Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental $\textit{Klebsiella pneumoniae}$

Abstract

$\textbf{BACKGROUND}$: $\textit{Klebsiella pneumoniae}$ is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly diverse population of $\textit{K. pneumoniae}$, the evolution and clinical significance of environmental $\textit{K. pneumoniae}$, as well as the relationship between clinical and environmental $\textit{K. pneumoniae}$, are poorly defined. $\textbf{METHODS}$: We isolated and sequenced $\textit{K. pneumoniae}$ from in-patients in a single hospital in Thailand, as well as hospital sewage, and surrounding canals and farms within a 20-km radius. $\textbf{RESULTS}$: Phylogenetic analysis of 77 K. pneumoniae (48 clinical and 29 non-clinical isolates) demonstrated that the two groups were intermixed throughout the tree and in some cases resided in the same clade, suggesting recent divergence from a common ancestor. Phylogenetic comparison of the 77 Thai genomes with 286 $\textit{K. pneumoniae}$ from a global collection showed that Thai isolates were closely related to the clinical sub-population of the global collection, indicating that Thai clinical isolates belonged to globally circulating lineages. Dating of four Thai $\textit{K. pneumoniae}$ clades indicated that they emerged between 50 and 150 years ago. Despite their phylogenetic relatedness, virulence factors and β-lactamase resistance genes were more numerous in clinical than in environmental isolates. Our results indicate that clinical and environmental $\textit{K. pneumoniae}$ are closely related, but that hospitals may select for isolates with a more resistant and virulent genotype. $\textbf{CONCLUSIONS}$: These findings highlight the clinical relevance of environmental K. pneumoniae isolates.