Molecular epidemiology of antibiotic resistant ESKAPE pathogens isolated from public sector hospitals in uMgungundlovu District, KwaZulu-Natal, South Africa.
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2017
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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.
Description
Doctor of Philosophy in Medical Microbiology. University of KwaZulu-Natal. Durban, 2017.