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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]

In recent years, the adsorption of heavy metal cations onto bacterial surfaces has been studied extensively. This paper reports the findings of a study conducted on the heavy metal ions found in mine effluents from a mining plant where Co(2+) and Ni(2+) bearing minerals are processed. Heavy metal ions are reported to be occasionally present in these mine effluents, and the proposed microbial sorption technique offers an acceptable solution for the removal of these heavy metals. The sorption affinity of microorganisms for metal ions can be used to select a suitable microbial sorbent for any particular bioremediation process. Interactions of heavy metal ions (Co(2+) and Ni(2+)) and light metal ions (Mg(2+) and Ca(2+)) with indigenous microbial cells (Brevundimonas spp., Bacillaceae bacteria and Pseudomonas aeruginosa) were investigated using the Langmuir adsorption isotherm, pseudo second-order reaction kinetics model and a binary-metal system. Equilibrium constants and adsorption capacities derived from these models allowed delineation of the effect of binding affinity and metal concentration ratios on the overall adsorption behaviour of microbial sorbents, as well as prediction of performance in bioremediation systems. Although microbial sorbents used in this study preferentially bind to heavy metal ions, it was observed that higher concentrations (>90 mg/ℓ) of light metal ions in multi-metal solutions inhibit the adsorption of heavy metal ions to the bacterial cell wall. However, the microbial sorbents reduced Ni(2+) levels in the mine-water used (93-100% Ni(2+) removal) to below the maximum acceptable limit of 350 μg/ℓ, established by the South African Bureau of Standards. Competition among metal ions for binding sites on the biomaterial surface can occur during the bioremediation process, but microbial sorption affinity for heavy metal ions can enhance their remediation in dilute (<5 mg/ℓ heavy metal) wastewaters., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

The Alexander Project, initiated in 1992 as an international, multicentre, longitudinal surveillance study of antimicrobial susceptibility among common respiratory pathogens, has been pivotal in defining the role of global surveillance. At the time, there were few studies in which data were collected in a way that allowed meaningful comparisons to be made between studies, locations or over time. The project instituted the use of a central laboratory and standardized methods for the collection of isolates and determination of susceptibility, and this was continued with the addition of two further reference laboratories. Data from the study have provided a resource for measuring trends in the susceptibility patterns of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis at country, regional and global levels. Determination and publication of quantitative MICs enabled detailed assessment of changes in susceptibility distributions and assessment of microbiological and potential clinical susceptibility using different breakpoints, including those based on pharmacokinetic/pharmacodynamic parameters. Comparisons of antimicrobial usage patterns and resistance prevalences over time allowed hypotheses to be examined with respect to the role of quantity and type of antimicrobial use in the selection and spread of resistance. The resulting collection of isolates has provided a valuable resource for molecular studies into the evolution of resistance over time and location; a substantial proportion of this collection is now in the public domain. This paper reviews the 10 years of the Alexander Project and the benefits it has brought to an understanding of the evolution of antibacterial resistance in community respiratory bacteria.

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]

Resource-limited communities throughout the developing world face significant environmental health problems related to the myriad of coliform sources within those communities. This study comprehensively investigated contamination sources and the biological and chemical mechanisms sustaining them in two adjacent communities in rural Limpopo, South Africa. An 8-month study was conducted of household () and source water quality, measurements of biofilm layers on the inside of household water storage containers and water transfer devices, and also hand-based coliforms and hand-washing effectiveness. A 7-day water container incubation experiment was also performed to determine the biological and chemical changes that occur in a household water storage container independent of human interference. Results indicate that household drinking water frequently becomes contaminated after collection but before consumption (197 versus 1,046 colony-forming ; ; ). The most important contamination sources include biofilm layers on the inside of storage containers ( colony-forming ; ), hands ( colony-forming ; ), and coliform regrowth resulting from high assimilable organic carbon (AOC) levels during storage. A maximum specific growth rate, , of was determined for total coliform bacteria on AOC, and a high correlation between AOC concentrations and the growth potential of total coliform bacteria was observed. These results support the implementation of point-of-use water treatment and other interventions aimed at maintaining the safe water chain and preventing biological regrowth. [ABSTRACT FROM AUTHOR]

