI 10.56 to 20.42), and the overall prevalence of genital mycoplasmas was 84% (185/220) (95% CI 78.47 to 88.58). BV was significantly associated with HIV infection with an OR of 2.84 (95% CI 1.08 to 7.46 and p value=0.034). However, BV was inversely associated with gestational age with an OR of 0.08 (95% CI 0.01 to 0.42 and p value=0.003) for second trimester pregnancies and an OR of 0.03 (95% CI 0.01 to 0.17 and p value

Background Bacterial vaginosis and genital mycoplasmas are reproductive tract infections that are associated with several infections and adverse pregnancy outcomes, such as pelvic inflammatory disease, preterm birth and spontaneous abortions in affected women. Bacterial vaginosis (BV), a polymicrobial condition, is reported to be prevalent in 15% to 20% of pregnant women while mycoplasmas colonise up to about 70% of sexually active women and antenatal patients. Methods Self-collected vaginal swabs were obtained from 221 pregnant women. Bacteria vaginosis was diagnosed using the Nugent scoring system and a multiplex PCR assay was performed to detect genital mycoplasmas. Mycoplasma hominis, M. genitalium, Ureaplasma urealyticum and U. parvum were targeted, respectively, for the 16S rRNA gene, 140-kDa adhesion protein and the multiple-banded antigen genes. Results The prevalence of bacterial vaginosis was 17.6% (39/221) with a total of 23.1% (9/39) of all BV-positive cases (score 7 to 10) being HIV positive. An intermediate grading according to the Nugent system (score 4 to 6) was given to 14.9% (33/221) of samples. Ureaplasma parvum was isolated from the majority of samples with a prevalence of 72.4% (160/221) followed by M. hominis, which was present in 50.7% (112/221) of all samples. The prevalence of M. genitalium and U. urealyticum was 14.5% (32/221) and 2.3% (5/221), respectively. Mycoplasma hominis was detected in 75% (27/36) of all HIV positive cases with U. parvum also present in 75% (27/36) of these cases. Conclusions The overall prevalence of genital mycoplasmas in antenatal patients was relatively high when compared to previous studies, while BV prevalence correlated with other reports. Ureaplasma parvum and M. hominis were notably present in HIV positive patients. The diagnosis of genital mycoplasmas and BV in pregnant women in HIV-prevalent South Africa is vital to allow early intervention and minimise complications, such as undesirable pregnancy outcomes.

Background Trichomoniasis caused by Trichomonas vaginalis affects both men and women, although the clinical presentation differs. Infected women are more likely to have symptoms compared to infected men. Approximately 75% to 100% of men are asymptomatic in comparison to approximately 50% to 75% of women who are identified as asymptomatic. In South Africa, data on the prevalence and detection of T. vaginalis is well-documented; however, data on the molecular characterization of T. vaginalis is limited. The study aimed to detect and characterise T. vaginalis isolates from HIV positive women attending an anti-retroviral clinic. Methods Self-collected vaginal swabs from 380 HIV positive women were included in the study. Trichomonas vaginalis was detected using wet mount microscopy, culture and a commercial PCR kit. The genetic relatedness of 92 culture positive T. vaginalis isolates was determined. Five primers (TV1, TV2, TV3, TV5 and TV6) were used for the RAPD assay. The PCR-IGS-RFLP products were digested with five enzymes, namely: Alu I , Hinf I , Rsa I , Sau 3AI and Tsp 509. Results A total of 8% (30/380) of specimens were positive for T. vaginalis using microscopy, 24% (92/380) of specimens were positive using culture and 31% (118/380) of the specimens were positive using the commercial PCR kit. RAPD assay analysis showed a high level of genetic diversity between the T. vaginalis isolates. The dendrogrammes obtained from the RAPD data grouped the 92 T.vaginalis isolates into between nine to 24 clusters with 70% similarity used to define clusters, while the PCR-IGS RFLP assay results for the isolates were genetically indistinguishable. Conclusion The PCR assay was the most sensitive diagnostic tool for the detection of T. vaginalis . A high prevalence of T. vaginalis , consisting of different strain types, was detected in the HIV positive women included in the study.