Bacterial diversity and functional profile of microbial populations on surfaces in public hospital environments in South Africa: A high throughput metagenomic analysis.

With the introduction of the One Health approach to global health advocated by the World Health Organization, the role of the environment as a reservoir and transmission route for diverse microorganisms is increasingly being recognised globally. This study investigated the diversity and functional profiles of bacterial communities using high-throughput metagenomics of the 16S rRNA gene in samples collected from environmental surfaces in different levels of healthcare in South Africa. A total of 150 samples were collected in three public hospitals [District (A), Regional (C) and Central (B)] from intensive care and paediatric wards. Military hospitals were excluded. Swabs were taken from mattresses, drip stands, ward telephones, patient files and sinks. A total of 7,996,346 reads were found, of which 7,319,569 were quality-filtered reads. Unique (and shared) microbial community structures were identified within the different hospital levels, locations and sample source. A total of 11 phyla, 29 classes, 50 orders, 105 families, 190 genera and 288 known species were identified. The primary phyla identified were Proteobacteria, Firmicutes and Actinobacteria. The dominant class identified was Gamma-proteobacteria, followed by Bacilli and Actinobacteria. Acinetobacter (16.08%), Citrobacter (13.64%), Staphylococcus (9.65%) and Corynebacterium (6.15%) were predominant genera. Although the functional profile analysis identified citrate cycle (TCA), signal transduction mechanisms, bisphenol degradation, tyrosine metabolism and transcription-factors as the dominant pathways, human disease functional classes, including involvement in antibiotic resistance, were significantly identified. The drip stands, patient files and ward telephones in all the wards of Hospitals A and C contained a higher number of human diseases functional classes. These findings highlight the potential of different hospital environments to serve as reservoirs and possible sources of bacterial pathogens; thus, the need for better monitoring and hygienic practices within the hospital environment.

Emergence and Spread of Extended Spectrum ß-Lactamase Producing Enterobacteriaceae (ESBL-PE) in Pigs and Exposed Workers: A Multicentre Comparative Study between Cameroon and South Africa.

Extended spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) represent a significant public health concern globally and are recognized by the World Health Organization as pathogens of critical priority. However, the prevalence of ESBL-PE in food animals and humans across the farm-to-plate continuum is yet to be elucidated in Sub-Saharan countries including Cameroon and South Africa. This work sought to determine the risk factors, carriage, antimicrobial resistance profiles and genetic relatedness of extended spectrum ß-lactamase producing Enterobacteriaceae (ESBL-PE) amid pigs and abattoir workers in Cameroon and South Africa. ESBL-PE from pooled samples of 432 pigs and nasal and hand swabs of 82 humans were confirmed with VITEK 2 system. Genomic fingerprinting was performed by ERIC-PCR. Logistic regression (univariate and multivariate) analyses were carried out to identify risk factors for human ESBL-PE carriage using a questionnaire survey amongst abattoir workers. ESBL-PE prevalence in animal samples from Cameroon were higher than for South Africa and ESBL-PE carriage was observed in Cameroonian workers only. Nasal ESBL-PE colonization was statistically significantly associated with hand ESBL-PE (21.95% vs. 91.67%; p = 0.000; OR = 39.11; 95% CI 2.02⁻755.72; p = 0.015). Low level of education, lesser monthly income, previous hospitalization, recent antibiotic use, inadequate handwashing, lack of training and contact with poultry were the risk factors identified. The study highlights the threat posed by ESBL-PE in the food chain and recommends the implementation of effective strategies for antibiotic resistance containment in both countries.