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TB is rated as one of the world’s deadliest diseases and South Africa ranks 9th out of the 22 countries with hardest hit of TB. Although many pieces of research have been carried out on this subject, this paper steps further by inculcating past knowledge into the model, using Bayesian approach with informative prior. Bayesian statistics approach is getting popular in data analyses. But, most applications of Bayesian inference technique are limited to situations of non-informative prior, where there is no solid external information about the distribution of the parameter of interest. The main aim of this study is to profile people living with TB in South Africa. In this paper, identical regression models are fitted for classical and Bayesian approach both with non-informative and informative prior, using South Africa General Household Survey (GHS) data for the year 2014. For the Bayesian model with informative prior, South Africa General Household Survey dataset for the year 2011 to 2013 are used to set up priors for the model 2014. [ABSTRACT FROM AUTHOR]

Introduction: Health Care Workers (HCWs) are among the highest risk groups for contracting tuberculosis (TB), which is ranked the third most common occupational health disease in South Africa. Little is known about the true extent of the burden of TB among South African HCWs and current surveillance approaches are inadequate. The study aimed to determine the feasibility of using postal and web-based surveys accessed through registries of registered professionals to estimate the prevalence of TB among HCWs in South Africa. Materials and methods: We conducted a cross sectional survey on a sample of professional nurses and doctors (general practitioners) registered on the Medpages database platform; a subscription based registry for practising health care professionals. The survey included professionals who were actively involved in the clinical management of patients, either in public or private health care facilities. The paper based survey, including pre-paid return envelopes, was distributed via the post office and web-based surveys were distributed via e-mail through a hyperlink. Descriptive statistics were used to summarize the data and the Chi-square test to determine associations between categorical variables. Active TB was defined as any history of TB Results: Out of a total of 3,400 health care professionals contacted, 596 (18%) responses were received: 401 (67%) web-based and 195 (33%) postal. A significantly higher percentage of complete forms were from postal compared to web-based (97% [189/195] versus 87% [348/401], p<0.001). Younger (<60 years) professionals were more likely to use the web-based compared to postal (87% [236/270] versus 71% [134/189], p<0.001). Overall, the prevalence of active TB infection was 8.7%, (95%CI: 6.3%–11.7%) and there was no difference observed between doctors and nurses (10.8% [18/167] versus 7.5% [22/292], p = 0.236). Conclusion: This novel approach demonstrated the feasibility of using an existing registry of professionals to conduct surveys to estimate the prevalence of TB. Our findings showed a high TB prevalence; however the estimate might have been biased by the low response rate. Further research to optimise our approach could lead to a viable option in improving surveillance among health care professionals. [ABSTRACT FROM AUTHOR]

Rhizobial nitrogen-fixing bacteria are the main inhabitants of the root nodules of legume plants. Studying the bacterial community of legume nodules is important in understanding plant growth and nutrient requirements. Culture-based technique was used to examine the bacterial community of these underground organs from Vigna subterranea L. Verdc (Bambara nut), an underutilized legume in Africa, for plant growth-promoting traits. In this study, Bambara nuts were planted to trap root-nodule bacteria, and the bacteria were morphologically, biochemically, and molecularly characterized. Five selected isolates were screened in vitro for their plant growth-promoting traits and exhibited differences in their phenotypic traits. The polymerase chain reaction (PCR) products were subjected to partial 16S rRNA gene sequencing for phylogenetic analysis. Based on 16S rRNA gene sequence, the isolates were identified as BA1 (Stenotrophomonas maltophilia), BA2 (Chryseobacterium sp.), BA3 (Pseudomonas alcaligenes), BA4 (Pseudomonas plecoglossicida), and BA5 (Pseudomonas hibiscicola). Results showed that four of the five isolates could produce IAA. The capability to solubilize phosphate in Pikovskaya's agar plates was positively shown by four isolates (BA2, BA3, BA4, and BA5). Three isolates could produce hydrogen cyanide while isolates BA1, BA3, BA4, and BA5 were found to have ammonia-production traits. The results suggest that these plant growth-promoting isolates can be used as inoculants for plant growth and productivity. [ABSTRACT FROM AUTHOR]