Objectives: To investigate knowledge of and practices regarding bottle-feeding preparation, as well as the nutrient content and microbial safety of bottles that are prepared by mothers and caregivers for infants aged 0-24 months. Design: Cross-sectional descriptive survey. Setting: Urban township, Mangaung, outside Bloemfontein. Subjects: A sample of 189 mothers or caregivers of healthy infants aged 0-24 months, who were exclusively formula fed or mixed fed with breast milk and infant formula or cow's milk, were randomly selected in a household survey. Outcome measures: An interviewer-administered questionnaire and/or observed practices were used for data collection. Bottle-feed samples were also collected and analysed for nutrient and microbial content. Results: Mother and caregiver knowledge on infant feeding was poor. An acceptable method for preparing a bottle feed in five steps was evaluated. Only 4.2% of the total sample applied all five steps. A total of 84.5% (n = 160) of all the collected feeds was contaminated with E coli. A lower level of maternal education was associated with a greater likelihood of feed contamination. The predominant source of bottle-feeding preparation information was clinic staff (28%). Conclusion: The findings were indicative of a lack of knowledge, and possibly resource limitations, to facilitate safe bottle-feeding practices. Acknowledgement of clinic staff as a source of infant-feeding information highlights the role of healthcare workers as facilitators of appropriate infant-feeding practices. [ABSTRACT FROM AUTHOR]

Background: Microbial infections and resulting inflammation and oxidative stress are common pathogenesis of gastrointestinal tract (GIT) disorders. In South Africa, several species of the genus Maytenus are used in traditional medicine to treat various infectious diseases. Most of the previous work on this genus was focused on nonpolar extracts from the root and bark. In this study, leaf extracts of polar extracts of Maytenus peduncularis, Maytenus procumbens, Maytenus senegalensis and Maytenus undata were evaluated for antimicrobial, anti-inflammatory and antioxidant activities to determine their efficacy as therapeutic agents in GIT disorders. Methods: Phenolic-enriched leaf extracts and fractions were prepared by extracting with acidified 70% methanol and solvent-solvent fractionation. The activities of the fractions against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Enterococcus faecalis as well as clinical isolates of Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans were determined using a serial microplate dilution method. Antioxidant activities were determined using 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2′-azinobis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), hydroxyl (OH) radical scavenging and linoleic acid peroxidation inhibitory assays. The phenolic composition as well as the cytotoxicity against Vero cell lines of the crude extracts was evaluated using various standard protocols. Results: The antimicrobial activities were concentrated in the non-polar fractions of hexane, dichloromethane and ethyl acetate (MICs 19-312 µg/ml). The crude extracts and polar fractions (butanol and water) had moderate to poor antimicrobial activity (MICs 312 to above 2500 µg/ml). The crude extracts and polar fractions had good antioxidant activity (EC50 values varied from 1.22 to 607 µg/ml, 1.71 to 312 µg/ml and 23 to 284 µg/ml for DPPH, ABTS and OH respectively. Linoleic acid peroxidation inhibition EC50 values of the crude extracts ranged between 27 and 39 µg/ml with relatively low toxicity against Vero cell lines (IC50 values 87 to 187 µg/ml). Fractionation of a crude extract with low activity could lead to fractions with more potent activity. Conclusion: This study justifies the traditional use of leaf crude extracts and fractions from these four plants to remedy gastrointestinal disorders resulting from infection, inflammation and oxidative stress complications. The study also provides rationale for the use of leaf extracts with same beneficial effects in place of unsustainable root and bark harvest. [ABSTRACT FROM AUTHOR]

