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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #349578
Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety and Quality

Title: Genetic context of antimicrobial-resistant Escherichia coli at the livestock-wildlife interface

Author
item CHANDLER, JEFFREY - Animal And Plant Health Inspection Service (APHIS)
item BLOUIN, NICOLAS - University Of Wyoming
item Bono, James - Jim
item FRANKLIN, ALAN - Animal And Plant Health Inspection Service (APHIS)
item GOODRIDGE, LAWRENCE - McGill University - Canada
item ROOT, JEFF - Animal And Plant Health Inspection Service (APHIS)
item SHRINER, SUSAN - Animal And Plant Health Inspection Service (APHIS)
item BISHA, BLEDAR - University Of Wyoming

Submitted to: Journal of Food Protection
Publication Type: Abstract Only
Publication Acceptance Date: 5/1/2018
Publication Date: 7/1/2018
Citation: Chandler, J.C., Blouin, N.A., Bono, J.L., Franklin, A.B., Goodridge, L.D., Root, J., Shriner, S., Bisha, B. 2018. Genetic context of antimicrobial-resistant Escherichia coli at the livestock-wildlife interface. Journal of Food Protection. 81 (Supplement A): P2-228.

Interpretive Summary:

Technical Abstract: Introduction: Previous studies show that livestock production is spatially correlated with increased prevalence of antimicrobial resistance (AMR) within the gut bacteria of associated wildlife. Thus, impacted wildlife potentially maintain, reintroduce, and disseminate AMR bacteria across food production landscapes. However, the genetic context underlying the apparent similarities of AMR phenotypes at the livestock-wildlife interface remains unclear. Purpose: Here, the genetic context of phenotypically similar AMR Escherichia coli harboring priority AMR phenotypes that were collected from cattle and raccoons was investigated. Methods: Phenotypic testing was performed on more than 1,000 bacteria isolated from cattle and wildlife feces collected at six livestock facilities in Colorado. From these isolates, two groups of Escherichia coli isolates resistant to cephems (n=8) and cephems/fluoroquinolones (n=3) were selected for whole genome sequencing analyses on the basis of identical antibiograms (18 different antibiotics tested) and presence in the feces of both raccoons and cattle on multiple farms. Complete closed and polished genomes (PacBio/HiSeq sequencing) were acquired for each isolate, and in silico (Parsnp, CARD-RGI, etc.) analyses were used to evaluate phylogenetic relationships and AMR phenotypes. Results: Three main clades of AMR E. coli isolates were identified, with the most highly conserved clade containing isolates from both cattle and raccoons. The variable genomes of isolates was primarily attributable to differential repertoires of Inc-like plasmids and prophage mosaics. Similarities between cattle and wildlife isolates were further highlighted by conserved AMR determinants. In total, 59 AMR determinants were detected, with 47 of these found in all isolates tested. Identical plasmid-encoded CMY-2 AmpC ß-lactamases were present in six isolates. Similarly, conserved mutations in gryA and parC were linked to fluoroquinolone resistance. Significance: Genetic conservation between AMR isolates from cattle and wildlife suggest a complex AMR livestock ecology that has inputs from multiple sources.