National Beef Quality Audit-2022: Transportation, mobility, live cattle, and hide assessments to determine producer-related defects that affect animal welfare and the value of market cows and bulls at processing facilities.

The National Beef Quality Audit (NBQA)-2022 serves as a benchmark of the current market cow and bull sectors of the U.S. beef industry and allows comparison to previous audits as a method of monitoring industry progress. From September 2021 through May 2022, livestock trailers (n = 125), live animals (n = 5,430), and post-slaughter hide-on animals (n = 6,674) were surveyed at 20 commercial beef processing facilities across the U.S. Cattle were transported in a variety of trailer types for an average distance of 490.6 km and a mean transport time of 6.3 h. During transit, cattle averaged 2.3 m2 of trailer space per animal indicating sufficient space was provided according to industry guidelines. Of all trailers surveyed, 55.3% transported cattle from an auction barn to a processing facility. When surveyed, 63.6% of all truck drivers reported to be Beef Quality Assurance certified. The majority (77.0%) of cattle were sound when evaluated for mobility. Mean body condition scores (9-point scale) for beef cows and bulls were 3.8 and 4.4, respectively, whereas mean body condition scores (5-point scale) for dairy cows and bulls were 2.3 and 2.6, respectively. Of the cattle surveyed, 45.1% had no visible live animal defects, and 37.9% had only a single defect. Of defects present in cows, 64.6% were attributed to an udder problem. Full udders were observed in 47.5% of all cows. Nearly all cattle were free of visible abscesses and knots (97.9% and 98.2%, respectively). No horns were observed in 89.4% of all cattle surveyed. Beef cattle were predominantly black-hided (68.9% and 67.4% of cows and bulls, respectively). Holstein was the predominant dairy animal observed and accounted for 85.7% of the cows and 98.0% of the bulls. Only 3.1% of all animals had no form of identification. Findings from the NBQA-2022 show improvements within the industry and identify areas that require continued education and research to improve market cow and bull welfare and beef quality.

National Beef Quality Audit-2022 Phase 1: face-to-face and digital interviews.

The National Beef Quality Audit (NBQA) has been conducted regularly since 1991 to assess and benchmark quality in the U.S. beef industry, with the most recent iteration conducted in 2022. The goal of NBQA Phase I is to evaluate what needs to be managed to improve beef quality and demand. Interviews (n = 130) of industry personnel were conducted with the aid of routing software. In total, packers (n = 24), retailers (n = 20), further processors (n = 26), foodservice (n = 18), and allied government agencies and trade organizations (n = 42) were interviewed. Interviews were routed in software based on interviewee involvement in either the fed steer and heifer market cow and bull sectors, or both. Interviews were structured to elicit random responses in the order of determining "must-have" criteria (quality factors that are required to make a purchase), best/worst ranking (of quality factors based on importance), how interviewees defined quality terms, a strength, weakness, opportunities, threats (SWOT) analysis, general beef industry questions, and sustainability goals (the latter four being open-ended). Quality factors were 1) visual characteristics, 2) cattle genetics, 3) food safety, 4) eating satisfaction, 5) animal well-being, 6) weight and size, and 7) lean, fat, and bone. Best/worst analysis revealed that "food safety" was the most (P < 0.05) important factor in beef purchasing decisions for all market sectors and frequently was described as "everything" and "a way of business." Culture surrounding food safety changed compared to previous NBQAs with interviewees no longer considering food safety as a purchasing criterion, but rather as a market expectation. The SWOT analysis indicated that "eating quality of U.S. beef" was the greatest strength, and cited that educating both consumers and producers on beef production would benefit the industry. Irrespective of whether companies' products were fed or market cow/bull beef, respondents said that they believed "environmental concerns" were among the major threats to the industry. Perceived image of the beef industry in the market sectors has improved since NBQA-2016 for both fed cattle and market cow/bull beef.

Efficacy of Antimicrobial Spray Treatments in Reducing Salmonella enterica Populations on Chilled Pork.

