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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Environmental Microbial & Food Safety Laboratory » Research » Publications at this Location » Publication #396425

Research Project: Evaluation of Genetic and Management Factors to Reduce Foodborne Pathogens and Antimicrobial Resistance in Dairy Cattle

Location: Environmental Microbial & Food Safety Laboratory

Title: Large scale genomic analysis identifies antimicrobial resistant and potentially pathogenic escherichia coli from dairy calves at commercial settings

item Salaheen, Serajus
item Kim, Seonwoo
item SPRINGER, HAYLEY - Pennsylvania State University
item HOVINGH, ERNEST - Pennsylvania State University
item Van Kessel, Jo Ann
item Haley, Bradd

Submitted to: ASM Conference
Publication Type: Abstract Only
Publication Acceptance Date: 8/14/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Background:Dairy calves carry a disproportionately large population of antimicrobial resistant (AMR) Escherichia coli compared with older animals. Currently, there is a paucity of information on the population structures, antimicrobial resistance gene (ARG) profiles, as well as virulence potential of AMR E. coli from dairy calves in commercial settings. Addressing these knowledge gaps will help strategize interventions and allow more informed antimicrobial stewardship programs to be developed. Methods: In total, the genomes of >1,000 non-redundant E. coli isolates (mostly AMR) previously isolated from feces collected from individual calves on 12 commercial dairy farms were sequenced (Illumina NextSeq 500, 2 x 150 bp reads). The genomes were evaluated with VirulenceFinder, ResFinder, MLST, and SerotypeFinder programs available at the Center for Genomic Epidemiology webserver and other publicly available programs. Results: The population of AMR E. coli in dairy calf feces was polyphyletic with at-least 150 known sequence types (STs) representing all major E. coli phylogroups, i.e., A, B1, B2, C, D, E, F, and G. The number of known E. coli STs in a single feces sample ranged between 1 and 8 (median 3). STs associated with extra-intestinal pathogenic E. coli (ExPEC), e.g., ST69 and ST117 were repeatedly detected. A diverse profile of ARGs and virulence factors were found in this group of isolates, including ARGs known to confer resistance to the drug classes Aminoglycoside, ß-lactam, Fosfomycin, Macrolide, Phenicol, Sulfonamide, Tetracycline, and Trimethoprim. In this analysis, 31 Shiga-toxin gene (stx) harboring E. coli isolates (STEC) were identified. The STEC isolates belonged to at-least 15 STs and 11 serogroups including two of the “big six” serogroups, O103 and O111. All the O103 and O111 isolates in this study harbored the stx gene along with the intimin gene, eae, and the translocated intimin receptor coding gene, tir. Two of the STEC isolates harbored gene markers of an ExPEC (e.g., aerobactin and Afa/Dr-adhesin) suggesting that they may be hybrid ExPEC/STECs. Conclusion: This study described the genomic attributes of potentially pathogenic AMR E. coli isolated from commercially raised dairy calves. Information presented herein will be useful for assessing public health risk and may help guide the development of preharvest prevention strategies of pathogenic and AMR E. coli in this important food animal reservoir.