A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome

Abstract

Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) can colonise humans, animals, and various environments, and frequently cause nosocomial and community-acquired infections in humans. While plasmid-borne AMR genes are prevalent in clinical strains, the diversity, distribution, and association of plasmids encoding AMR and virulence across ecological niches remain poorly characterised. Understanding the traits governing successful plasmid transmission within and between ecological niches is critical for developing effective AMR prevention strategies. Here, we characterise the diversity and distribution of KpSC plasmids and identify potential niche associations of AMR, heavy metal resistance, virulence factors, and plasmid clusters. We analysed the plasmidome (i.e. total genetic content attributable to plasmids) of 578 whole-genome sequenced KpSC isolates collected in Norway between 2001-2020 from human (n=453), terrestrial animal (n=102), and marine (n=23) sources. Plasmids from complete hybrid assemblies were annotated and clustered to evaluate the plasmid diversity and content across niches. Additionally, the representativeness of this plasmid collection was determined by clustering with a global collection of 8656 circularised KpSC plasmids. In total, 1415 circularised plasmids were identified and grouped according to rearrangement distance using Pling, resulting in 130 clusters (containing >1 plasmid), of which 36% (n=47) contained plasmids from >1 niche. The plasmids exhibited significant diversity, as 37% (n=524) remained singletons after clustering. AMR and virulence genes existed across diverse clusters and singletons, but predominantly resided on 120-250 kbp conjugative or mobilisable plasmids harbouring various transposable elements. The human niche exhibited a significantly higher prevalence of plasmids with AMR genes compared to animal or marine niches (p<0.001), whereas the animal niche displayed a significantly higher prevalence of virulence-encoding plasmids compared to human or marine niches (p<0.001), which was largely due to an enrichment of iuc3 plasmids in pigs. The high diversity of the KpSC plasmids underscores the dynamic nature of plasmid evolution, driven by horizontal gene transfer, and selective pressures. The presence of variable clusters, marked by high genetic diversity, indicates a dynamic plasmidome capable of rapid adaptation to environmental pressures through the acquisition and rearrangement of accessory genes.