Whole-genome sequencing of MDR K. pneumoniae circulating in Moroccan river ecosystems: a comprehensive genomic analysis of environmental isolates

Abstract

BACKGROUND: Klebsiella pneumoniae is a major opportunistic pathogen and a recognized contributor to the global burden of antimicrobial resistance (AMR). Although traditionally associated with healthcare settings, it is increasingly detected in environmental compartments influenced by anthropogenic activities. Aquatic ecosystems may act as reservoirs and dissemination hubs for multidrug-resistant (MDR) lineages and resistance genes. However, genomic data on environmental K. pneumoniae in Morocco remain scarce. This pilot study aimed to characterize a targeted subset of MDR K. pneumoniae isolates recovered from Moroccan rivers using whole-genome sequencing (WGS), with a focus on resistance determinants, virulence-associated loci, plasmid content, and phylogenetic relationships. RESULTS: in a subset of isolates. The genomes also carried multiple determinants associated with resistance to other major antimicrobial classes. In addition, the isolates showed diverse plasmid backgrounds, heterogeneous virulence-associated loci, and substantial capsular diversity. Phylogenetic and pangenome analyses further indicated high intraspecific variability and extensive genome plasticity across the collection. CONCLUSIONS: This pilot study provides the first whole-genome-based characterization of river-derived MDR K. pneumoniae in Morocco. It demonstrates that aquatic ecosystems harbor genetically diverse lineages carrying clinically relevant resistance and virulence determinants. These findings underscore the imperative of integrating environmental surveillance into national AMR monitoring strategies within a One Health framework.