Genetic Relatedness of NDM-Producing Klebsiella pneumoniae Co-Occurring VIM, KPC, and OXA-48 Enzymes from Surveillance Cultures from an Intensive Care Unit.

Abstract

Klebsiella pneumoniae is an opportunistic bacterial pathogen most commonly associated with nosocomial infections, especially in intensive care unit (ICU) patients. Routine surveillance cultures for carbapenemase-producing Enterobacteriaceae have become a common practice for hospital infection prevention. The objective of this study was to investigate the genetic relatedness of carbapenem-resistant K. pneumoniae carrying blaNDM gene across multilocus sequence typing (MLST) scheme. Surveillance rectal swabs from 4,463 ICU patients admitted to the Rio de Janeiro hospital (March 2016-2017) were screened on CHROMagar mSuperCARBA. Of these, 631 isolates were subjected to VITEK 2 system for phenotypic microbial identification and antibiotic susceptibility testing. Out of 631 isolates, 108 were identified as K. pneumoniae, 103 of which were confirmed by PCR of 16S-23S rDNA internal transcribed spacer (ITS). Eleven blaNDM-positive isolates were subsequently screened for blaKPC, blaBKC, blaIMP, blaVIM, blaSPM, blaOXA-48, and mcr-1-8 genes. Twenty-seven percent (3/11) revealed co-occurrence with KPC, OXA-48, and VIM, 46% (5/11) with KPC and VIM, and 18% (2/11) with VIM type. No strains harbored the blaBKC, blaSPM, blaIMP, and mcr-1 to 8 resistance genes. All 11 isolates were resistant to β-lactams, ciprofloxacin 90%, tigecycline 82%, gentamicin 73%, and amikacin 18%, and were classified as multidrug resistant (MDR), extensively drug resistant (XDR), and pandrug resistant (PDR). Molecular epidemiology data based on MLST revealed 11 different STs, 8 of which were novel and 3 were previously described. Six out of the eight new STs were associated with MDR and PDR strains and two clonal complexes were reported, including CC258 and CC15. The coexistence of NDM-producing K. pneumoniae and other carbapenemase has been frequently described worldwide. Moreover, we report for the first time K. pneumoniae co-harboring up to four carbapenemases from active surveillance cultures.