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

Mitul A Patel; Aparna Pandey; A C Patel; S S Patel; H C Chauhan; M D Shrimali; Pankaj A Patel; S K Mohapatra; B S Chandel

doi:10.3389/fmicb.2022.996214

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

Front Microbiol. 2022 Oct 14:13:996214. doi: 10.3389/fmicb.2022.996214. eCollection 2022.

Authors

Mitul A Patel¹, Aparna Pandey², A C Patel³, S S Patel³, H C Chauhan³, M D Shrimali⁴, Pankaj A Patel⁵, S K Mohapatra⁴, B S Chandel⁴

Affiliations

¹ Department of Biotechnology, Sankalchand Patel University, Visnagar, India.
² Department of Biochemistry, Dental College, Sankalchand Patel University, Visnagar, India.
³ Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India.
⁴ Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India.
⁵ Department of Physiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India.

Abstract

Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli 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 E. coli in the Gujarat state of India. This study included 108 E. coli 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, bla _TEM (63.88%) was found to be the predominant genotype, followed by bla _SHV (30.55%) and bla _OXA (28.70%). In the bla _CTX-M group, a higher occurrence was observed in bla _CTX-M-9 (23.14%), followed by bla _CTX-M-2 (24.07%) and bla _CTX-M-1 (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 E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli 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 viz., tetA, qnrS1, dfrA14, sul2, aph(3")-lb, aph(6)-ld, and Aph(3')-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.

Keywords: ESBL; Escherichia coli; SNPs; antimicrobial resistance; plasmids; polymerase chain reaction; whole genome sequencing.