Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products

Abstract

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

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

“…Production system differences in carcass meat trimmings were not apparent in predominant classes of AMR. This finding was similar to another targeted shotgun metagenomic study [45] that compared conventional to raised-without-antibiotics ground beef that also found no differences in the predominant classes of resistance between the two groups (in this case 91% of the resistance gene were associated with tetracycline resistance). In a culture-based study, when conventional versus organic beef has been evaluated in terms of AMR, Escherichia coli and Staphylococcus aureus were found to harbor lower rates of AMR in organic versus conventional beef samples; although, no production differences were found in Listeria monocytogenes isolates [46].…”

Oxygen Sensor-Based Respirometry and the Landscape of Microbial Testing Methods as Applicable to Food and Beverage Matrices

“…Similar to the above, this study found that product management had a greater influence on the ground beef microbiome than the resistome. Furthermore, the novel target-enriched shotgun sequencing implemented in this study allowed for the analysis of samples with low microbial abundance [40].…”

Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities

“…Current research on foodborne bacteria primarily focuses on individual pathogens and identifier microbes [24]. ARGs allow bacteria to survive throughout the face of antibiotics, and the resistance to antibiotics is reliably evaluated by phenotypic testing of isolates to a variety of antibiotics in food microbiology labs [25].…”