Genomic Surveillance of ESBL-Producing Klebsiella pneumoniae Across Municipal Wastewater and Food Animal Production Environments

Extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-K. pneumoniae) is a priority antimicrobial-resistant pathogen with the capacity to persist and disseminate across environmental and food animal production systems. This study conducted genomic surveillance of ESBL-K. pneumoniae recovered from municipal wastewater treatment plants and food animal production environments in Fayetteville, North Carolina. A total of 449 wastewater and livestock farm environment samples were analyzed. K. pneumoniae was recovered from 162 (36.1%) samples, including 68 (15.1%) ESBL-producing isolates. Antimicrobial susceptibility testing showed that 77.9% of ESBL-producing isolates were multidrug-resistant. Polymerase chain reaction identified blaCTX-M-1, blaSHV, and blaACT as the predominant resistance genes. Whole-genome sequencing of selected isolates identified diverse antimicrobial resistance determinants, virulence-associated genes, and plasmid replicons, with IncFIB(K) being the predominant plasmid type. Phylogenetic analysis demonstrated close genetic relatedness between wastewater and farm environment isolates, with some differing by only 0–6 single-nucleotide polymorphisms, suggesting possible dissemination between environmental reservoirs. These findings highlight municipal wastewater and food animal production environments as important reservoirs of ESBL-K. pneumoniae and reinforce the value of integrated genomic surveillance within a One Health framework to monitor the emergence and spread of antimicrobial resistance.