Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 87
Filtrar
1.
Front Microbiol ; 13: 882419, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35572696

RESUMO

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.

2.
Anim Microbiome ; 4(1): 21, 2022 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-35272712

RESUMO

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.

3.
J Food Sci Technol ; 58(9): 3661-3665, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34366483

RESUMO

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.

4.
Front Microbiol ; 12: 647434, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33868205

RESUMO

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.

5.
Foods ; 10(4)2021 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-33924021

RESUMO

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.

6.
mSystems ; 6(2)2021 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-33653941

RESUMO

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.

7.
J Food Prot ; 84(5): 827-842, 2021 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-33302298

RESUMO

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.


Assuntos
Antibacterianos , Anti-Infecciosos , Animais , Antibacterianos/farmacologia , Bovinos , Farmacorresistência Bacteriana , Escherichia coli , Testes de Sensibilidade Microbiana
8.
PLoS One ; 15(12): e0242673, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33264353

RESUMO

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.


Assuntos
Resíduos de Drogas/análise , Gorduras/química , Intestino Grosso/química , Músculos/química , Fenetilaminas/farmacologia , Carne Vermelha/análise , Animais , Bovinos , Análise dos Mínimos Quadrados , Limite de Detecção , Fenetilaminas/análise
9.
Front Microbiol ; 11: 541972, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33240224

RESUMO

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.

10.
Data Brief ; 32: 106064, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32775575

RESUMO

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].

11.
Emerg Infect Dis ; 26(9): 2108-2117, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32818395

RESUMO

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).


Assuntos
Intoxicação Alimentar por Salmonella , Infecções por Salmonella , Animais , Antibacterianos/farmacologia , Bovinos , Resistência Microbiana a Medicamentos , Microbiologia de Alimentos , Salmonella , Intoxicação Alimentar por Salmonella/epidemiologia , Infecções por Salmonella/epidemiologia , Estados Unidos/epidemiologia
12.
J Food Prot ; 83(12): 2216-2228, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32730612

RESUMO

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.


Assuntos
Anti-Infecciosos , Doenças dos Bovinos , Animais , Antibacterianos/farmacologia , Bovinos , Farmacorresistência Bacteriana , Escherichia coli , Feminino , Salmonella , Estados Unidos
13.
J Am Vet Med Assoc ; 257(1): 87-96, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32538697

RESUMO

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.


Assuntos
Anti-Infecciosos , Preparações Farmacêuticas , Médicos Veterinários , Animais , Antibacterianos/uso terapêutico , Atitude , Bovinos , Estudos Transversais , Farmacorresistência Bacteriana , Humanos , Percepção , Prescrições , Inquéritos e Questionários , Suínos
14.
J Proteomics ; 222: 103794, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32330628

RESUMO

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.


Assuntos
Proteoma , Carne Vermelha , Animais , Bovinos , Carne , Contração Muscular , Músculo Esquelético , Mudanças Depois da Morte , Proteômica , Carne Vermelha/análise
15.
Nucleic Acids Res ; 48(D1): D561-D569, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31722416

RESUMO

Antimicrobial resistance (AMR) is a threat to global public health and the identification of genetic determinants of AMR is a critical component to epidemiological investigations. High-throughput sequencing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysis of AMR within metagenomic samples (i.e. the resistome). Along with MEGARes, we released AmrPlusPlus, a bioinformatics pipeline that interfaces with MEGARes to identify and quantify AMR gene accessions contained within a metagenomic sequence dataset. Here, we present MEGARes 2.0 (https://megares.meglab.org), which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 2.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 57 classes, 220 mechanisms of resistance, and 1,345 gene groups that classify the 7,868 accessions. In addition, we present an updated version of AmrPlusPlus (AMR ++ version 2.0), which improves accuracy of classifications, as well as expanding scalability and usability.