Bioflocculant-producing bacteria were isolated from activated sludge of a wastewater treatment plant located in Durban, South Africa, and identified using standard biochemical tests as well as the analysis of their 16S rRNA gene sequences. The bioflocculants produced by these organisms were ethanol precipitated, purified using 2% (w/v) cetylpyridinium chloride solution and evaluated for removal of wastewater dyes under different pH, temperature and nutritional conditions. Bioflocculants from these indigenous bacteria were very effective for decolourizing the different dyes tested in this study, with a removal rate of up to 97.04%. The decolourization efficiency was largely influenced by the type of dye, pH, temperature, and flocculant concentration. A pH of 7 was found to be optimum for the removal of both whale and mediblue dyes, while the optimum pH for fawn and mixed dye removal was found to be between 9 and 10. Optimum temperature for whale and mediblue dye removal was 35 °C, and that for fawn and mixed dye varied between 40-45 °C and 35-40 °C, respectively. These bacterial bioflocculants may provide an economical and cleaner alternative to replace or supplement present treatment processes for the removal of dyes from wastewater effluents, since they are biodegradable and easily sustainable. [ABSTRACT FROM AUTHOR]

Authigenic calcite and dolomite and biogenic aragonite occur in Holocene pan sediments in a Mediterranean-type climate on the western coastal plain of South Africa. Sediment was analysed from a Late Pleistocene coastal pan at Yzerfontein and four Holocene inland pans ranging from brackish to hypersaline. The pans are between 0·08 and 0·14 km2 in size. The δ18OPDB values of carbonate minerals in the pan sediments range from −2·41 to 5·56‰ and indicate precipitation from evaporative waters. Covariance of total organic content and percentage carbonate minerals, and the δ13CPDB values of pan carbonate minerals (−8·85 to −1·54‰) suggest that organic matter degradation is a significant source of carbonate ions. The precipitation of the carbonate minerals, especially dolomite, appears to be mediated by sulphate-reducing bacteria in the black sulphidic mud zone found in the brine-type hypersaline pans. The knobbly, sub-spherical texture of the carbonate minerals suggests that the precipitation of the carbonate minerals, particularly dolomite, is related to microbial processes. The 87Sr/86Sr ratios of pan carbonate minerals (0·7108 to 0·7116) are slightly higher than modern sea water and indicate a predominantly sea water (marine aerosol) source for calcium (Ca2+) ions with relatively minor amounts of Ca2+ derived from the chemical weathering of bedrock. [ABSTRACT FROM AUTHOR]

The reliability of a field test kit for the detection and the persistence of Synergistes jonesii bacteria in sheep was investigated in two trials for 12 months. The test kit consisted of a culture medium (Fe2), serum test tubes, disposable syringes and needles, stomach tube, cheesecloth and ferric chloride reagent. The objectives were to test a field kit for practicality and reliability, to assess the spread of the bacteria among sheep flocks within the farm in Phase 1, and to monitor the persistence of the bacteria with and without Leucaena forage in the diet for 5 months in Phase 2. Three sheep flocks (20 young ewes, 30 older ewes and 11 wethers) were screened in Phase 1; and in Phase 2, four wethers were monitored for 19 weeks with and without Leucaena forage in the diet. In Phase 1, wethers tested positive within 6.364 ± 0.48 d, while the ewes took longer (16.5 ± 0.14 d). All flocks were infested with the bacteria even without prior inoculation. In Phase 2, the four wethers on Leucaena diet tested positive within 5.0 ± 0.0 d, but without Leucaena in the diet it took 12.08 ± 0.0, 11.0 ± 4.46, 11.67 ± 5.76, and 6.92 ± 0.0 d, respectively. The bacteria persisted for 5 months without Leucaena in the diet. This confirmed that the field test kit was simple, reliable and fast, and the bacteria are contagious and very persistent. [ABSTRACT FROM AUTHOR]

