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

Doster, Enrique; Thomas, K.; Weinroth, Margaret D.; Parker, Jennifer; Crone, K.K.; Arthur, Terrance M.; Schmidt, J. W.; Wheeler, T. L.; Belk, K. E.; Morley, Paul S.

doi:10.3389/fmicb.2020.541972

Cited by 16 publications

(8 citation statements)

References 42 publications

(55 reference statements)

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“…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].…”

Section: Discussionsupporting

confidence: 87%

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

et al. 2022

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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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Section: Discussionsupporting

confidence: 87%

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

et al. 2022

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“…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].…”

Section: Next-generationation Sequencing Methodsmentioning

confidence: 99%

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

Papkovsky

Kerry

2023

Sensors

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The current status of microbiological testing methods for the determination of viable bacteria in complex sample matrices, such as food samples, is the focus of this review. Established methods for the enumeration of microorganisms, particularly, the ‘gold standard’ agar plating method for the determination of total aerobic viable counts (TVC), bioluminescent detection of total ATP, selective molecular methods (immunoassays, DNA/RNA amplification, sequencing) and instrumental methods (flow cytometry, Raman spectroscopy, mass spectrometry, calorimetry), are analyzed and compared with emerging oxygen sensor-based respirometry techniques. The basic principles of optical O2 sensing and respirometry and the primary materials, detection modes and assay formats employed are described. The existing platforms for bacterial cell respirometry are then described, and examples of particular assays are provided, including the use of rapid TVC tests of food samples and swabs, the toxicological screening and profiling of cells and antimicrobial sterility testing. Overall, O2 sensor-based respirometry and TVC assays have high application potential in the food industry and related areas. They detect viable bacteria via their growth and respiration; the assay is fast (time to result is 2–8 h and dependent on TVC load), operates with complex samples (crude homogenates of food samples) in a simple mix-and-measure format, has low set-up and instrumentation costs and is inexpensive and portable.

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“…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].…”

Section: Introductionmentioning

confidence: 99%

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

Song

Wang

Han

et al. 2022

Genes

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Suancai, as a traditional fermented food in China with reputed health benefits, has piqued global attention for many years. In some circumstances, the microbial-driven fermentation may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers. To better utilize beneficial traits, a deeper comprehension of the composition and functionality of the bacterial species harboring enzymes of catalytically active is required. On the other hand, ingestion of fermented food increases the likelihood of microbial antibiotic resistance genes (ARGs) spreading in the human gastrointestinal tract. Besides, the diversity and taxonomic origin of ARGs in suancai are little known. In our study, a metagenomic approach was employed to investigate distribution structures of CAZymes and ARGs in main bacterial species in suancai. Functional annotation using the CAZy database identified a total of 8796 CAZymes in metagenomic data. A total of 83 ARGs were detected against the CARD database. The most predominant ARG category is multidrug-resistant genes. The ARGs of antibiotic efflux mechanism are mostly in Proteobacteria. The resistance mechanism of ARGs in Firmicutes is primarily antibiotic inactivation, followed by antibiotic efflux. Due to the abundance of species with different ARGs, strict quality control including microbial species, particularly those with lots of ARGs, is vital for decreasing the risk of ARG absorption via consumption. Ultimately, we significantly widen the understanding of suancai microbiomes by using metagenomic sequencing to offer comprehensive information on the microbial functional potential (including CAZymes and ARGs content) of household suancai.

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

Cited by 16 publications

References 42 publications

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

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

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

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

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