One Health genomic surveillance of Klebsiella pneumoniae in Belgium demonstrates large genomic diversity, presence of ESBLs and carbapenemases and circulation of clones across sectors
Abstract
Klebsiella pneumoniae is an important reservoir and disseminator of antimicrobial resistance (AMR) genes. Multidrug-resistant lineages, particularly extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant strains, represent an important public health threat. This study characterized antimicrobial resistance and genomic diversity of K. pneumoniae across One Health compartments in Belgium and investigated genomic relatedness within and across sectors. Between 2019 and 2022, 888 presumptive K. pneumoniae isolates were collected from diseased animals ( n = 311), wastewater ( n = 299), the food chain ( n = 178), and human clinical samples ( n = 100). Following selection based on isolation source and AMR characteristics, 286 WGS-confirmed K. pneumoniae isolates were characterized for AMR and virulence determinants, plasmid replicons, population structure, and phylogenomic relatedness. Phenotypic and genotypic resistance showed high concordance for third-generation cephalosporins (93.4%) and carbapenems (89.2%). Carbapenemase genes encoding KPC, NDM, OXA-48-like, and VIM enzymes were detected in 67 isolates from humans ( n = 56) and wastewater ( n = 11), but not in food-chain or diseased-animal isolates. Population structure was highly diverse, with ST307, ST15, ST147, and ST11 representing the most frequently detected high-risk lineages. Thirteen novel STs were identified in 18 K. pneumoniae isolates. Seventeen genomic clusters were identified, including 13 within-sector and four cross-sector clusters. Notably, an ST147 cluster comprising two poultry-meat isolates and a human clinical isolate showed no SNP differences, indicating very close genomic relatedness across sectors. Overall, our findings demonstrate a genetically diverse K. pneumoniae population alongside the circulation of clinically relevant high-risk lineages across One Health compartments and support integrated genomic surveillance to better understand their dissemination.