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

## TL;DR

This study explores the diversity of plasmids in Klebsiella pneumoniae across different environments, revealing their adaptability and role in spreading antibiotic resistance and virulence.

## Contribution

The study identifies shared plasmid clusters across ecological niches and highlights their potential for rapid adaptation and gene transfer.

## Key findings

- Plasmids from human, animal, and marine isolates form shared genetic clusters spanning ecological boundaries.
- Human isolates carry higher plasmid burdens and most AMR-encoding plasmids.
- Animal isolates are enriched for virulence plasmids, particularly iuc3 plasmids in pigs.

## Abstract

Plasmids play a pivotal role in the horizontal gene transfer (HGT) of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) can colonize 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 characterized. Understanding the traits governing successful plasmid transmission within and between ecological niches is critical for developing effective AMR prevention strategies. Here, we identify ecological and structural factors shaping plasmid persistence and dissemination. We analysed the plasmidome (i.e. total genetic content attributable to plasmids) of 578 whole-genome sequenced KpSC isolates collected in Norway between 2001 and 2020 from human (n=453), 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 8,656 circularized KpSC plasmids. In total, 1,415 circularized plasmids were identified and grouped according to rearrangement distance using Pling, resulting in 130 clusters (≥2 plasmids each), of which 36% (n=47) contained plasmids from more than one 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 mobilizable plasmids harbouring various transposable elements. Human isolates carried higher overall plasmid burdens and harboured most AMR-encoding plasmids, while animal isolates were significantly enriched for virulence plasmids (P<0.001), largely due to iuc3 plasmids in pigs. Plasmids from human, animal and marine isolates formed shared genetic clusters spanning ecological boundaries, revealing the existence of widely distributed backbones already primed for AMR gene acquisition. The extensive diversity of KpSC plasmids highlights the dynamic nature of plasmid evolution, driven by HGT 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.