Background: Honey has been shown to have wound healing properties which can be ascribed to its antimicrobial activity. The antimicrobial activity can be effective against a broad spectrum of bacterial species especially those of medical importance. It has also been shown that there is considerable variation in the antimicrobial potency of different types of honey, which is impossible to predict. With this in mind we tested the antimicrobial activity of honeys produced from plants grown in South Africa for their antibacterial properties on selected standard strains of oral microorganisms. Methods: The honeys used were produced from the blossoms of Eucalyptus cladocalyx (Bluegum) trees, an indigenous South African plant Leucospermum cordifolium (Pincushion), a mixture of wild heather shrubs, mainly Erica species (Fynbos) and a Leptospermum scoparium (Manuka) honey. Only pure honey which had not been heated was used. The honeys were tested for their antimicrobial properties with a broth dilution method. Results: Although the honeys produced some inhibitory effect on the growth of the microorganisms, no exceptionally high activity occurred in the South African honeys. The carbohydrate concentration plays a key role in the antimicrobial activity of the honeys above 25%. However, these honeys do contain other antimicrobial properties that are effective against certain bacterial species at concentrations well below the hypertonic sugar concentration. The yeast C. albicans was more resistant to the honeys than the bacteria. The species S. anginosus and S. oralis were more sensitive to the honeys than the other test bacteria. Conclusion: The honeys produced from indigenous wild flowers from South Africa had no exceptionally high activity that could afford medical grade status. [ABSTRACT FROM AUTHOR]

Usnea barbata is a lichen of the Usneaceae family that grows epiphytieally on trunks and branches of trees. It is widespread in Hogsback South Africa. Extracts of the lichen were investigated for antimicrobial activity against 10 bacterial and 5 fungal strains by dilution method on solid agar medium. The extracts showed significant activity against the Gram-positive bacteria with minimum inhibitry concentration as low as 0.1 mg/ml on Bacillus subtillis, Entercoccus faecalis, Micrococcus viradans and Staphylococcus aureus. The acetone extract was the most active while the water extract showed the least activity against the microbes. Our findings have validated the use of the lichens for the treatment of various infections in man and livestock. [ABSTRACT FROM AUTHOR]

Trophic cascading resulting from the coupling between components of the microbial food comprising bacteria, phytoplankton and protozooplankton [nano- (2–20 μm) and microzooplankton (20–200 μm)] and mesozooplankton (copepods) (200–2000 μm) was investigated at three stations in the oligotrophic temperate Kariega estuary during the summer (February) and winter (May) 2001. Total chlorophyll a (Chl a) was dominated by picophytoplankton (<2 μm) throughout the study comprising between 55 and 74% of the total pigment during summer and between 64 and 78% of the total during winter. Among the heterotrophic components of the pelagic food web, nanozooplankton (HNAN) were identified as the most important consumers of bacteria and microzooplankton (MICRO) the primary consumers of Chl a. The low impact of the mesozooplankton (MESO) on the Chl a appears to be related to the size structure of the phytoplankton community in the estuary which is too small to be grazed efficiently by the larger zooplankton. In response to the unfavourable size structure of the phytoplankton community in the estuary, it is suggested that the MESO consume HNAN, MICRO and/or detritus. The negative impact of the MESO on the net growth rates of the HNAN and MICRO resulted in a decrease in the feeding impact of these organisms on the Chl a < 2 μm and bacteria. This result is consistent with the expectations of predator–prey cascades. [ABSTRACT FROM PUBLISHER]

Bacterial streak disease of maize is currently causing some concern among breeders in South Africa. The causal organism of this previously undescribed disease was successfully isolated and its pathogenicity established using KoCH's postulates. Standard physiological and biochemical tests used to identify phytopathogenic bacteria indicated that the bacterium is a Xantbomonas campestris pathovar. Comparisons between this organism and other recognized X. campestris pathovars of the Poaceae indicated that apart from some minor differences the maize streak pathogen is physiologically similar to X. campestris pv. holcicola. However, in repeated reciprocal inoculation experiments all attempts to induce disease symptoms in sorghum with the maize streak pathogen were unsuccessful. Conversely, X. campestris pv. holcicola did produce symptoms in maize leaves. In all the maize cultivars tested the symptoms produced by the maize streak pathogen were, however, always considerably more severe than those caused by X. campestris pv. holcicola. Notwithstanding its physiological similarity to X. campestris pv. holicola it would appear that on the grounds of host specificity the maize streak pathogen warrants new pathovar status. The name X. campestris pv. zeae is proposed. [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]