Evaluating surface water for genomic surveillance of community-linked antimicrobial resistance in ESBL-producing Klebsiella pneumoniae

Abstract

ABSTRACT A major limitation in wastewater-based epidemiology is its application in communities without centralised sewage systems necessitating alternative approaches. We evaluated surface water as an alternate antimicrobial resistance (AMR) monitoring interface by comparing the resistome, virulome, and phylogeny of extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) from surface water (SW), healthy residents (HR), and clinical (CL) settings. Ninety-six (SW=32, HR=32, CL=32) ESBL-Kp isolates collected over eight-months underwent comparative genomic analysis of antibiotic resistance genes (ARGs), virulence determinants, multilocus sequence types, and phylogenetic relatedness. Sixteen sequence types (STs) were identified across all sources. ST983 was shared by all sources, ST25 and ST219 were exclusive to SW-HR, and ST152 to SW-CL. More SW (93.8%) isolates shared STs with HR than with CL (9.4%). Phylogenomic analysis was lineage-driven rather than source-structured, with SW isolates forming stronger subclades with HR through ST25 and ST219. Resistome composition showed substantial overlap with differences ( p = 0.003). The dominant β-lactamase ARG in all sources was bla CTX-M-15 , alongside non-β-lactam sul2 and dfrA14 . Pairwise exclusive ARGs totalled 20 (CL-HR), seven (SW-HR), and two (SW-CL); source-restricted ARGs totalled fourteen, nine, and none for CL, HR, and SW, respectively. SW-HR. Virulome overlap was driven by ST25/KL2 and ST219/KL114, a limited SW-CL link was observed through ST152/KL149, and source-restricted lineages were concentrated mainly in clinical and healthy resident isolates. SW shared major ESBL-Kp AMR features with both HR and CL, but distribution differed across sources. SW more closely resembled HR, supporting its use as a complementary tool rather than a standalone approach for AMR surveillance.