KPC-2 and VIM-1 producing Klebsiella pneumoniae ST39 high-risk clone isolated from a clinical sample in Volos, Greece.

Abstract

Klebsiella pneumoniae is a major human pathogen, because it causes both community- and hospital-acquired infections. Several multidrug-resistant high-risk clones of K. pneumoniae have been reported worldwide, and these are responsible for high numbers of difficult-to-treat infections. In Greece, a K. pneumoniae ST39 high-risk clone was detected in 2019 in a survey of carbapenem- and/or colistin-resistant Enterobacteriacae. The present study included nine carbapenem-resistant K. pneumoniae (CRKP) isolates collected during a retrospective analysis from October 2020 to December 2020. They were isolated from nine different patients hospitalized in the intensive care unit (ICU) of a hospital in Volos, Greece, and they were selected for analysis due to their phenotypic profile. In this study, we analyzed A165 strain K. pneumoniae ST39 isolated from a blood culture in November 2020. Whole-genome sequencing (WGS) was performed using Ion Torrent Platform, and resistance genes, virulence determinants, capsular types, insertion sequences, phage regions, and clustered regularly interspaced palindromic repeats (CRISPR) regions were detected by bioinformatic analysis. The molecular characterization revealed antimicrobial resistance genes, including sul2 for sulfamethoxazole; dfrA1 for trimethoprim; blaVIM-1 and blaKPC-2 for carbapenems; aac(6')-II for aminoglycosides; fosA for fosfomycin and aad1 for streptomycin, blaSHV-40, blaSHV-85, blaSHV-79, blaSHV-56, and blaSHV-89 for beta-lactams. Point mutations were identified in ompK36, and ompK37 and in acrR, gyrA, parC. Several replicons were found, including CoIRNA, IncC, IncFIB(K), IncFIB(pQiL), and IncFII(K). The capsular typing revealed that the strain was KL23, O2afg. The genome sequence of A165 was submitted to NCBI under PRJNA1074377 and have been assigned to Genbank accession number JAZIBV000000000.