Genomic epidemiology of carbapenemase producing klebsiella pneumoniae strains at a northern portuguese hospital enables the detection of a misidentified klebsiella variicola kpc-3 producing strain

João Perdigão, Cátia Caneiras, Rita Elias, Ana Modesto, Anton Spadar, Jody Phelan, Susana Campino, Taane G. Clark, Eliana Costa, Maria José Saavedra, Aida Duarte

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)

Abstract

The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicola n = 1; K. pneumoniae n = 2) and Tn4401d isoform (K. pneumoniae n = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.

Original languageEnglish
Article number1986
Pages (from-to)1-18
Number of pages18
JournalMicroorganisms
Volume8
Issue number12
DOIs
Publication statusPublished - Dec 2020
Externally publishedYes

Keywords

  • Carbapenemase
  • Enterobacteriaceae
  • Gram-negative
  • KPC-3
  • Klebsiella pneumoniae
  • Klebsiella variicola
  • Molecular epidemiology
  • OXA-48
  • Portugal
  • Whole-genome sequencing

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