Abstract
BackgroundMultidrug-resistant (MDR) E. coli with extended-spectrum β-lactamases (ESBLs) is becoming endemic in health care settings around the world. Baseline data on virulence and antimicrobial resistance (AMR) of specific lineages of E. coli circulating in developing countries like India is currently lacking.MethodsWhole-genome sequencing was performed for 60 MDR E. coli isolates. The analysis was performed at single nucleotide polymorphism (SNP) level resolution to identify the presence of their virulence and AMR genes.ResultsGenome comparison revealed the presence of ST-131 global MDR and ST410 as emerging-MDR clades of E. coli in India. AMR gene profile for cephalosporin and carbapenem resistance differed between the clades. Genotypes blaCTX-M-15 and blaNDM-5 were common among cephalosporinases and carbapenemases, respectively. For aminoglycoside resistance, rmtB was positive for 31.7% of the isolates, of which 95% were co-harboring carbapenemases. In addition, the FimH types and virulence gene profile positively correlated with the SNP based phylogeny, and also revealed the evolution of MDR clones among the study population with temporal accumulation of SNPs. The predominant clone was ST167 (blaNDM lineage) followed by ST405 (global clone ST131 equivalent) and ST410 (fast spreading high risk clone).ConclusionsThis is the first report on the whole genome analysis of MDR E. coli lineages circulating in India. Data from this study will provide public health agencies with baseline information on AMR and virulent genes in pathogenic E. coli in the region.
Highlights
Escherichia coli is the leading cause of bloodstream infections (BSIs) [1] and other common infections including urinary tract infections (UTIs)
The analysis was performed at single nucleotide polymorphism (SNP) level resolution to identify the presence of their virulence and antimicrobial resistance (AMR) genes
AMR gene profile for cephalosporin and carbapenem resistance differed between the clades
Summary
Escherichia coli is the leading cause of bloodstream infections (BSIs) [1] and other common infections including urinary tract infections (UTIs). It has recently been reported that a large proportion of multi-drug resistant (MDR) E. coli carried by people is food acquired, especially from farm animals [3]. Most of the MDR E. coli are reported to be community acquired, recently MDR E. coli, which produce extended-spectrum β-lactamases (ESBLs) have been found to be endemic in health care settings [4,5]. Among MDR E. coli, AMR caused by ESBL is mainly due to the blaCTX-M family, blaCTX-M-15 and -14, compared to the less frequently observed blaSHV and blaOXA families [6,7,8]. Multidrug-resistant (MDR) E. coli with extended-spectrum β-lactamases (ESBLs) is becoming endemic in health care settings around the world. Baseline data on virulence and antimicrobial resistance (AMR) of specific lineages of E. coli circulating in developing countries like India is currently lacking
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