Lignin recalcitrance is a key issue in producing value-added products from lignocellulose biomass. In situ biodegradable lignin-modifying enzymes-producing bacteria are considered a suitable solution to lignin biodegradation problems, but exploitation of ligninolytic bacteria is still limited to date. Hence, this study aimed to isolate and characterize potential lignin peroxidase ligninolytic bacteria from decomposing soil, sawdust, and cow dung at Richard Bay, South Africa. The samples were collected and cultured in the lignin-enriched medium. Pure isolated colonies were characterized through 16S rRNA gene sequencing. The ability of the isolates to grow and utilize aromatic monomers (veratryl and guaiacol alcohol) and decolorize lignin-like dyes (Azure B, Congo Red, Remazol Brilliant Blue R) was evaluated. Of the twenty-six (26) bacteria isolates 10 isolates, including Pseudomonas spp. (88%), Enterobacter spp. (8%), and Escherichia coli (4%) were identified as true lignin peroxidase producers. Pseudomonas aeruginosa (CP031449.2) and E. coli (LR025096.1) exhibited the highest ligninolytic activities. These isolates could potentially be exploited in the industry and wastewater treatment as effective lignin degrading agents. [ABSTRACT FROM AUTHOR]

Background. Inappropriate empirical antibiotics promote antibiotic resistance. Antibiograms guide empirical antibiotic therapy by outlining the percentage susceptibility of each pathogen to individual antibiotics. In 2016, the Trauma Intensive Care Unit at Charlotte Maxeke Johannesburg Academic Hospital escalated empirical antibiotic therapy for nosocomial infections from piperacillin-tazobactam to imipenem plus amikacin. Objectives. This study assessed the impact of escalation in empirical antimicrobial treatment on organism prevalence and resistance profile. Methods. A retrospective analysis of bacterial and fungal microscopy, culture and susceptibility reports from the laboratory information system of the National Health Laboratory Services, from 1 January 2015 to 31 December 2015 and 1 January 2017 to 31 December 2017, was conducted. Data were de-duplicated according to standard guidelines. Fisher's exact test was used to determine p-values. Results. Organism prevalence shifted between the years, with a 2.7% increase in streptococci (p=0.0199), 1.7% increase in Candida auris (p=0.0031) and 4.6% and 4.4% reduction in Acinetobacter baumannii (p=0.0508) and Pseudomonas aeruginosa (p=0.0196), respectively. Similarly, there was a change in the resistance profile, with a 28.9% reduction in multi-drug resistant (MDR) A. baumannii (p=0.0001), 60.4% reduction in MDR P aeruginosa (p=0.0001) and a 6.5% increase in carbapenem-resistant Enterobacterales (p=0.007). The predominant specimen type differed between the years, with significantly more pus, tissue and fluid samples and fewer respiratory samples sent for investigation in 2017 than 2015. Conclusion. Escalation in the use of empirical antibiotics showed a change in organism prevalence and an improvement in the susceptibility profile of MDR non-fermenters. [ABSTRACT FROM AUTHOR]

