Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST147 Carrying Both mcr-1 and blaNDM-1 Genes in Peru

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 beta-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.

Automated summary

The study identified a high-risk clone ST147 Klebsiella pneumoniae carrying multiple resistance genes including mcr-1 and bla(NDM-1), posing a serious public health risk. The findings support the need for implementation of genomic surveillance studies.