Resistomes and microbiomes of meat trimmings and colon content from culled cows raised in conventional and organic production systems

The potential to distribute bacteria resistant to antimicrobial drugs in the meat supply is a public health concern. Market cows make up a fifth of the U.S. beef produced but little is known about the entire population of bacteria (the microbiome) and entirety of all resistance genes (the resistome) that are found in this population. The objective of this study was to characterize and compare the resistomes and microbiomes of beef, dairy, and organic dairy market cows at slaughter. Fifty-four (N = 54) composite samples of both colon content and meat trimmings rinsate samples were collected over six visits to two harvest facilities from cows raised in three different production systems: conventional beef, conventional dairy, and organic dairy (n = 9 samples per visit per production system). Metagenomic DNA obtained from samples were analyzed using target-enriched sequencing and 16S rRNA gene sequencing to characterize the microbiomes and resistomes, respectively. All colon-content samples had at least one identifiable antimicrobial resistance gene (ARG), while 21 of the 54 meat trimmings samples harbor at least one identifiable ARGs. Tetracycline ARGs were the most abundant class in both colon content and carcass meat trimmings. Beta-lactam ARGs were the most abundant class in final meat trimmings. The resistome found on carcass meat trimmings were not significantly different by production system (P = 0.835, R2 = 0.00) or harvest facility (P = 0.104, R2 = 0.09). However, the resistome of colon contents differed (P = 0.013; R2 = 0.05) among production systems, but not among the harvest facilities (P = 0.41; R2 = 0.00). Amplicon sequencing revealed differences (P < 0.05) in microbial population structure in both meat trimmings and colon content between harvest facilities but not production system (P > 0.05). These data provide a baseline characterization of an important segment of the beef industry and highlight the effect that the production system where cattle are raised in as well as facility's environmental factors can impact associated microbiomes and resistomes.