At present, there is no comprehensive soil quality assessment practice for soil stockpiles in the South African coal mining industry. Soil microorganisms and enzymes are suitable indicators for soil quality monitoring. Therefore, this study investigated the microbial community and enzyme (beta-glucosidase and urease) activities in soil stockpiles of opencast coal mines in the coal-rich region of South Africa. Soil stockpiles of three opencast coal mines were sampled at depths of 0–20 cm ('topsoil') and >20 cm ('subsoil') across three seasons. Beta-glucosidase and urease activities were mostly higher in soil stockpiles than in unmined soils and were significantly influenced (P < 0.05) by the interaction of site and seasonal factors. However, analyses of PCR-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of partial 16S rRNA gene and internally transcribed spacer 2 (ITS2) sequences revealed higher microbial diversity in unmined (reference) soils compared to soil stockpiles across all seasons. Redundancy analysis further revealed that microbial communities of topsoil were not significantly (P > 0.05) influenced by soil properties, whereas microbial communities of subsoils were significantly (P < 0.05) influenced by pH, organic carbon, total nitrogen and phosphorus contents. Furthermore, operational taxonomic units (OTUs) belonging to genera of known phytobeneficial species such as Azomonas, Aureobasidium, Phialocephala, Phoma and Sordariomycetes were detected in these soils. Overall, results suggest that the microbial community structure and diversity observed in stockpiles is impaired (compared to the unmined site), although variations in the microbial community structure of soil stockpiles across seasons are site-specific. The impaired microbial community of stockpiles may have negative implications on soil biological processes driven by microbes; especially those that are critical for nutrient cycling and ecosystem sustainability. More importantly, such alteration in soil biodiversity may impair post-mining land use capability of stockpile soils. [ABSTRACT FROM AUTHOR]

South Africa ranks third among 22 high burden countries in the world. TB which remains a leading cause of death causes one in five adult deaths in South Africa. An in-depth understanding of knowledge, attitudes and practices of young people towards TB is required to implement meaningful interventions. We analysed young men and women (18–24 years)'s TB knowledge including TB/HIV coinfections, testing rates and factors associated with them. A cross sectional cluster-based household survey was conducted in two provinces. Participants completed computer-assisted self-interviews on TB knowledge, testing history and TB/HIV coinfections. A participant was regarded as knowledgeable of TB if s/he correctly answered the WHO-adopted TB knowledge questions. We built three multivariate regression models in Stata 13.0 to assess factors associated with knowing TB alone, testing alone and both knowing and testing for TB. 1955 participants were interviewed (89.9% response rate). Their median age was 20 years (IQR19-22). Sixteen percent (16.2%) of the participants were social grant recipients, 55% were enrolled in a school/college and 5% lived in substandard houses. A total of 72% had knowledge of TB, 21% underwent screening tests for TB and 14.7% knew and tested for TB. Factors associated with TB knowledge were being female, younger, a student, social grant recipient, not transacting sex and having positive attitudes towards people living with HIV (PLWH). Factors associated with TB testing were being a student, receiving a social grant, living in OR Tambo district, HIV knowledge and having a family member with TB history. Factors associated with both TB knowledge and testing were being female, a student, using the print media, living in OR Tambo district and having a family member with a TB history. The study demonstrates the importance of demographic factors (gender, economic status, family TB history, and location) and HIV factors in explaining TB knowledge and testing. We recommend extending community TB testing services to increase testing. [ABSTRACT FROM AUTHOR]

Background: Compounds having both anticancer and antimicrobial activity have promising therapeutic potential due to their selective cytotoxicity and their potential to reduce the occurrence of bacterial and fungal infections in immune-compromised cancer patients. In our quest to find new antimicrobial agents with potent anticancer activity, the biological potential of leaves from the three medicinal plants Centella asiatica, Warburgia salutaris and Curtisia dentata as used by Zulu traditional healers for the treatment of cancer is investigated. Methods: Extracts were assayed for antibacterial activity using the agar well diffusion and micro plate dilution assay. In addition, minimum bactericidal concentrations (MBC), lactate dehydrogenase (LDH) release assay and rhodamine 6G intake assay were used to ascertain the antibacterial activity. The cytotoxic effects of the plant extracts were determined using tetrazolium-based colorimetric (MTT) cell proliferation assay against MCF-7, human colorectal carcinoma cells (Caco-2), A549 and HeLa cancerous cell lines. Results: The acetone extracts from Waburgia salutaris revealed noteworthy anti-proliferative effect yielding IC50 value of 34.15 μg/ml against MCF-7 cell line, while acetone extract from Curtisia dentata significantly (P ≤ 0.05) revealed promising IC50 values of 41.55, 45.13, 57.35 and 43.24 μg/ml against A549, HeLa, CaCo-2 and MCF-7 cell lines. The extracts further revealed a broad-spectrum antibacterial activity against bacterial strains used in the study. An acetone extract from W. salutaris revealed the highest zone of inhibition and the lowest minimum inhibitory concentration (MIC) of 21.0 mm and 0.16 mg/ml respectively against Staphylococcus aureus. Methanol extract from W. salutaris and ethyl acetate extract from C. dentata revealed 53% inhibition of R6G inside the cell against Staphylococcus aureus and Escherichia coli respectively in a cytosolic lactate dehydrogenase assay, suggesting that the mode of action of such extracts may be through efflux pump. Conclusions: Overall, the extracts had good antibacterial activity and anti-proliferative effects against selected cancerous cell lines. Given the good antibacterial activity of the extracts the plants may act as an immune booster and prevent infection in immunosuppressed cancer patients. This is further supported by the plants' anti-proliferative potential, bacteriostatic, bactericidal properties and also their ability to block bacterial efflux pump systems. [ABSTRACT FROM AUTHOR]