Studies reporting on alternative antimicrobial interventions for pathogen control on chilled pork carcasses and cuts are limited. In this study, the antimicrobial effects of various spray treatments against Salmonella enterica inoculated on skin-on pork samples were evaluated. Chilled pork jowls were portioned (10 by 5 by 1 cm) and inoculated, on the skin side, with a mixture of six S. enterica serotype strains to target levels of 6 to 7 log CFU/cm2 (high inoculation level) or 3 to 4 log CFU/cm2 (low inoculation level). Samples were then left nontreated (control) or were treated (10 s) using a laboratory-scale spray cabinet with water, formic acid (1.5%), a proprietary blend of sulfuric acid and sodium sulfate (SSS, pH 1.2), peroxyacetic acid (PAA, 400 ppm), or PAA (400 ppm) that was pH-adjusted (acidified) with acetic acid (1.5%), formic acid (1.5%), or SSS (pH 1.2). Samples (n = 6) were analyzed for Salmonella populations after treatment application (0 h) and after 24 h of refrigerated (4°C) storage. Irrespective of inoculation level, all spray treatments effectively reduced (P < 0.05) Salmonella levels immediately following their application. Overall, pathogen reductions for the chemical treatments, compared to the respective high and low inoculation level nontreated controls, ranged from 1.2 to 1.9 log CFU/cm2 (high inoculation level) and 1.0 to 1.7 log CFU/cm2 (low inoculation level). Acidification of PAA with acetic acid, formic acid, or SSS did not (P ≥ 0.05) enhance the initial bactericidal effects of the nonacidified PAA treatment. Salmonella populations recovered from all treated samples following 24 h of storage were, in general, similar (P ≥ 0.05) or up to 0.6 log CFU/cm2 lower (P < 0.05) than those recovered from samples analyzed immediately after treatment application. The results of the study may be used by processing establishments to help identify effective decontamination interventions for reducing Salmonella contamination on pork.

More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments.

Widely considered an anthropogenic phenomenon, antimicrobial resistance (AMR) is a naturally occurring mechanism that microorganisms use to gain competitive advantage. AMR represents a significant threat to public health and has generated criticism towards the overuse of antimicrobial drugs. Livestock have been proposed as important reservoirs for AMR accumulation. Here, we show that assemblages of AMR genes in cattle and ungulates from natural environments (Yellowstone and Rocky Mountain National Parks) are all dominated by genes conferring resistance to tetracyclines. However, cattle feces contained higher proportions of erm(A-X) genes conferring resistance to macrolide antibiotics. Medically important AMR genes differed between cattle and natural ungulates, but cumulatively were more predominant in natural soils. Our findings suggest that the commonly described predominance of tetracycline resistance in cattle feces is a natural phenomenon among multiple ungulate species and not solely a result of antimicrobial drug exposure. Yet, the virtual absence of macrolide resistance genes in natural ungulates suggests that macrolide usage in agriculture may enrich these genes in cattle. Our results show that antimicrobial use in agriculture may be promoting a potential reservoir for specific types of AMR (i.e., macrolide resistance) but that a significant proportion of the ungulate resistome appears to have natural origins.

Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.

Introduction: Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle. Methods: This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics. Results: Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively). Discussion: Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.

Bacteroidetes and Firmicutes Drive Differing Microbial Diversity and Community Composition Among Micro-Environments in the Bovine Rumen.

Ruminants are a critical human food source and have been implicated as a potentially important source of global methane emissions. Because of their unique digestive physiology, ruminants rely upon a symbiotic relationship with the complex and rich community of microorganism in the foregut to allow digestion of complex carbohydrates. This study used 16S rRNA gene sequencing to investigate the composition of microbial communities from three rumen micro-environments of cattle fed identical diets: (1) free fluid, (2) the fibrous pack, and (3) the mucosa. Community composition analysis revealed that while a phylogenetic core including the most abundant and most common ruminal taxa (members of Bacteroidetes and Firmicutes) existed across micro-environments, the abundances of these taxa differed significantly between fluid- and mucosa-associated communities, and specific lineages were discriminant of individual micro-environments. Members of Firmicutes, specifically Clostridiales, Lachnospiraceae, Mogibacteriaceae, Christenellaceae, and Erysipelotrichaceae were significantly more abundant in fluid communities, while members of Bacteroidetes, namely Muribaculaceae and Prevotellaceae were more abundant in mucosa-associated communities. Additionally, Methanobacteriaceae, a family of methanogenic Archaea, was more abundant in fluid-associated communities. A set of four more diverse lineages were discriminant of pack-associated communities that included Succinivibrionaceae, RFP12 (Verruco-5), Fibrobacteraceae, and Spirochaetaceae. Our findings indicate that different ecological niches within each micro-environment have resulted in significant differences in the diversity and community structure of microbial communities from rumen fluid, pack, and mucosa without the influence of diet that will help contextualize the influence of other environmental factors.

