Abstract
Colistin is a last-resort antimicrobial used for the treatment of human infections caused by multidrug-resistant Gram-negative bacteria. However, colistin is still widely used in intensive poultry production in Bangladesh. We aimed to investigate the dynamics and genetic diversity of colistin-resistant commensal Escherichia coli from broiler chickens. A total of 1200 E. coli strains were characterized from 20 broiler farms at three-time points along the production period. All strains were screened for mcr-1 to mcr-5 genes by a multiplex PCR, and their genetic diversity was measured by repetitive extragenic palindromic (REP)-PCR fingerprinting. Genomic diversity and characterization were performed by whole genome sequencing (WGS). Twenty-five percent of the commensal E. coli strains harbored mcr-1 genes. Frequency of mcr-1 gene detection correlated positively (odds ratio 1.71; 95% CI 0.96–3.06; p = 0.068) with the use of colistin in poultry flocks. REP-PCR profiles and WGS analysis showed diverse E. coli population carrying multiple antimicrobial resistance genes. Phylogenetic comparison of mcr-1-bearing strains recovered from this study with a global strain collection revealed wide phylogenetic relationship. This study identified a high prevalence of mcr-1 gene among genetically diverse E. coli populations from broiler chickens in Bangladesh suggesting a massive horizontal spread of mcr-1 rather than by clonal expansion.
Highlights
The gut of warm-blooded animals is the primary habitat to Escherichia coli, and the type of relationship between E. coli and its host is mainly that of commensalism
It is well documented that the use of antimicrobial in food animal production is a possible source of AMR in humans through horizontal transfer of either antimicrobial resistance genes (ARGs) to human pathogens or through direct transfer of AMR bacteria[7,8]
The objectives of the current study were to investigate the genetic diversity of commensal E. coli in poultry, to explore the distribution and genetic background of colistin-resistant strains among the commensal E. coli population, and to characterize the phylogenetic relationship of the colistin-resistant commensal E. coli strains in the global population structure of E. coli
Summary
The gut of warm-blooded animals is the primary habitat to Escherichia coli, and the type of relationship between E. coli and its host is mainly that of commensalism. There is no systematic investigation on the colistin resistance commensal E. coli population in animals in this production system where imprudent use of antimicrobial is very frequent. The overall genetic diversity of the commensal E. coli population in broiler chicken over the entire production stage has not been investigated before. The genetic diversity of commensal E. coli from broiler chicken in Bangladesh was thoroughly investigated throughout the production period, and the prevalence of plasmid-encoded colistin resistance genes (mcr) was determined. The objectives of the current study were to investigate the genetic diversity of commensal E. coli in poultry, to explore the distribution and genetic background of colistin-resistant strains among the commensal E. coli population, and to characterize the phylogenetic relationship of the colistin-resistant commensal E. coli strains in the global population structure of E. coli
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