Objectives: To estimate trends in prevalence and incidence of syphilis, gonorrhea and chlamydia in adult men and women in South Africa. Methods: The Spectrum-STI tool estimated trends in prevalence and incidence of active syphilis, gonorrhea and chlamydia, fitting South African prevalence data. Results were used, alongside programmatic surveillance data, to estimate trends in incident gonorrhea cases resistant to first-line treatment, and the reporting gap of symptomatic male gonorrhea and chlamydia cases treated but not reported as cases of urethritis syndrome. Results: In 2017 adult (15–49 years) the estimated female and male prevalences for syphilis were 0.50% (95% CI: 0.32–0.80%) and 0.97% (0.19–2.28%), for gonorrhea 6.6% (3.8–10.8%) and 3.5% (1.7–6.1%), and for chlamydia 14.7% (9.9–21%) and 6.0% (3.8–10.4%), respectively. Between 1990 and 2017 the estimated prevalence of syphilis declined steadily in women and men, probably in part reflecting improved treatment coverage. For gonorrhea and chlamydia, estimated prevalence and incidence showed no consistent time trend in either women or men. Despite growing annual numbers of gonorrhea cases − reflecting population growth − the estimated number of first line treatment-resistant gonorrhea cases did not increase between 2008 and 2017, owing to changes in first-line antimicrobial treatment regimens for gonorrhea in 2008 and 2014/5. Case reporting completeness among treated male urethritis syndrome episodes was estimated at 10–28% in 2017. Conclusion: South Africa continues to suffer a high STI burden. Improvements in access and quality of maternal, STI and HIV health care services likely contributed to the decline in syphilis prevalence. The lack of any decline in gonorrhea and chlamydia prevalence highlights the need to enhance STI services beyond clinic-based syndromic case management, to reinvigorate primary STI and HIV prevention and, especially for women, to screen for asymptomatic infections. [ABSTRACT FROM AUTHOR]

Background: Tithonia diversifolia and T. rotundifolia belong to the Asteraceae family and are native to Mexico and Central America. These plants have become invasive in parts of tropical Africa and Asia where they have become an ecological, agricultural and economic burden. Tithonia diversifolia is exploited by locals in its native and most parts of its invasive range as a source of medicines; however, T. rotundifolia is only used for medicinal purposes in one country in the native range (Venezuela) and none in the invasive range. Although T. diversifolia has been studied for different biological activities, little or no attention has been given to T. rotundifolia. This study compared the antimicrobial activity, phytochemistry, identification of bioactive compound(s) and toxicity levels of different leaf extracts and fractions of T. diversifolia and T. rotundifolia. Methods: Antimicrobial activity was evaluated against seven pathogenic bacteria, four non-pathogenic Mycobacterium species and three fungal species using serial microdilution assays. Phytochemical contents were determined through standard methods of analysis. UPLC/MS was used to analyse the fractions to identify possible bioactive compounds that may be responsible for bioactivity, while toxicity tests were carried out using the colorimetric MTT assay and the Ames test. Results: Both species had a range of antimicrobial activity against bacterial, mycobacterial and fungal species. However, T. rotundifolia displayed better activity against most of the strains tested with minimum inhibitory concentration values ranging between 0.01 and 0.07 mg/ml. Both species were rich in phenolics, flavonoids and tannins. Tagitinin A was identified as the main compound present in both species, and this compound may be responsible for the antimicrobial activity displayed. Toxicity tests showed that T. diversifolia was cytotoxic at concentrations used in this study, while T. rotundifolia was not. Both species did not show any mutagenic/genotoxic effects. Conclusion: The above results suggest that both species may be further developed as a source of antimicrobials for the treatment of infections caused by opportunistic pathogens. They may also serve as alternatives to highly exploited plant species with the same medicinal properties. However, T. diversifolia should be used with caution as it may be toxic. [ABSTRACT FROM AUTHOR]

