AUTHOR=Patel Mitul A. , Pandey Aparna , Patel A. C. , Patel S. S. , Chauhan H. C. , Shrimali M. D. , Patel Pankaj A. , Mohapatra S. K. , Chandel B. S. 

TITLE=Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.996214

DOI=10.3389/fmicb.2022.996214

ISSN=1664-302X

ABSTRACT=<p>Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing <italic>Escherichia coli</italic> constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL <italic>E. coli</italic> infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL <italic>E. coli</italic> in the Gujarat state of India. This study included 108 <italic>E. coli</italic> strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, <italic>bla</italic><sub>TEM</sub> (63.88%) was found to be the predominant genotype, followed by <italic>bla</italic><sub>SHV</sub> (30.55%) and <italic>bla</italic><sub>OXA</sub> (28.70%). In the <italic>bla</italic><sub>CTX-M</sub> group, a higher occurrence was observed in <italic>bla</italic><sub>CTX-M-9</sub> (23.14%), followed by <italic>bla</italic><sub>CTX-M-2</sub> (24.07%) and <italic>bla</italic><sub>CTX-M-1</sub> (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL <italic>E. coli</italic> isolated. We examined the genetic relatedness of a human pathogenic <italic>E. coli</italic> strain by comparing its sequence with the broad geographical reference <italic>E. coli</italic> sequences. <italic>Escherichia coli</italic> ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of <italic>Escherichia coli</italic> str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes <italic>viz.</italic>, <italic>tetA</italic>, <italic>qnrS1, dfrA14</italic>, <italic>sul2</italic>, <italic>aph(3”)-lb</italic>, <italic>aph(6)-ld</italic>, and <italic>Aph(3’)-la</italic>. The ST 681 was found to have <italic>Cib</italic>, <italic>traT</italic>, and <italic>terC</italic> virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL <italic>E. coli</italic> detected in poultry.</p>