Decoding genotypic antimicrobial resistance amongst colistin-resistant Gram-negative bloodstream isolates at a South African academic healthcare facility

BACKGROUND: Genotyping is essential for identifying the relatedness of multidrug-resistant organisms (MDROs), particularly in outbreak situations. This study outlines the genotypic antimicrobial resistance (AMR) characteristics of Gram-negative bacteria (GNB) isolated from bloodstream infections (BSI) in paediatric patients admitted to a tertiary academic hospital in Soweto from January 2023 to August 2024. METHODS: Whole genome sequencing (WGS) using Illumina (USA) short-read technology, followed by bioinformatics analysis, was performed on phenotypically confirmed colistin-resistant (CR) Klebsiella pneumoniae (CRKP; n = 24), CR Acinetobacter baumannii (CRAB; n = 3), and CR Escherichia coli (CREC; n = 1) isolates. RESULTS: High-risk global clones of CRKP carrying New Delhi metallo-β-lactamase (blaNDM) and oxacillinase (blaOXA-48) included all sequence type (ST) 17 isolates and a single ST2497 isolate exhibiting mgrB gene mutations denoting colistin-resistance. Phylogenetic clustering of seventeen ST2497 isolates indicated possible outbreak-related strains. The mechanism of the two-component system sensor histidine kinase PmrB was the source of the colistin-resistance expressed in the E. coli O157:H7 (ST11), a notable enterohaemorrhagic diarrhoeal strain that exhibited diverse AMR. No plasmid or chromosomal-mediated colistin-resistance was detected among the CRAB isolates (Two belonged to ST2, and one was ST1). CONCLUSION: This study highlights mgrB and PmrB mutants as chromosomal mechanisms of colistin-resistance amongst the K. pneumoniae and E. coli causing paediatric BSI. Genomic surveillance is necessary for monitoring high-risk bacterial clones that cause invasive infections in paediatric wards. Further research is warranted into the molecular characterisation of GN bacteria causing healthcare-associated infections from sites other than BSI.