Background: Sexually transmitted infections (STIs) and bacterial vaginosis (BV) are associated with increased transmission of HIV, and poor reproductive and sexual health. The burden of STIs/BV among young people is unknown in many high HIV prevalence settings. We conducted an acceptability, feasibility, and prevalence study of home-based sampling for STIs/BV among young men and women aged 15-24 years old in a health and demographic surveillance site (HDSS) in rural KwaZulu-Natal, South Africa.Methods and Findings: A total of 1,342 young people, stratified by age (15-19 and 20-24 years) and sex were selected from the HDSS sampling frame; 1,171/1,342 (87%) individuals had ≥1 attempted home visit between 4 October 2016 and 31 January 2017, of whom 790 (67%) were successfully contacted. Among the 645 who were contacted and eligible, 447 (69%) enrolled. Consenting/assenting participants were interviewed, and blood, self-collected urine (men), and vaginal swabs (women) were tested for herpes simplex virus type 2 (HSV-2), chlamydia, gonorrhoea, syphilis, trichomoniasis, and BV. Both men and women reported that sample collection was easy. Participants disagreed that sampling was painful; more than half of the participants disagreed that they felt anxious or embarrassed. The weighted prevalence of STIs/BV among men and women, respectively, was 5.3% and 11.2% for chlamydia, 1.5% and 1.8% for gonorrhoea, 0% and 0.4% for active syphilis, 0.6% and 4.6% for trichomoniasis, 16.8% and 28.7% for HSV-2, and 42.1% for BV (women only). Of the women with ≥1 curable STI, 75% reported no symptoms. Factors associated with STIs/BV included having older age, being female, and not being in school or working. Among those who participated in the 2016 HIV serosurvey, the prevalence of HIV was 5.6% among men and 19% among women. Feasibility was impacted by the short study duration and the difficulty finding men at home.Conclusions: A high prevalence of STIs/BV was found in this rural setting with high HIV prevalence in South Africa. Most STIs and HIV infections were asymptomatic and would not have been identified or treated under national syndromic management guidelines. A nested STI/BV survey within a HDSS proved acceptable and feasible. This is a proof of concept for population-based STI surveillance in low- and middle-income countries that could be utilised in the evaluation of STI/HIV prevention and control programmes. [ABSTRACT FROM AUTHOR]

