Antibiotics used during food-animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower antimicrobial resistance (AMR) levels than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from 6 U. S. cities. Samples with a RWA or USDA Organic claim ( N = 299) were assigned to the RWA production system. Samples lacking these claims ( N = 300) were assigned to the CONV production system. Each sample was cultured for the detection of five antimicrobial resistant bacteria. Genomic DNA was isolated from each sample and qPCR was used to determine the abundance of ten antimicrobial resistance genes (ARGs). Tetracycline-resistant Escherichia coli (CONV = 46.3%; RWA = 34.4%, P < 0.01) and erythromycin-resistant Enterococcus (CONV = 48.0%; RWA = 37.5%, P = 0.01) were more frequently detected in CONV. Salmonella were detected in 1.2% of samples. The ARG bla CTX-M (CONV = 4.1 log 10 normalized abundance, RWA = 3.8 log 10 normalized abundance, P < 0.01) was more abundant in CONV ground beef. The ARGs mecA (CONV = 4.4 log 10 normalized abundance, RWA = 4.9 log 10 normalized abundance, P = 0.05), tet (A) (CONV = 3.9 log 10 normalized abundance, RWA = 4.5 log 10 normalized abundance, P < 0.01), tet (B) (CONV = 3.9 log 10 normalized abundance, RWA = 4.5 log 10 normalized abundance, P < 0.01), and tet (M) (CONV = 5.4 log 10 normalized abundance, RWA = 5.8 log 10 normalized abundance, P < 0.01) were more abundant in RWA ground beef. Although these results suggest that antimicrobial use during U. S. cattle production does not increase human exposure to AMR via ground beef quantitative microbiological risk assessments are required for authoritative assessments regarding the human health impacts of antimicrobial uses during beef production.
Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bacterial species, but these techniques are unable to describe the whole community of microbial species (microbiome) and the profile of AMR genes they carry (resistome), which is critical for getting a holistic perspective of AMR. The objective of this study was to characterize the microbiome and resistome of retail ground beef products labeled as coming from conventional or raised without antibiotics (RWA) production systems. Sixteen ground beef products were purchased from 6 retail grocery outlets in Fort Collins, CO, half of which were labeled as produced from cattle raised conventionally and half of products were from RWA production. Total DNA was extracted and isolated from each sample and subjected to 16S rRNA amplicon sequencing for microbiome characterization and target-enriched shotgun sequencing to characterize the resistome. Differences in the microbiome and resistome of RWA and conventional ground beef were analyzed using the R programming software. Our results suggest that the resistome and microbiome of retail ground beef products with RWA packaging labels do not differ from products that do not carry claims regarding antimicrobial drug exposures during cattle production. The resistome predominantly consisted of tetracycline resistance making up more than 90% of reads mapped to resistance gene accessions in our samples. Firmicutes and Proteobacteria predominated in the microbiome of all samples (69.6% and 29.0%, respectively), but Proteobacteria composed a higher proportion in ground beef from conventionally raised cattle. In addition, our results suggest that product management, such as packaging type, could exert a stronger influence on the microbiome than the resistome in consumer-ready products. Metagenomic analyses of
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.
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