Molecular epidemiology and emergence of sequence type 25 hypervirulent Klebsiella pneumoniae in pigs in the Netherlands (2013-2020): a global comparative analysis with human and pig isolates

Abstract

Klebsiella pneumoniae (Kp), a ubiquitous pathogen found in diverse ecological niches, poses a threat to human and animal health. Hypervirulent Kp (hvKp) is concerning for its acquisition of virulence and antimicrobial resistance genes through plasmids. This study investigates hvKp as a cause of septicaemia in piglets in the Netherlands and examines the role of plasmids in virulence and host association. We collected 41 Kp isolates cultured from necropsies submitted from 15 different farms (2013-2020) and sequenced them using long-read sequencing. We identified sequence type (ST) 25 as the dominant Kp (67%, 10/15 farms) associated with septicaemia in pigs in the Netherlands. ST25 isolates displayed a hypervirulent profile, including the K2 hyper-capsule type and carried an iuc3 virulence plasmid. Further analysis revealed two ST25 clonal groups: CG25 and CG3804, a novel porcine clone. Multidrug resistance was identified in CG25 isolates from five pig farms. There was one colistin-resistant isolate carrying mcr-1 on a plasmid. Comparative genomic analysis was performed by including a large dataset of related publicly available Kp genomes from ST25 humans (n=230) and pigs (n=12) of all STs for phylogenetic and plasmid analysis. Pangenomic analysis revealed significantly higher iuc3 prevalence in global CG25 pig isolates (98%, 40/41) compared to humans (10%, 24/234) correlating with their enhanced virulence (scores 3-4 vs 0-1). The study highlights ST25 hvKp causing septicaemia in piglets in the Netherlands for the first time. Aerobactin lineage iuc3 on a plasmid is associated with infections in pigs and is responsible for an increased virulence score.