Background: The World Health Organization (WHO) aims to reduce tuberculosis (TB) deaths by 95% by 2035; tracking progress requires accurate measurement of TB mortality. International Classification of Diseases (ICD) codes do not differentiate between HIV-associated TB and HIV more generally. Verbal autopsy (VA) is used to estimate cause of death (CoD) patterns but has mostly been validated against a suboptimal gold standard for HIV and TB. This study, conducted among HIV-positive adults, aimed to estimate the accuracy of VA in ascertaining TB and HIV CoD when compared to a reference standard derived from a variety of clinical sources including, in some, minimally-invasive autopsy (MIA). Methods and findings: Decedents were enrolled into a trial of empirical TB treatment or a cohort exploring diagnostic algorithms for TB in South Africa. The WHO 2012 instrument was used; VA CoD were assigned using physician-certified VA (PCVA), InterVA-4, and SmartVA-Analyze. Reference CoD were assigned using MIA, research, and health facility data, as available. 259 VAs were completed: 147 (57%) decedents were female; median age was 39 (interquartile range [IQR] 33–47) years and CD4 count 51 (IQR 22–102) cells/μL. Compared to reference CoD that included MIA (n = 34), VA underestimated mortality due to HIV/AIDS (94% reference, 74% PCVA, 47% InterVA-4, and 41% SmartVA-Analyze; chance-corrected concordance [CCC] 0.71, 0.42, and 0.31, respectively) and HIV-associated TB (41% reference, 32% PCVA; CCC 0.23). For individual decedents, all VA methods agreed poorly with reference CoD that did not include MIA (n = 259; overall CCC 0.14, 0.06, and 0.15 for PCVA, InterVA-4, and SmartVA-Analyze); agreement was better at population level (cause-specific mortality fraction accuracy 0.78, 0.61, and 0.57, for the three methods, respectively). Conclusions: Current VA methods underestimate mortality due to HIV-associated TB. ICD and VA methods need modifications that allow for more specific evaluation of HIV-related deaths and direct estimation of mortality due to HIV-associated TB. [ABSTRACT FROM AUTHOR]

Pathogenic free-living amoebae (FLA), such as Naegleria fowleri, Balamuthia mandrillaris and Acanthamoeba species isolated from aquatic environments have been implicated in central nervous system, eye and skin human infections. They also allow the survival, growth and transmission of bacteria such as Legionella, Mycobacteria and Vibrio species in water systems. The purpose of this study was to investigate the co-occurrence of potentially pathogenic FLA and their associated bacteria in hospital water networks in Johannesburg, South Africa. A total of 178 water ( n = 95) and swab ( n = 83) samples were collected from two hospital water distribution systems. FLA were isolated using the amoebal enrichment technique and identified using PCR and 18S rDNA sequencing. Amoebae potentially containing intra-amoebal bacteria were lysed and cultured on blood agar plates. Bacterial isolates were characterized using the VITEK®2 compact System. Free-living amoebae were isolated from 77 (43.3 %) of the samples. Using microscopy, PCR and 18S rRNA sequencing, Acanthamoeba spp. (T3 and T20 genotypes), Vermamoeba vermiformis and Naegleria gruberi specie were identified. The Acanthamoeba T3 and T20 genotypes have been implicated in eye and central nervous system infections. The most commonly detected bacterial species were Serratia marcescens, Stenotrophomonas maltophilia, Delftia acidovorans, Sphingomonas paucimobilis and Comamonas testosteroni. These nosocomial pathogenic bacteria are associated with systematic blood, respiratory tract, the urinary tract, surgical wounds and soft tissues infections. The detection of FLA and their associated opportunistic bacteria in the hospital water systems point out to a potential health risk to immune-compromised individuals. [ABSTRACT FROM AUTHOR]