Not All Liver Abscesses Are Created Equal: The Impact of Tylosin and Antibiotic Alternatives on Bovine Liver Abscess Microbial Communities and a First Look at Bacteroidetes-Dominated Communities.

Liver abscesses (LAs) are extremely prevalent in cattle and result in significant economic losses due to liver condemnation, decreased growth and production, and lower carcass quality. LAs are commonly attributed to the transition to diets high in rapidly fermentable starch which results in rumen epithelial inflammation that allows pathogenic bacteria to gain entry to liver through transport via the hepatic portal vein. The most common intervention for LAs is the inclusion of antibiotics in feedlot diets, under the supervision of a veterinarian; this treatment is associated with reduced occurrence of LAs in this and other studies. Here, through the largest LA 16S rRNA gene sequencing study to date, we demonstrate that the inclusion of tylosin and antibiotic alternatives (the essential oil limonene and Saccharomyces cerevisiae fermentation product) had little impact on LA microbial community composition. Importantly, members of Bacteroidetes (Bacteroides spp. and Porphyromonas spp.) were identified as the dominant taxa in conjunction with low proportions of Fusobacteria in nearly a quarter (61/259) of all LA communities analyzed in this study. The relative abundances of the phyla Fusobacteria and Bacteroidetes had a strongly negative correlation, and LA microbial communities rarely contained high abundances of both of these dominant phyla. Further, based on the presence of taxa discriminant of Bacteroidetes-dominated LAs within over 400 bovine gut communities, we provide evidence suggestive of Bacteroidetes-dominated abscess communities originating in more distal portions of the bovine gut. Together, these findings suggest that some LA microbial communities may originate from portions of the gut other than the rumen.

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

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.

Nix Pro Color Sensor provides comparable color measurements to HunterLab colorimeter for fresh beef.

The HunterLab MiniScan (HunterLab) colorimeter is used in meat quality research worldwide for measuring meat color; however, the Nix Pro Color Sensor (Nix) could be a less expensive alternative that is easier to operate. Therefore, the objective of this study was to compare the two colorimeters to objectively evaluate fresh beef color. Longissimus thoracis muscle from one side of A maturity beef carcasses (n = 200) was evaluated using both the HunterLab (3 technical replicate scans) and Nix (3, 5, 7, and 9 technical replicate scans) colorimeters. The correlation between the HunterLab and Nix for L* (lightness), a* (redness), and b* (yellowness) values ranged between r = 0.80 to 0.85 and the Bland Altman Limits of Agreement analysis indicated good agreement between the Nix and HunterLab colorimeters for all the color parameters. These results indicated that the Nix colorimeter could be a viable alternative for HunterLab colorimeters.

Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes.

A comparative whole genome analysis was performed on three newly sequenced Escherichia coli O157:H7 strains with different stx profiles, previously isolated from feedlot cattle [C1-010 (stx1-, stx2c+), C1-057 (stx-), and C1-067 (stx1+, stx2a+)], as well as five foodborne outbreak strains and six stx-negative strains from NCBI. Phylogenomic analysis demonstrated that the stx2c-carrying C1-010 and stx-negative C1-057 strains were grouped with the six NCBI stx-negative E. coli O157:H7 strains in Cluster 1, whereas the stx2a-carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one stx2a-carrying strain, and the six NCBI stx-negative strains and identify their prophages at the stx insertion sites. All stx-carrying prophages contained both the three Red recombination genes (exo, bet, gam) and their repressor cI. On the other hand, the majority of the stx-negative prophages carried only the three Red recombination genes, but their repressor cI was absent. In the absence of the repressor cI, the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of stx genes. We further investigated each of the 10 selected E. coli O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two stx2a-carrying strains and one in the single stx2c-carrying and seven stx-negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in stx2a-carrying E. coli O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the stx2c-carrying and stx-negative E. coli O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic E. coli O157:H7 in livestock and downstream food production environments.

