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

Authors: Ducey, Thomas; Durso, Lisa; Ibekwe, Abasiofiok - Mark; Dungan, Robert - Rob; Jackson, Charlene; Frye, Jonathan; Castleberry, Bobbie - Lana; RASHASH, DIANA - North Carolina Cooperative Extension; Rothrock, Michael; Boykin, Deborah; Whitehead, Terence; Ramos, Zeanmarj; McManus, Morgan; Cook, Kimberly - Kim

Submitted to: Journal of Hazardous Materials
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2019
Publication Date: 1/15/2020
Citation: Ducey, T.F., Durso, L.M., Ibekwe, A.M., Dungan, R.S., Jackson, C.R., Frye, J.G., Castleberry, B., Rashash, D.M., Rothrock Jr, M.J., Boykin, D.L., Whitehead, T.R., Ramos, Z.D., McManus, M.N., Cook, K.L. 2020. 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. Journal of Hazardous Materials. 382. https://doi.org/10.1016/j.jhazmat.2019.120991.
DOI: https://doi.org/10.1016/j.jhazmat.2019.120991

Interpretive Summary: Bacteriological studies sometimes rely on the use of isolate panels, which are collections of similarly, but not identically, related microorganisms, often of the same species. While such isolate panels exist for the study of Escherichia coli, they are typically designed either: (i) to optimize genetic and/or phenotypic diversity; (ii) are restrictive in their geographical reach; or (iii) are isolated from a limited number of species. Such panels therefore do not give a sufficiently broad look at agricultural production in the United States as a whole. The isolate panel in this study provides a random sampling of E. coli isolates from all four major animal food production commodities in the United States, ranging from beef, dairy, poultry, to swine while also including several isolates from agriculturally-impacted environments as well as other commodity groups. This panel demonstrates a high degree of genetic diversity and should provide the research community with an isolate set representative of E. coli for study of issues pertinent to U.S. animal food production.

Technical Abstract: There are a limited number of Escherichia coli isolate panels that represent all the major United States animal production groups. To address this shortfall in resources, we have assembled an isolate collection from all four major animal production commodities in the United States, ranging from beef, dairy, poultry, to swine while also including several isolates from agriculturally-impacted environments as well as other commodity groups. This publicly available isolate panel consists of 300 E. coli isolates. Analysis of diversity by both phylotyping and pulsed-field gel electrophoresis reveal a highly diverse composition, with isolates clustered into a total of 74 sub-types. The panel was further utilized to assay tetracycline and sulfonamide resistance genes. A total of 131 isolates harbored genes that confer tetracycline resistance, while 41 isolates harbored genes to confer sulfonamide resistance. There was strong overlap in the two pools of isolates, with 38 of the 41 sulfonamide resistance gene harboring isolates containing tetracycline resistance genes as well. Further analysis of antibiotic resistance genes revealed significant differences along commodity and geographical lines.