Genetic characterization of a clinical extensively drug resistant Klebsiella pneumoniae isolated in Ho Chi Minh City

Abstract

Klebsiella pneumoniae is one of the leading causes of hospital-acquired infections. The choice of effective antibiotic for treatment the extensively drug resistant (XDR) bacteria, which remain susceptible to only one or two antimicrobial categories, is in a serious predicament. We conducts this study aimed to describe, the genetic characterization of a clinical XDR Klebsiella pneumoniae (designed PIKP27) using whole-genome data which was sequenced by the Illumina MiSeq and Oxford Nanopore MinION platforms. The results indicated that PI15KP27 consisted of a 5,247,824-bp chromosome and three circular plasmids pKP27-MCR1, pKP27-NDM4 and pKP27-MPHA with sizes of 222.330bp, 144.138bp and 121.851bp, respectively. In addition to 29 genes identifed by Resfnder database, containing colistin resistance gene mcr-1 and carbapenem resistance gene blaNDM-4,
the CARD database provided more 14 genes involving in four antimicrobial resistance mechanisms including efux, inactivation, target alteration and reduced permeability to antibiotic. The presence of mobile genetic elements, such as
the plasmids, ISs, tra genes, gene cassette play important roles in evolution and diversity of multidrug resistant characteristic. The accumulation of multiple antibiotic resistance mechanisms in this clinical isolate raise alarm on potential spread of XDR K. pneumoniae in healthcare settings.