Molecular epidemiology of antibiotic resistant ESKAPE pathogens isolated from public sector hospitals in uMgungundlovu District, KwaZulu-Natal, South Africa.

Abstract

Multi-drug resistant Enterococcus faecium, staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp termed ESKAPE pathogens are commonly implicated in difficult-to-treat infectious diseases in developed and developing countries. The prevalence, risk factors, phenotypic and genotypic profiles including but not limited to clonal relatedness, genetic diversity, resistance and virulence associated with ESKAPE bacteria were investigated in carriage and clinical isolates from patients in a rural, district and an urban tertiary hospital in the public health sector in uMgungundlovu District, Kwazulu- Natal, South Africa. The overall carriage of MDR ESKAPE Gram-negative bacteria in both hospitals was 37.21%, 42.31% and 57.14% at admission, after 48 hours and at discharge, respectively. The prevalence of MDR ESKAPE Gram-negative bacteria in faecal carriage (46%) was higher than clinical samples (28%) and colonization was mainly associated with referral from the district to the tertiary hospital with high statistical significance (OR: 14.40, 95% CI 0.98-210.84). blaCTX-M-group-9, blaCTX-M-group-1 and blaSHV were the main resistance genes identified. Similarly, the overall prevalence of faecal VRE carriage was 53% with patients at the district hospital being more likely to be colonized by VRE at admission (44%), after 48 hours (64%) and discharge (100%) than those of the tertiary level. Fifteen (39%) E. faecium and 23 (61%) E. faecalis, were detected and displayed high level of antibiotic resistance. Extensive genetic diversity of E. faecalis and E. faecium and clonal dissemination of various lineages were observed across wards and within hospitals. The high levels of resistance in S. aureus were attributed to the multi-drug resistant efflux pumps mepA, mexE, AcrB, MATE, qac and qacA. Whole genome analysis revealed that the circulating S. aureus isolates belonged to the extremely virulent ST121 clone that harboured a total of 18 virulence genes. The high prevalence, genetic diversity and virulence of antibiotic-resistant ESKAPE bacteria elucidated in this study necessitates routine screening and surveillance in communities and hospitals, stringent infection prevention and control measures and antibiotic stewardship to monitor epidemiological changes, to contain their spread and inform appropriate antibiotic treatment options respectively.