Assuntos
Anti-Infecciosos/farmacologia , Bases de Dados Genéticas , Bases de Dados de Produtos Farmacêuticos , Resistência Microbiana a Medicamentos , Genes Bacterianos , Metagenômica/métodos , Software , Anti-Infecciosos/química , Bactérias/efeitos dos fármacos , Bactérias/genética , Desinfetantes/química , Desinfetantes/farmacologia , Metagenoma , Metais/química , Metais/farmacologia
16.
Adv Nutr ; 11(1): 41-51, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31408089

RESUMO

This systematic review and landscape analysis describes patterns in dietary meat (skeletal muscle and associated tissues from mammalian, avian, and aquatic species; i.e., muscle foods) categories (CAT) and descriptions (DESCR) used throughout nutrition-related chronic disease literature, as there is anecdotally noted variation. A total of 1020 CAT and 776 DESCR were identified from 369 articles that assessed muscle food consumption and primary prevention of cardiovascular disease, obesity, type 2 diabetes, or cancer in adults ≥19 y from PubMed, Cochrane, and CINAHL up to March 2018. Specificity of CAT was analyzed on an empirical 1-7 ordinal scale as: 1) broad/undescriptive, "fish"; 2) muscle food type, "red meat"; 3) species, "poultry"; 4) broad + 1 descriptor, "processed meat"; 5) type/species + 1 descriptor, "fresh red meat"; 6) broad/type + 2 descriptors, "poached lean fish"; and 7) specific product, "luncheon meat." Median CAT specificity for randomized controlled trials (RCTs) and observational studies (OBSs) was 3 and 2 points out of 7, respectively, with no differences between chronic disease types. Specificity of OBS CAT was higher in recent articles but RCT CAT became less specific starting in the 2000s. RCT CAT were 400% more likely to include species, 500% more likely to include leanness, but 400% less likely to include processing degree compared with OBS CAT. A DESCR was included for 76% and 82% of OBS and RCT CAT, respectively. Researchers described processed meat, red meat, and total meat CAT more commonly than poultry or fish CAT. Among processed meat DESCR, 31% included a common term used in public regulatory definitions. In conclusion, muscle food categories and descriptions are substantively different within and between experimental and observational studies and do not match regulatory definitions. A practical muscle food classification system is warranted to improve interpretation of evidence regarding muscle food consumption and chronic disease.


Assuntos
Pesquisa Biomédica/métodos , Doenças Cardiovasculares , Diabetes Mellitus Tipo 2 , Dieta , Carne , Neoplasias , Obesidade , Doenças Cardiovasculares/etiologia , Doenças Cardiovasculares/prevenção & controle , Doença Crônica , Diabetes Mellitus Tipo 2/etiologia , Diabetes Mellitus Tipo 2/prevenção & controle , Comportamento Alimentar , Humanos , Carne/classificação , Neoplasias/etiologia , Neoplasias/prevenção & controle , Avaliação Nutricional , Obesidade/etiologia , Obesidade/prevenção & controle , Projetos de Pesquisa
17.
Front Microbiol ; 10: 2499, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31736924

RESUMO

This study was conducted to compare aerobic culture, polymerase chain reaction (PCR), lateral flow immunoassay (LFI), and shotgun metagenomics for identification of Salmonella enterica in feces collected from feedlot cattle. Samples were analyzed in parallel using all four tests. Results from aerobic culture and PCR were 100% concordant and indicated low S. enterica prevalence (3/60 samples positive). Although low S. enterica prevalence restricted formal statistical comparisons, LFI and deep metagenomic sequencing results were discordant with these results. Specifically, metagenomic analysis using k-mer-based classification against the RefSeq database indicated that 11/60 of samples contained sequence reads that matched to the S. enterica genome and uniquely identified this species of bacteria within the sample. However, further examination revealed that plasmid sequences were often included with bacterial genomic sequence data submitted to NCBI, which can lead to incorrect taxonomic classification. To circumvent this classification problem, we separated all plasmid sequences included in bacterial RefSeq genomes and reassigned them to a unique taxon so that they would not be uniquely associated with specific bacterial species such as S. enterica. Using this revised database and taxonomic structure, we found that only 6/60 samples contained sequences specific for S. enterica, suggesting increased relative specificity. Reads identified as S. enterica in these six samples were further evaluated using BLAST and NCBI's nr/nt database, which identified that only 2/60 samples contained reads exclusive to S. enterica chromosomal genomes. These two samples were culture- and PCR-negative, suggesting that even deep metagenomic sequencing suffers from lower sensitivity and specificity in comparison to more traditional pathogen detection methods. Additionally, no sample reads were taxonomically classified as S. enterica with two other metagenomic tools, Metagenomic Intra-species Diversity Analysis System (MIDAS) and Metagenomic Phylogenetic Analysis 2 (MetaPhlAn2). This study re-affirmed that the traditional techniques of aerobic culture and PCR provide similar results for S. enterica identification in cattle feces. On the other hand, metagenomic results are highly influenced by the classification method and reference database employed. These results highlight the nuances of computational detection of species-level sequences within short-read metagenomic sequence data, and emphasize the need for cautious interpretation of such results.

