Molecular epidemiology of antibiotic resistant ESKAPE and escherichia coli pathogens isolated from bloodstream infections in public sector hospitals in uMgungundlovu district, KwaZulu-Natal, South Africa.

Abstract

Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. (ESKAPE) pathogens and Escherichia coli (ESKAPEEc) are major contributors to bloodstream infections (BSIs) and pose significant treatment challenges. This study describes the molecular epidemiology and genomic profiles of ESKAPEEc isolates from BSIs in two public hospitals in the uMgungundlovu District, South Africa. Blood samples (n = 195) were collected from adult and paediatric patients with suspected BSIs between November 2017 and December 2018. Isolates were identified using VITEK 2 system, and confirmed by polymerase chain reaction (PCR). Antimicrobial susceptibility testing was performed using the Kirby–Bauer disk diffusion method and interpreted according to EUCAST/CLSI guidelines. Whole-genome sequencing (WGS) and bioinformatics tools were used to determine the resistome, virulome, mobilome, clonality and phylogenies of selected K. pneumoniae, K. oxytoca, and S. aureus isolates. Out of 195 presumptive isolates, 159 were confirmed as ESKAPEEc. K. pneumoniae (28.9%) and S. aureus (28.3%) were the most predominant pathogens. In total, 151 (94.9%) of isolates were multi-drug resistant (MDR). K. pneumoniae and K. oxytoca carried β-lactamase genes including the blaCTX-M-15, blaOXA-1, blaTEM-1B, blaSHV, and blaOXY genes. The blaCTX-M-15 and blaTEM-1 genes were associated with Tn3 transposons and insertion sequences (ISs) (ISEc9, IS91). Virulence genes detected in Klebsiella spp. were associated with ISs (IS1, IS3, IS630) and integrase. Six sequenced S. aureus isolates harboured ARGs including blaZ, aac(6′ )- aph(2′′), ant(9)-Ia, ant(6)-Ia, and fosB among others. Most ARGs were associated with ISs (IS6, IS1182) and recombinase. Virulence genes identified in S. aureus isolates were mostly associated with ISs, recombinases and integrases. Phylogenetic analysis of selected K. pneumoniae and S. aureus isolates revealed clear grouping patterns based on Multilocus Sequence Typing (MLST) and geographic origin. WGS and bioinformatics analysis revealed that Klebsiella strains and S. aureus have a rich repertoire of ARGs, virulence genes, and MGEs in several permutations and combinations, indicating a complex situation of mobilized antibiotic resistance and pathogenic characteristics in clonal and multi-clonal strains responsible for BSIs in this healthcare context.