Prevalence and Molecular Epidemiology of Clinical Isolates of <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> Harboring Extended-Spectrum Beta-Lactamase and Carbapenemase Genes in Bangladesh

Abstract

Spread of Gram-negative bacteria producing extended-spectrum beta-lactamases (ESBLs) and carbapenemases constitutes a growing challenge in control of bacterial infections. In this study, prevalence and genetic characteristics of <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> harboring ESBL and/or carbapenemase genes, with other beta-lactamase/resistance genes, were investigated for a total of 375 clinical isolates in Mymensingh located in north-central Bangladesh. The major ESBL gene was <i>bla</i>_CTX-M-1 group, which was detected in 33.9% and 51.4% of <i>E. coli</i> and <i>K. pneumoniae</i>, respectively, with CTX-M-15 gene being dominant. SHV-type beta-lactamase genes, including newly identified alleles (SHV-201 and SHV-202) were detected at higher rate in <i>K. pneumoniae</i> (27%). Nine isolates of <i>E. coli</i> (3.9%) harbored carbapenemase genes; <i>bla</i>_NDM-1 (phylogenetic group A-sequence type 2104 (A-ST2104), B2-ST73), <i>bla</i>_NDM-5 (A-ST167, B2-ST38/ST2659-related STs), and <i>bla</i>_NDM-7 (B1-ST101/ST224, D-ST6682). AmpC beta-lactamase genes (<i>bla</i>_CMY-2 and <i>bla</i>_CMY-42) were detected in <i>E. coli</i>, which mostly harbored <i>bla</i>_CTX-M-15 and plasmid-mediated quinolone resistance (PMQR) determinants (<i>aac6'-Ib-cr</i>, <i>qnrB</i>, <i>qnrS</i>, <i>qepA</i>, and <i>oqxAB</i>). A new CMY allele (CMY-160) belonging to CMY-2 group was identified in phylogenetic group D <i>E. coli</i>. Among <i>K. pneumoniae</i>, carbapenemase gene was detected in three isolates (2%); <i>bla</i>_NDM-1 in ST11 and ST1322, and <i>bla</i>_OXA-181 in ST43 isolate. As well as higher rate of <i>aac6'-Ib-cr</i> in <i>K. pneumoniae</i> (39%), PMQR gene <i>oqxAB</i> was also commonly found among isolates analyzed. These findings indicated spread of <i>bla</i>_NDM genes to diverse <i>E. coli</i> clones and emergence of <i>bla</i>_OXA-181 in <i>K. pneumoniae</i>, with increased prevalence of ESBLs represented by CTX-M-15 in Bangladesh.