Evaluation of Immersion and Spray Applications of Antimicrobial Treatments for Reduction of Campylobacter jejuni on Chicken Wings.

The decontamination efficacy of antimicrobial treatments against Campylobacter jejuni on chicken wings was evaluated. Chicken wings surface-inoculated with C. jejuni (3.9 log colony-forming units [CFU]/mL) were left untreated (control) or were treated by immersion (5 s) or in a spray cabinet (4 s) with water, a sulfuric acid and sodium sulfate blend (SSS; pH 1.2), formic acid (1.5%), peroxyacetic acid (PAA; 550 ppm), or PAA (550 ppm) that was pH-adjusted (acidified) with SSS (pH 1.2) or formic acid (1.5%). All evaluated immersion and spray chemical treatments effectively (p < 0.05) lowered C. jejuni populations on chicken wings. Spray application of chemical treatments resulted in immediate pathogen reductions ranging from 0.5 to 1.2 log CFU/mL, whereas their application by immersion lowered initial pathogen levels by 1.7 to 2.2 log CFU/mL. The PAA and acidified PAA treatments were equally (p ≥ 0.05) effective at reducing initial C. jejuni populations, however, following a 24 h refrigerated (4 °C) storage period, wings treated with acidified PAA had lower (p < 0.05) pathogen levels than samples that had been treated with PAA that was not acidified. Findings of this study should be useful to the poultry industry in its efforts to control Campylobacter contamination on chicken parts.

Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.

The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.

Antimicrobial Resistance in U.S. Retail Ground Beef with and without Label Claims Regarding Antibiotic Use.

ABSTRACT: 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 levels of antimicrobial-resistant bacteria than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from six U.S. cities. Samples with an RWA or U.S. Department of Agriculture 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 a quantitative PCR assay was used to determine the abundance of 10 antimicrobial resistance (AMR) genes. Prevalence of 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) was higher in CONV ground beef. Salmonella was detected in 1.2% of samples. The AMR gene blaCTX-M (CONV, 4.1 log-normalized abundance; RWA, 3.8 log-normalized abundance; P < 0.01) was more abundant in CONV ground beef. The AMR genes mecA (CONV, 4.4 log-normalized abundance; RWA, 4.9 log-normalized abundance; P = 0.05), tet(A) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), tet(B) (CONV, 3.9 log-normalized abundance; RWA, 4.5 log-normalized abundance; P < 0.01), and tet(M) (CONV, 5.4 log-normalized abundance; RWA, 5.8 log-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 antimicrobial-resistant bacteria via ground beef, quantitative microbiological risk assessments are required for authoritative determination of the human health impacts of the use of antimicrobial agents during beef production.

Effects of differing withdrawal times from ractopamine hydrochloride on residue concentrations of beef muscle, adipose tissue, rendered tallow, and large intestine.

