Whole-Genome Analysis of a High-Risk Clone of <i>Klebsiella pneumoniae</i> ST147 Carrying Both <i>mcr-1</i> and <i>bla</i> _NDM-1 Genes in Peru

Abstract

The increasing prevalence and dissemination of carbapenemase-producing Enterobacterales represent a serious concern for public health. We studied the genetic features of a multidrug-resistant isolate of high-risk clone ST147 Klebsiella pneumoniae coharboring mcr -1 and bla NDM-1 recovered from a human clinical urine sample in 2017 in Peru. Whole-genome sequencing and conjugation assays identified mcr-1 and bla NDM-1 genes on two different conjugative plasmids, which belong to IncI2 and IncFIB/HI1B incompatibility groups, respectively. The presence of bla CTX-M-15 (in the studied isolate, located on the chromosome) and mutations in GyrA S83I and ParC S80I were detected, as expected for ST147. In addition, other β-lactamases ( bla TEM-26 and bla OXA-1 ) and PMQR ( qnrE2 and aac(6′)-Ib-cr ) among several resistance determinants were identified. The coexistence not previously described of these genes in the same high-risk clone is a cause for serious concern that supports the need for implementation of genomic surveillance studies.