Population structure of multidrug resistant Klebsiella oxytoca within hospitals across the UK and Ireland identifies sharing of virulence and resistance genes with K. pneumoniae.

Danesh Moradigaravand,Julian Parkhill,Veronique Martin,Sharon J Peacock

doi:10.1093/gbe/evx019

Abstract

Klebsiella oxytoca, a member of the Enterobacteriaceae, is a gram-negative pathogenic bacterium of environmental origin, which can cause infection in healthcare settings. Outbreaks of multidrug-resistant K. oxytoca infection have been increasingly reported in hospitalized patients. Despite the growing importance of this pathogen, there is limited knowledge about the population structure and epidemiology of antimicrobial resistant K. oxytoca. We investigated the population structure and genomic basis of antimicrobial resistance of 41 multidrug resistant K. oxytoca isolates recovered from bloodstream infections across the UK and Ireland. Our results show that K. oxytoca has a highly diverse population, which is composed of several distinct clades, and we identified one recent expansion of a clone within our dataset. Although the K. oxytoca genomes are clearly distinct from the genomes of a global collection of Klebsiella pneumoniae complex, pre-dominantly composed of K. pneumoniae, we found evidence for sharing of core genes through recombination, as well as the exchange of accessory antimicrobial resistance and virulence factor genes between the species. Our findings also suggest that the different K. oxytoca clades have acquired antimicrobial resistance and virulence factor genes independently. This highlights the clinical and therapeutic importance of genetic flexibility in K. oxytoca and the relevance of this in its role as an opportunistic pathogen.

Highlights

Klebsiella oxytoca is an important member of the genusKlebsiella, which contains species that cause nosocomial and community acquired infections worldwide (Bagley 1985; Broberg et al 2014; Podschun and Ullmann 1998).Originating from the environment, K. oxytoca typically resides in the intestinal tract as a commensal bacterium but can spread to the bloodstream and cause disease, in particular in patients with a compromised immune system (Al-Anazi et al.2008; Tang and Chen 1995)
It is known that the variants of the chromosomally encoded beta-lactamase-OXY define major phylogroups of this species, and the evolution of blaoxy was thought to have occurred congruently with the evolution of K. oxytoca (Fevre et al 2005)
We found that four variants of blaoxy are present in the isolates and correspond to the phylogenetic groups KoI, KoII, KoVI, and KoV on the whole genome tree, respectively

Summary

Introduction

Klebsiella oxytoca is an important member of the genusKlebsiella, which contains species that cause nosocomial and community acquired infections worldwide (Bagley 1985; Broberg et al 2014; Podschun and Ullmann 1998).Originating from the environment, K. oxytoca typically resides in the intestinal tract as a commensal bacterium but can spread to the bloodstream and cause disease, in particular in patients with a compromised immune system (Al-Anazi et al.2008; Tang and Chen 1995). Klebsiella, which contains species that cause nosocomial and community acquired infections worldwide (Bagley 1985; Broberg et al 2014; Podschun and Ullmann 1998). Klebsiella oxytoca outbreaks generally have environmental sources, and are subsequently propagated by the dissemination of the pathogen in healthcare settings, for example, in transplant, intensive care, or neonatal units (Bagley 1985; Decre et al 2004; Lowe et al 2012; Zarate et al 2008). Outbreaks of K. oxytoca usually involve strains with extended-spectrum beta-lactamases and carbapenamases (Decre et al 2004; Lowe et al 2012; Schulz-Stubner and Kniehl 2011; Zarate et al 2008), which enable bacterial resistance to betalactam antibiotics and lead to therapeutic problems (Wu et al 1991, 1999).

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