Deciphering the Epidemiological Characteristics and Molecular Features of blaKPC–2- or blaNDM–1-Positive Klebsiella pneumoniae Isolates in a Newly Established Hospital

Abstract

The emergence of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) was regarded as an emerging threat in clinical settings. Here, we investigated the prevalence of CRKP strains among inpatients in a new hospital over 1 year since its inception with various techniques, and carried out a WGS-based phylogenetic study to dissect the genomic background of these isolates. The genomes of three representative blaNDM–1-positive strains and the plasmids of four blaKPC–2-positive strains were selected for Nanopore long-read sequencing to resolve the complicated MDR structures. Thirty-five CRKP strains were identified from 193 K. pneumoniae isolates, among which 30 strains (85.7%) harbored blaKPC–2, whereas the remaining five strains (14.3%) were positive for blaNDM–1. The antimicrobial resistance profiles of blaNDM–1-positive isolates were narrower than that of blaKPC–2-positive isolates. Five isolates including two blaNDM–1-positive isolates and three blaKPC–2-positive strains could successfully transfer the carbapenem resistance phenotype by conjugation. All CRKP strains were categorized into six known multilocus sequence types, with ST11 being the most prevalent type. Phylogenetic analysis demonstrated that the clonal spread of ST11 blaKPC–2-positive isolates and local polyclonal spread of blaNDM–1-positive isolates have existed in the hospital. The blaNDM–1 gene was located on IncX3, IncFIB/IncHI1B, and IncHI5-like plasmids, of which IncFIB/IncHI1B plasmid has a novel structure. By contrast, all ST11 isolates shared the similar blaKPC–2-bearing plasmid backbone, and 11 of them possessed pLVPK-like plasmids. In addition, in silico virulome analysis, Galleria mellonella larvae infection assay, and siderophore secretion revealed the hypervirulence potential of most blaKPC–2-positive strains. Given that these isolates also had remarkable environmental adaptability, targeted measures should be implemented to prevent the grave consequences caused by hv-CRKP strains in nosocomial settings.

Epidemiological characteristics and molecular features of carbapenem-resistant Enterobacter strains in China: a multicenter genomic study

“…In this study, bla NDM -harbouring IncX3-type plasmids were the most common plasmids among all carbapenemase-encoding plasmids. The IncX3-type plasmid was self-transmissible, which has been confirmed in this study and previous reports [ 18 , 19 ]. Furthermore, the same IncX3-type plasmid was detected in E. xiangfangensis strains belonging to different clones.…”

Genomic and functional characterization of carbapenem-resistant Klebsiella pneumoniae from hospital wastewater

“…Meanwhile, many studies characterized the genetic environments of bla KPC-2 and various mobile genetic elements played a critical role in the rapid spread of bla KPC-2 [ 35 , 36 ]. In this study, we found that the genetic environments of bla KPC−2 shared the core structure with IS Kpn27 - bla KPC−2 -IS Kpn6 , which was similar to the previous study [ 37 ]. Bacteria could acquire preexisting resistance determinants to promote drug resistance, which was achieved through the concerted activities of mobile genetic elements (such as IS, transposons) and plasmids and integrative conjugative elements [ 38 ].…”

Epidemiology of carbapenem-resistant Klebsiella pneumoniae ST15 of producing KPC-2, SHV-106 and CTX-M-15 in Anhui, China

“…imipenem, meropenem and doripenem) have become the last line of defense in the treatment of K. pneumoniae infections [ 3 ]. Unfortunately, due to the spread of mobile genetic elements has led to a steady increasing in CRKP [ 4 ]. The World Health Organisation (WHO) issued a report in 2017 highlighting the serious threat posed by carbapenem-resistant K. pneumoniae (CRKP) [ 5 ].…”