Companion animals harbour globally circulating human-associated Klebsiella pneumoniae lineages and high-risk antimicrobial resistance clones.

Abstract

Companion animals are increasingly recognised within One Health antimicrobial-resistance (AMR) surveillance, yet the global genomic structure of dog- and cat-associated Klebsiella pneumoniae remains poorly defined. We assembled a global dataset of 712 domestic dog (Canis lupus familiaris)– and cat (Felis catus)–derived K. pneumoniae genomes to define lineage diversity, AMR burden, host-associated patterns, and overlap with human-associated populations. Companion-animal isolates comprised 263 sequence types (STs), but recurrent high-risk lineages, including ST307, ST11, ST15, and ST147, were prominent. Among 706 isolates from 25 countries, extended-spectrum β-lactamase (ESBL) and carbapenemase genes were widely distributed, detected in 303 (42.9%) and 98 (13.9%) isolates, respectively. Cat-derived isolates showed higher multidrug-resistance (MDR) prevalence than dog-derived isolates; 80.0% versus 56.3%, partly reflecting enrichment of epidemic clones, especially ST147. MDR was not confined to infection-associated samples, indicating that colonisation may represent an important reservoir state. Comparison with 38,106 human-associated K. pneumoniae isolates revealed extensive ST overlap, with 71.1% of companion-animal STs and 87.2% of companion-animal isolates belonging to STs also detected in humans. Focused recombination-filtered phylogenomics of ST147 identified a closely related MDR cluster containing cat-, dog- and human-associated genomes, consistent with recent common ancestry and cross-host cocirculation. Together, these findings reveal domestic dogs and cats harbour globally distributed K. pneumoniae lineages and high-risk AMR clones also represented in human-associated populations.