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

Abstract

Background 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 microbiome of beef, dairy, and organic dairy market cows at slaughter. Methods 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 = 3 samples per visit per production system). Metagenomic DNA obtained from samples were analyzed using target-enriched sequencing (resistome) and 16S rRNA gene sequencing (microbiome). Results All colon content samples had at least one identifiable antimicrobial resistance gene (ARG), while 21 of the 54 meat trimmings samples harbored at least one identifiable ARGs. Tetracycline ARGs were the most abundant class in both colon content and carcass meat trimmings. The resistome found on carcass meat trimmings was not significantly different by production system (P = 0.84, R2 = 0.00) or harvest facility (P = 0.10, R2 = 0.09). However, the resistome of colon content differed (P = 0.01; 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 populations in both meat trimmings and colon content between harvest facilities but not production systems (P > 0.05). Conclusions 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 and the harvest facilities where an animal is processed can impact associated microbiome and resistomes.

Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment

“…Administration of tylosin has been associated with co-selection for bacterial resistance to the entire macrolide class of 14-, 15-, and 16- membered ring molecules ( Marshall and Levy, 2011 ; Beukers et al, 2015 ); these include multiple antibiotics that are classified by the World Health Organization (WHO) as critically important for human health ( World Health Organization [WHO], 2017 ). Tylosin administration may promote carriage of antimicrobial resistance (AMR) determinants in cattle, which may increase the risk of human infections associated with AMR pathogens from beef food products and the environment ( Noyes et al, 2016 ; Huebner et al, 2019 ; Weinroth et al, 2019 , 2022 ). There is a critical need to find alternative therapies that provide the same benefits of antibiotics without the risk of AMR selection and propagation in food animal production systems.…”

Nanopore Sequencing Assessment of Bacterial Pathogens and Associated Antibiotic Resistance Genes in Environmental Samples

“…The residues from the pork meat factory are rich in nitrogen compounds, which decrease the abundance of Burkholderiaceae in samples S1, S2, and S3. Another abundant family in samples S1, S2, and S3 was Moraxellaceae, a family usually isolated from meat, which is recorded in high abundance, even in processed meat products [35].…”

Transmission of antimicrobial resistance (AMR) during animal transport

“…In summary, young age is generally a risk factor for harbouring ARB/ARGs even though this may not be valid for all species, management conditions, bacteria and AMR determinants. Conventional farms are at greater risk for housing ARB than organic or antimicrobial‐free farms (Tenhagen et al., 2018 ; Pesciaroli et al., 2020 ; Innes et al., 2021 ; Mencía‐Ares et al., 2021 ; Weinroth et al., 2022 ). In all species, antimicrobial consumption is a major driver for an increase of ARB/ARGs.…”