18.
J Agric Food Chem ; 67(48): 13327-13332, 2019 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-31715101

RESUMO

The biochemical basis of lower metmyoglobin reducing activity (MRA) in high-oxygen modified atmospheric packaged (HiOx-MAP) beef than those in vacuum and polyvinyl chloride (PVC) packaging is not clear. To explore this, the effects of lipid oxidation products with varying carbon chain length on lactate dehydrogenase (LDH) and NADH-dependent metmyoglobin reductase activity were evaluated. Surface color, MRA, and lipid oxidation of beef longissimus lumborum steaks (n = 10) were measured during 6-day display. Further, two enzymes, LDH and NADH-dependent metmyoglobin reductase (n = 5), critical for MRA were incubated with or without (control) lipid oxidation products of varying carbon chain length: malondialdehyde (3-carbon), hexenal (6-carbon), and 4-hydroxynonenal (9-carbon). Steaks in HiOx-MAP had greater (P < 0.05) redness than vacuum and PVC, but had lower (P < 0.05) MRA and greater (P < 0.05) lipid oxidation on day 6. LDH and NADH-dependent metmyoglobin reductase activities were differentially influenced by lipid oxidation products (P < 0.05). The results indicate that the difference in reactivity of various lipid oxidation products on LDH (HNE > MDA = hexenal) and NADH-dependent metmyoglobin reductase (HNE = MDA > hexenal) activity could be responsible for lower MRA in HiOx-MAP.


Assuntos
Carbono/química , L-Lactato Desidrogenase/química , Lipídeos/química , NADH NADPH Oxirredutases/química , Carne Vermelha/análise , Animais , Carbono/metabolismo , Bovinos , Embalagem de Alimentos , L-Lactato Desidrogenase/metabolismo , Metamioglobina/química , Metamioglobina/metabolismo , Músculo Esquelético/química , Músculo Esquelético/enzimologia , Músculo Esquelético/metabolismo , NAD/química , NAD/metabolismo , NADH NADPH Oxirredutases/metabolismo , Oxirredução
19.
J Anim Sci ; 97(11): 4567-4578, 2019 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-31563955

RESUMO

Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.


Assuntos
Antibacterianos/administração & dosagem , Doenças dos Bovinos/prevenção & controle , Suplementos Nutricionais/análise , Abscesso Hepático/veterinária , Microbiota/efeitos dos fármacos , Tilosina/administração & dosagem , Ração Animal/análise , Animais , Bovinos , Doenças dos Bovinos/epidemiologia , Doenças dos Bovinos/microbiologia , Farmacorresistência Bacteriana , Fezes/microbiologia , Feminino , Geografia , Abscesso Hepático/epidemiologia , Abscesso Hepático/microbiologia , Abscesso Hepático/prevenção & controle , Masculino , Metagenômica , Microbiota/genética , Modelos Estatísticos , Prevalência , Microbiologia do Solo
20.
Front Microbiol ; 10: 1980, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31555225

RESUMO

Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide-lincosamide-streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the ß-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause-effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms' records (tetracyclines and macrolides in feedlots, ß-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the "resistance potential" of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA