A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage

[Display omitted] •Agricultural Escherichia coli panel (AgEC) generated from the four major animal production commodities of the United States.•The 300 isolates are highly diverse, clustering into 71 PFGE groups.•Tetracycline and sulfonamide resistance PCR gene screening identified 131 tet and 41 su...

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Bibliographic Details
Published in:Journal of hazardous materials 2020-01, Vol.382, p.120991-120991, Article 120991
Main Authors: Ducey, Thomas F., Durso, Lisa M., Ibekwe, Abasiofiok M., Dungan, Robert S., Jackson, Charlene R., Frye, Jonathan G., Castleberry, B. Lana, Rashash, Diana M.C., Rothrock, Michael J., Boykin, Debbie, Whitehead, Terence R., Ramos, Zeanmarj, McManus, Morgan, Cook, Kimberly L.
Format: Article
Language:English
Subjects:
Animal production
Antimicrobial resistance genes
Escherichia coli
Isolate panel
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Summary:[Display omitted] •Agricultural Escherichia coli panel (AgEC) generated from the four major animal production commodities of the United States.•The 300 isolates are highly diverse, clustering into 71 PFGE groups.•Tetracycline and sulfonamide resistance PCR gene screening identified 131 tet and 41 sul harboring isolates.•This isolate panel is a publicly available resource for the agricultural community. There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel’s utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.
ISSN:0304-3894
1873-3336
DOI:10.1016/j.jhazmat.2019.120991