PS2-17. Mapping the Livestock Resistome: Antimicrobial Resistance Genes Across Oklahoma Farms.

Abstract Studying the antimicrobial resistome in livestock farms helps monitor the spread of antimicrobial resistance (AMR) from animals to humans, promotes safer antibiotic use in agriculture, and contributes to the protection of public health. Therefore, the objective of this study was to assess various AMR genes (ARGs) in livestock farms across Oklahoma. Fecal samples were collected from 12 farms located in 12 counties, including beef and dairy cattle, sheep, goats, and horses. Three of the 12 farms had mixed livestock species, including Holstein and Jersey dairy cattle, beef cattle and horses, and beef cattle and goats. Livestock species grazed on natural grazing lands without supplementation, except for dairy cattle and one feedlot beef operation. Six fecal samples were collected for each species from different farms, resulting in a total of 90 samples. Genomic DNA was extracted from the samples and amplified using the Illumina AMR Research Panel targeting 815 amplicons corresponding to 478 ARGs across 28 antibiotic classes. The amplified ARGs were sequenced, generating approximately one million reads, which were analyzed using the Resistance Gene Identifier in BWT mode against the Comprehensive Antibiotic Resistance Database. There were 605 ARGs identified across samples with a mean of 116 ± 66.6 (standard deviation) identified per animal type and only 17 core ARGs were shared across farms and species. Among the detected ARGs, lnuC, tet(Q), tet(W), tet(44), ANT(6)-Ib, tet(40), tet(O/W), and Escherichia coli mdfA were highly prevalent across different farms. In terms of antibiotic classes, lincosamide resistance was the most prevalent, followed by tetracycline, tetracycline-phenicol-disinfecting agents, and aminoglycoside antibiotics. Principal component analysis combined with pairwise PERMANOVA indicated that AMR patterns differed significantly (P < 0.05) across farms and species, except between Jersey and Holstein cattle within the same farm. The ARG patterns in grazing ruminants were closely related to each other but were distantly related to those observed in dairy and feedlot cattle, whereas the ARG patterns in horses were highly divergent. In co-grazing beef cattle and horses, horses exhibited higher (P < 0.05) prevalence of Bcl, Escherichia coli mdfA, tet(M), tet(L), tet(33), and tet(W/N/W), whereas cattle showed higher (P < 0.05) abundances of tet(W/32/O), tet(O/W), and tet(Q). In Jersey and Holstein cattle housed on the same premises, Holstein dairy cattle exhibited higher (P < 0.05) prevalence of ErmX and CMY-40, whereas Jersey cattle harbored higher (P < 0.05) abundances of tet(W/N/W), APH(3’)-Ia, and cfxA2. Overall, these results indicate that lincosamide, tetracycline, and aminoglycoside resistance genes are highly prevalent across Oklahoma farms, with AMR patterns shaped by farm, feeding system, species, and breed, underscoring the complex dynamics of the livestock resistome.