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bioRxiv · 10.64898/2026.06.13.732079

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

Fordham, S. M. E.·Sheridan, E.·Drobniewski, F.
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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- and cat-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 {beta}-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 recent host-spanning MDR sub-lineage linking cat-, dog- and human-associated genomes. Together, these findings show that domestic dogs and cats are not epidemiologically separate from the wider K. pneumoniae AMR landscape, but harbour globally circulating human-associated lineages and high-risk AMR clones.

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Fordham, S. M. E., Sheridan, E., Drobniewski, F.. 2026-06-15. Companion animals harbour globally circulating human-associated Klebsiella pneumoniae lineages and high-risk antimicrobial resistance clones. https://doi.org/10.64898/2026.06.13.732079

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