COMPARATIVE GENOMIC ANALYSIS OF MULTIDRUG RESISTANT BACTERIAL ISOLATES FROM CLINICAL AND ENVIRONMENTAL SOURCES

Abstract

Multidrug-resistant Escherichia coli is found in clinical and environmental settings, and there is a need to understand the variation in the range of resistances, genomic lineage or mobile genetic elements between these settings. This study compared six multidrug-resistant E. coli  genome assemblies comprising three clinical and three environmental isolates. Comparative whole-genome bioinformatics included genome characterisation, multilocus sequence typing, acquired antimicrobial resistance gene (ARG) profiling, resistance-class analysis, plasmid replicon typing, Mash-based genomic relatedness, and ARG Jaccard similarity. Environmental genomes carried 11–16 unique ARGs compared with 8–10 in clinical genomes and collectively contained 25 distinct ARGs versus 21 among clinical isolates. Eight ARGs were shared between sources, with an overall source-level Jaccard similarity of 0.211. ST69 occurred in both clinical and environmental isolates, while the closest genomic pair also comprised isolates from different sources. Mash distance showed a negative but non-significant association with resistome similarity (Spearman ρ = −0.500, P = 0.0577). Plasmid replicon richness ranged from one to seven per genome, with IncFIB(AP001918) being the most widely distributed replicon, while replicon richness was not associated with ARG burden (ρ = −0.058, P = 0.9131). These results show both unique and overlapping resistomes and genomic relatedness across multiple sources, providing a basis for genomic surveillance of antimicrobial resistance integrated across clinical and environmental compartments.