RESUMO
Atypical Escherichia coli forms exhibit unusual characteristics compared to typical strains. The H2S-producing variants of some atypical E. coli strains cause a wide range of illnesses in humans and animals. However, there are sparse reports on such strains worldwide. We performed whole-genome sequencing (WGS) and detailed characterization of four H2S-producing E. coli variants from poultry and human clinical sources in Dhaka, Bangladesh. All four isolates were confirmed as E. coli using biochemical tests and genomic analysis, and were multidrug-resistant (MDR). WGS analysis including an additional Chinese strain, revealed diverse STs among the five H2S-producing E. coli genomes, with clonal complex ST10 being detected in 2 out of 5 genomes. The predominant phylogroup detected was group A (n = 4/5). The blaTEM1B (n = 5/5) was the most predominant extended-spectrum beta-lactamase (ESBL) gene, followed by different alleles of blaCTX-M (blaCTX-M -55,-65,-123; n = 3/5). Multiple plasmid replicons were detected, with IncX being the most common. One E. coli strain was classified as enteropathogenic E. coli. The genomes of all five isolates harbored five primary and four secondary function genes related to H2S production. These findings suggest the potential of these isolates to cause disease and spread antibiotic resistance. Therefore, such atypical E. coli forms should be included in differential diagnosis to understand the pathogenicity, antimicrobial resistance and evolution of H2S-producing E. coli.
RESUMO
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 Escherichia coli and Klebsiella pneumoniae 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 blaCTX-M-1 group, which was detected in 33.9% and 51.4% of E. coli and K. pneumoniae, 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 K. pneumoniae (27%). Nine isolates of E. coli (3.9%) harbored carbapenemase genes; blaNDM-1 (phylogenetic group A-sequence type 2104 (A-ST2104), B2-ST73), blaNDM-5 (A-ST167, B2-ST38/ST2659-related STs), and blaNDM-7 (B1-ST101/ST224, D-ST6682). AmpC beta-lactamase genes (blaCMY-2 and blaCMY-42) were detected in E. coli, which mostly harbored blaCTX-M-15 and plasmid-mediated quinolone resistance (PMQR) determinants (aac6'-Ib-cr, qnrB, qnrS, qepA, and oqxAB). A new CMY allele (CMY-160) belonging to CMY-2 group was identified in phylogenetic group D E. coli. Among K. pneumoniae, carbapenemase gene was detected in three isolates (2%); blaNDM-1 in ST11 and ST1322, and blaOXA-181 in ST43 isolate. As well as higher rate of aac6'-Ib-cr in K. pneumoniae (39%), PMQR gene oqxAB was also commonly found among isolates analyzed. These findings indicated spread of blaNDM genes to diverse E. coli clones and emergence of blaOXA-181 in K. pneumoniae, with increased prevalence of ESBLs represented by CTX-M-15 in Bangladesh.
