Genomic epidemiology revealed the emergence and worldwide dissemination of ST383 carbapenem-resistant hypervirulent Klebsiella pneumoniae and hospital acquired infections of ST196 Klebsiella quasipneumoniae in Qatar

Abstract

The emergence of carbapenem-resistant (CR) hypervirulent Klebsiella pneumoniae (hvKp) is a new threat to healthcare. In this study, we studied the molecular epidemiology of CR Klebsiella isolates in Qatar using whole genome sequence data. We also characterised the prevalence and genetic basis of hypervirulent phenotypes, and established the virulence potential using a Galleria mellonella model. One hundred CR Klebsiella isolates were recovered, and NDM and OXA-48 were the most common carbapenemases. Phylogenetic analysis indicated the presence of diverse sequence types and clonal lineages; one of them belonged to K. quaisipneumoniae ST196 that may be disseminated among several health care centres. Ten K. pneumoniae isolates carrying rmpA and/or rmpA2, and 2 isolates belonged to KL2, indicating the prevalence of classical hypervirulent (hv) isolates was not high. Isolates carrying CR and hv genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated the blaNDM was located on an IncHI1B type plasmid (pFQ61_ST383_NDM-5), which also harbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from inversion and recombination events. In contrast, blaOXA-48 was located in an IncL-type plasmid. Comparative genomes indicated the recent evolution and emergence of CR-hv Kp ST383 via the acquisition of hybrid plasmids with both carbapenemase and virulence genes. CR-hv K. pneumoniae ST383 pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.

BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes

“…and Klebsiella spp. [ 39 , 40 , 41 , 42 ], implying that the ST028 isolate may be contaminated with Salmonella spp. and/or Klebsiella spp.…”

Case Report of blaNDM-7-Harboring IncX3 Plasmid in ST196 Klebsiella quasipneumoniae in China

“…ST196 K. quasipneumoniae has rarely been reported but can be present in health care centers worldwide, possibly leading to hospital-acquired infections. 7 …”

“…ST196 K. quasipneumoniae has rarely been reported but can be present in health care centers worldwide, possibly leading to hospital-acquired infections. 7 In 2013, bla NDM-7 was identified for the first time in Escherichia coli from a patient who had traveled to Burma and was hospitalized in France. 8 Owing to Asp-130-Asn and Met-154-Leu substitutions, NDM-7 has greater carbapenemhydrolyzing activity than NDM-1.…”