Co-occurrence of Rapid Gene Gain and Loss in an Interhospital Outbreak of Carbapenem-Resistant Hypervirulent ST11-K64 Klebsiella pneumoniae.

Xiaotuan Zhang,Linlin Zhou,Haijian Zhou,Logen Liu,Zhuoran Liu,Tong Zeng,Hongtao Jiang,Wenwen He,Bin Liu,Yunsheng Zhang,Jinglin Ouyang

doi:10.3389/fmicb.2020.579618

Abstract

We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals that undergo frequent patient transfers. Analysis of 11 completely assembled genomes showed that the bacteria were ST11-K64 strains. Moreover, 12 single nucleotide polymorphisms (SNPs) identified the strains as having originated from the same cluster, and were also indicative of the interhospital transmission of infection. Five plasmids were assembled in each of the strains. One plasmid carried several virulence genes, including the capsular polysaccharide regulators rmpA and rmpA2. Two others carried antimicrobial-resistance genes, including one for carbapenem resistance, blaKPC–2. Comparative genomic analysis indicated the occurrence of frequent and rapid gain and loss of genomic content along transmissions and the co-existence of progeny strains in the same ward. A 10-kbp fragment harboring antimicrobial resistance-conferring genes flanked by insert sequences was missing in a plasmid from strain KP20194c in patient 3, and this strain also likely subsequently infected patient 4. However, strains containing the 10-kbp fragment were also isolated from the ward environment at approximately the same time, and harbored different chromosome indels. Tn1721 and multiple additional insert sequence-mediated transpositions were also seen. These results indicated that there is a rapid reshaping and diversification of the genomic pool of K. pneumoniae facilitated by mobile genetic elements, even a short time after outbreak onset. ST11-K64 CR-hvKP strains have the potential to become new significant superbugs and a threat to public health.

Highlights

MATERIALS AND METHODSKlebsiella pneumoniae is a gram-negative bacterium that can cause both community-acquired and nosocomial infections
Our 13 isolates were cultured from samples obtained from five patients and from the environment during an outbreak of multidrug-resistant K. pneumoniae in two hospitals that had frequent interhospital patient transfer
Between late March and April 2019, four CR-hypervirulent K. pneumoniae (hvKP) strains were isolated from the sputum of two patients presenting with critical lung infections at the neurosurgery unit of a secondary hospital, and one strain was isolated from the bedsheets of patient 1

Summary

Introduction

MATERIALS AND METHODSKlebsiella pneumoniae is a gram-negative bacterium that can cause both community-acquired and nosocomial infections. Recently reported cases or outbreaks of K. pneumoniae infection showed convergent virulence and resistance, resulting in the emergence of CRhvKP, and the K47 and K64 serotypes, in addition to K1 and K2 (Zhang et al, 2016; Feng et al, 2018; Gu et al, 2018; Shen et al, 2019; Zhao et al, 2019).

Results

Conclusion