Background: We assessed the diagnostic accuracy of Determine TB-LAM (LF-LAM) to screen for tuberculosis among ambulatory adults established in HIV care in South Africa. Methods: A systematic sample of adults attending for HIV care, regardless of symptomatology, were enrolled in the XPHACTOR study, which tested a novel algorithm for prioritising investigation with Xpert MTB/RIF. In this substudy, restricted to participants with enrolment CD4<200x106/l, urine was stored at enrolment for later testing with LF-LAM. Sputum was sent for immediate Xpert MTB/RIF if any of: current cough, fever ≥3 weeks, body mass index (BMI)<18.5kg/m2, CD4<100x106/l (or <200x106/l if pre-ART), weight loss ≥10% or strong clinical suspicion were present; otherwise, sputum was stored for Xpert testing at study completion. Participants were reviewed monthly, with reinvestigation if indicated, to 3 months, when sputum and blood were taken for mycobacterial culture. We defined tuberculosis as “confirmed” if Xpert, line probe assay or culture for M. tuberculosis within six months of enrolment were positive, and “clinical” if tuberculosis treatment started without microbiological confirmation. Results: Amongst 424 participants, 61% were female and 57% were taking ART (median duration 22 months); median age, CD4 and BMI were 39 years, 111x106/l, and 23 kg/m2. 56/424 (13%) participants had tuberculosis (40 confirmed, 16 clinical). 24/424 (5.7%) vs. 8/424 (1.9%) were LAM-positive using grade 1 vs. grade 2 cut-off. Using grade 1 cut-off, sensitivity for confirmed TB (all clinical TB excluded) was 12.5% (95% CI 4.2%, 26.8%) and in CD4<100x106/l vs. CD4 ≥100x106/l was 16.7% (95% CI 4.7%, 37.4%) vs. 6.3% (95% CI 0.2%, 30.2%). Specificity was >95% irrespective of diagnostic reference standard, CD4 stratum, or whether grade 1 or grade 2 cut-off was used. Conclusion: Sensitivity of LF-LAM is too low to recommend as part of intensified case finding in ambulatory patients established in HIV care. [ABSTRACT FROM AUTHOR]

The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches. [ABSTRACT FROM AUTHOR]

Routine diagnostic methods for the aetiologic agents of diarrhoea in most developing countries are usually not sensitive enough, leading to under-diagnosis. Thus, this study investigated possible mixed diarrhoeal aetiology by using cultures and real-time polymerase chain reactions (PCR) in children younger than four years old in the Northwest Province, South Africa. In total, 505 stool samples were collected from symptomatic and asymptomatic children who were attending three clinics and the Brits hospital in Madibeng District, between September 2016 and December 2017. Rotavirus, norovirus, Campylobacter, Arcobacter, and diarrhoeagenic Escherichia coli (DEC) were targeted. Campylobacter spp. (24.6%), Arcobacter (15.8%) and DEC (19.6%) were detected using PCR; only Campylobacter spp. (29.7%) and DEC (26.9%) were detected through the culture. Campylobacter jejuni (36%), Campylobacter coli (28%), Campylobacter upsalensis (12%), and Arcobacter butzleri (15.8%) were the only spp. of Campylobacter and Arcobacter identified. The eaeA gene (31.4%) of enteropathogenic E. coli/enterohaemorrhagic E. coli (EPEC/EHEC) was the most prevalent DEC virulence gene (VG) identified. Rotavirus and norovirus were detected at 23.4% and 20%, respectively. Mixed viral aetiology (7.3%) and the co-infection of A. butzleri and Campylobacter (49%) were recorded. A mixed bacterial-viral aetiology was observed in 0.6% of the specimens. Sensitive diagnostic procedures like PCR should be considered to provide the best treatment to children experiencing diarrhoea. [ABSTRACT FROM AUTHOR]

Next-generation sequencing provides new insights into the diversity and structure of bacterial communities, as well as the fate of pathogens in wastewater treatment systems. In this study, the bacterial community structure and the presence of pathogenic bacteria in three wastewater treatment plants across Gauteng province in South Africa were studied. The physicochemical results indicated that the quality of wastewater varies considerably from one plant to the others. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla across the three wastewater treatment plants, while Alphaproteobacteria, Actinobacteria, Bacilli, and Clostridia were the dominant classes. The dominant bacterial functions were highly associated with carbohydrate, energy, and amino acid metabolism. In addition, potential pathogenic bacterial members identified from the influent/effluent samples included Roseomonas, Bacillus, Pseudomonas, Clostridium, Mycobacterium, Methylobacterium, and Aeromonas. The results of linear discriminant analysis (LDA) effect size analysis also confirmed that these bacterial pathogens were significantly abundant in the wastewater treatment systems. Further, the results of this study highlighted that the presence of bacterial pathogens in treated effluent pose a potential contamination risk, transmitted through soil, agriculture, water, or sediments. There is thus a need for continuous monitoring of potential pathogens in wastewater treatment plants (WWTPs) in order to minimize public health risk. [ABSTRACT FROM AUTHOR]