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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 #337054

Title: Genomic and metagenomic diversity of antibiotic resistance in dairy animals

item Haley, Bradd
item KIM, SEON-WOO - University Of Maryland
item CAO, HUILIN - University Of Maryland
item KARNS, JEFFREY - Retired ARS Employee
item Van Kessel, Jo Ann

Submitted to: American Society for Microbiology Conference
Publication Type: Abstract Only
Publication Acceptance Date: 2/15/2017
Publication Date: 6/4/2017
Citation: Haley, B.J., Kim, S., Cao, H., Karns, J., Van Kessel, J.S. 2017. Genomic and metagenomic diversity of antibiotic resistance in dairy animals. American Society for Microbiology Conference. New Orleans, LA on June 1-5, 2017.

Interpretive Summary:

Technical Abstract: Antibiotic resistance in food animals has received increased scrutiny in recent years due to the increased prevalence of antibiotic resistant infections in the human clinical setting. The extent to which antibiotic usage in food animals is responsible for the burden of antibiotic resistance in human infections is not well known. Thus, there is a need to further evaluate the diversity of genes conferring antibiotic resistance in bacteria isolated from these animals. To further evaluate the prevalence of antibiotic resistance in the feces of dairy animals, we sequenced the genomes of 160 antibiotic resistant Escherichia coli and 28 fecal metagenomes isolated from adult dairy cows, veal calves, and pre-weaned calves. E. coli isolates were collected from composite fecal samples and fecal grab samples taken directly from the animal. Isolates were screened for susceptibility to a panel of 14 antibiotics and 150 showing resistance to at least one antibiotic and 10 antibiotic susceptible isolates were selected for whole genome shotgun sequencing. Twenty-eight fecal grab samples collected from animals shedding variable levels of antibiotic resistant E. coli were selected for shotgun metagenomics sequencing. At least four E. coli isolates from each of the major phylogroups were detected with phylogroups A, B1, and D detected more frequently than all others. The most frequently detected sequence types were the phylogroup C ST88 (10% of all isolates), phylogroup B1 ST10 (9%), and the phylogroup B2 ExPEC ST117 (6%). Within these sequence types isolates from different animals on the same farm and isolates from different farms were closely related indicating that some strains of antibiotic resistant E. coli may be circulating among dairy herds within the same region. Interestingly several MDR ST117 isolates, which are reported to be shed by cattle worldwide, were closely related to pathogenic human ExPEC isolates and isolates recovered from chickens with colibacillosis. Metagenomic analyses indicated that for all samples tetracycline resistance genes were the most frequently identified resistance genes followed by aminoglycoside, macrolide, beta-lactam, trimethoprim, and sulphonamide resistance genes. In veal calf fecal samples trimethoprim and floroquinolone resistance genes were more frequently detected than in pre-weaned dairy calf samples. Future work will identify genomic features that may confer persistence of high frequency antibiotic resistant E. coli strains and sequence types in the dairy cow hindgut and factors that influence the presence of antibiotic resistance in pre-weaned calves.