Ractopamine hydrochloride (RAC) is a beta-agonist approved by the U.S. Food and Drug Administration (FDA) as a medicated feed ingredient for cattle during the final days of finishing to improve feed efficiency and growth. Maximum residue limits and U.S. FDA residue tolerances for target tissues have defined management practices around RAC usage in the U.S. However, many countries have adopted zero tolerance policies and testing of off-target tissues, presenting a major challenge for international export. Therefore, the objective this study was to determine the necessary withdrawal time among cattle group-fed RAC to achieve residue concentrations below tolerance levels in muscle and off-target tissues. Specifically, both total and parent RAC residues were quantified in muscle, adipose tissue, rendered tallow, and large intestines from animals group-fed RAC and subjected to withdrawal 2, 4, or 7 days before harvest. Ractopamine (parent and total) residues were below the assay limit of detection (< 0.12 ng/g) in all muscle and adipose tissue samples from animals in control groups (no RAC). However, RAC residues were detectable, but below the limit of quantitation, in 40% of tallow and 17% of large intestine samples from control animals. As expected, mean RAC residue concentrations in muscle, adipose tissue, and large intestine samples decreased (P < 0.05) as the RAC withdrawal duration (days) was extended. Irrespective of RAC withdrawal duration, mean parent RAC residue concentrations in muscle, adipose tissue, and large intestine ranged from 0.33 to 0.76 ng/g, 0.16 to 0.26 ng/g, 3.97 to 7.44 ng/g, respectively and all tallow samples were > 0.14 ng/g (detectable but below the limit of quantitation). Results of this study provide a baseline for the development of management protocol recommendations associated with withdrawal following group-feeding of RAC to beef cattle in countries that allow RAC use and intend to export to global markets which may be subject to zero tolerance policies and off-target tissue testing.

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

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 ground beef is a promising tool to investigate community-wide shifts in retail ground beef. Importantly, however, results from metagenomic sequencing must be carefully considered in parallel with traditional methods to better characterize the risk of AMR in retail products.

Tandem mass tagged dataset used to characterize muscle-specific proteome changes in beef during early postmortem period.

Bovine longissimus lumborum (LL) and psoas major (PM) muscles biopsy samples were collected from four carcasses (n = 4) at 45 min, 12 h, and 36 h postmortem from a commercial beef processing facility. Proteins present in the early postmortem LL and PM proteomes were identified and quantified using tandem mass tag (TMT) labelled, fractionated peptides coupled to liquid chromatography tandem mass spectrometry (LC-MS/MS). The data are supplied in this article and are related to "Tandem mass tag labeling to characterize muscle-specific proteome changes in beef during early postmortem period" by Zhai et al. [1].

No Change in Risk for Antibiotic-Resistant Salmonellosis from Beef, United States, 2002-2010.

Restricting antibiotic use in food production animals is a target for reducing antimicrobial drug-resistant infections in humans. We used US surveillance data to estimate the probability of antibiotic-resistant nontyphoidal salmonellosis per meal made with beef during 2002-2010. Applying data for nontyphoidal Salmonella in raised-without-antibiotics cattle, we tested the effect of removing antibiotic use from all beef cattle production. We found an average of 1.2 (95% credible interval 0.6-4.2) antibiotic-resistant nontyphoidal salmonellosis cases per 1 million beef meals made with beef initially contaminated with antibiotic-resistant nontyphoidal Salmonella at slaughter or retail and 0.031 (95% credible interval 0.00018-0.14) cases per 1 million meals irrespective of beef contamination status. Neither outcome showed sustained change except for increases in 2003 and 2009 (>98% confidence) when larger or more outbreaks occurred. Switching all beef production to a raised-without-antibiotics system may not have a significant effect on antibiotic-resistant nontyphoidal salmonellosis (94.3% confidence).

Antimicrobial Resistance at Two U.S. Cull Cow Processing Establishments.

ABSTRACT: Culled beef cows (cows that have reached the end of their productive life span in cow-calf operations) and culled dairy cows represent approximately 18% of the cattle harvested in the United States annually, but data on antimicrobial resistance (AMR) in these cull cattle are extremely limited. To address this data gap, colon contents were obtained from 180 culled conventional beef cows, 179 culled conventional dairy cows, and 176 culled organic dairy cows (produced without using antimicrobials). Sponge samples were also collected from 181 conventional beef, 173 conventional dairy, and 180 organic dairy cow carcasses. These samples were obtained on 6 days (3 days each at two beef harvest and processing establishments). At one establishment, 30 samples of beef manufacturing trimmings from conventional cows and 30 trim samples from organic dairy cows were acquired. All 1,129 samples were cultured for Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella, and 3GCrSalmonella. Metagenomic DNA was isolated from 535 colon content samples, and quantitative PCR assays were performed to assess the abundances of the following 10 antimicrobial resistance genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For colon contents, only TETrE. coli (P < 0.01), 3GCrE. coli (P < 0.01), and erm(B) (P = 0.03) levels were higher in conventional than in organic cows. Sampling day also significantly affected (P < 0.01) these levels. Production system did not affect the levels of any measured AMR on carcasses or trim. The human health impact of the few significant AMR differences could not be determined due to the lack of standards for normal, background, safe, or basal values. Study results provide key heretofore unavailable data that may inform quantitative microbial risk assessments to address these gaps.

Survey of production animal veterinarians' prescription practices, factors influencing antimicrobial drug use, and perceptions of and attitudes toward antimicrobial resistance.

OBJECTIVE: To assess production animal medicine veterinarians' prescription practices and identify factors influencing their use of antimicrobial drugs (AMDs) and their perceptions of and attitudes toward antimicrobial resistance (AMR). SAMPLE: 157 production animal veterinarians in the United States. PROCEDURES: An online cross-sectional survey and digital diary were used to gather information regarding perceptions on AMD use and AMR and on treatment recommendations for production setting-specific disease scenarios. Results were compared across respondents grouped by their selected production setting scenarios and reported years as veterinarians. RESULTS: The most commonly selected production setting disease scenarios were dairy cattle (96/157 [61.1%]), backgrounding cattle (32/157 [20.4%]), and feedlot cattle (20/157 [12.7%]). Because few respondents selected swine (5/157 [3.2%]) or poultry (4/157 [2.5%]) scenarios, those responses were excluded from statistical analysis of AMD prescription practices. Most remaining respondents (147/148 [99.3%]) reported that they would recommend AMD treatment for an individual ill animal; however, responses differed for respondents grouped by their selected production setting scenarios and reported years as veterinarians when asked about AMD treatment of an exposed group or high-risk disease-free group. Most respondents reported that government regulations influenced their AMD prescribing, that owner and producer compliance was a veterinary-related factor that contributed to AMR, and that environmental modifications to prevent disease could be effective to mitigate AMR. CONCLUSIONS AND CLINICAL RELEVANCE: Results of the present study helped fill important knowledge gaps pertaining to prescription practices and influencing factors for AMD use in production animal medicine and provided baseline information for future assessments. This information could be used to inform future interventions and training tools to mitigate the public health threat of AMR.

Tandem mass tag labeling to characterize muscle-specific proteome changes in beef during early postmortem period.

Previous research has indicated that variation in the proteome profile of longissimus lumborum (LL) and psoas major (PM) post-rigor influences meat quality attributes such as tenderness and color stability during retail display. Tandem mass tag (TMT) labeling is a chemical labeling approach using isobaric mass tags for accurate mass spectrometry-based quantification and identification of biological macromolecules. The objective of this study was to use TMT labeling to examine proteome profile variation between beef LL and PM during the early postmortem period (45 min, 12 h, and 36 h). We identified a total of 629 proteins, of which 71 were differentially abundant (fold change > 1.5, P < .05) from three comparisons between the muscles (PM vs. LL at 45 min, 12 h and 36 h). These proteins were mainly involved in oxidative phosphorylation and ATP-related transport, tricarboxylic acid cycle, NADPH regeneration, fatty acid degradation, muscle contraction, calcium signaling, chaperone activity, oxygen transport, as well as degradation of the extracellular matrix. At early postmortem, more abundant antiapoptotic proteins in LL could cause high metabolic stability, enhanced autophagy, and delayed apoptosis, while overabundant metabolic enzymes and pro-apoptotic proteins in PM could accelerate the generation of reactive oxygen species and initiation of cell death. SIGNIFICANCE: Longissimus lumborum and psoas major are two highly valuable cuts in beef carcass exhibiting different quality attributes such as color and tenderness, partly due to their distinct muscle fiber proportion and metabolic property. We characterized the proteomic change of these two muscles at early postmortem using tandem mass tag labeling for the first time, which highlighted the potential relationships between metabolism, cell death, and color stability. Our work provides a new perspective on muscle-to-meat conversion, especially on the potential effect of muscle-specific cell death on meat color stability.