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Aims: Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle. Methods and Results: Two arrival date blocks of high‐risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac lymph nodes were collected the day before and the day of harvest. Samples were cultured for antimicrobial‐resistant Salmonella, Escherichia coli and Enterococcus spp. The effect of treatment varied by day across all targeted bacterial populations (p ≤ 0.01) except total E. coli. Total E. coli counts were greatest on days 112, 182 and study end (p ≤ 0.01). Tulathromycin resulted in greater counts and prevalence of Salmonella from faeces than CON at study end (p ≤ 0.01). Tulathromycin and CEF yielded greater Salmonella hide prevalence and greater counts of 128ERYRE. coli at study end than CON (p ≤ 0.01). No faecal Salmonella resistant to tetracyclines or third‐generation cephalosporins were detected. Ceftiofur was associated with greater counts of 8ERYREnterococcus spp. at study end (p ≤ 0.03). By the day before harvest, antimicrobial use did not increase prevalence or counts for all other bacterial populations compared with CON (p ≥ 0.13). Conclusions: Antimicrobial resistance (AMR) in feedlot cattle is not caused solely by using a metaphylactic antimicrobial on arrival, but more likely a multitude of environmental and management factors. [ABSTRACT FROM AUTHOR]

Intramuscular adipose tissue (IMAT; marbling) deposition is a highly desired trait in beef cattle. Unlike excessive subcutaneous (SCAT) and visceral (VIAT) adipose tissue, which have relatively low value, increased marbling is associated with meat sensory traits and is a primary factor influencing beef quality grading in the U.S. However, this trait is difficult to achieve. Our objective was to assess depot-specific characteristics and gene profile of IMAT, SCAT, and VIAT in beef cattle. IMAT and SCAT samples from the longissimus muscle (9-11th ribs), and VIAT from the greater omentum were collected from four beef animals at harvest. Adipose tissue (AT) samples were flash frozen in liquid nitrogen, followed by RNA extraction (Trizol reagent) and RNA sequencing analysis on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. DESeq2 R package was used for differential gene expression analysis (DEG) and DEG (P = 0.05, log2FC = 1) were evaluated for KEGG enrichment pathways. Remainder tissue samples were assessed for viscoelasticity (rheometer), collagen fibrillogenesis (kinetics), and adipocyte size (K2 Cellometer). Transcriptome analysis revealed over 4,000 DEG between IMAT and SCAT, over 3,000 DEG between VIAT and IMAT, and 1,018 DEG between VIAT and SCAT, thus indicating substantial transcriptional diversity among AT depots (Figure 1). Top upregulated genes in SCAT vs. IMAT were associated with increased lipid accumulation and regulation such as LIPE, LEP, ADIPOQ, PPARG, and extracellular matrix (ECM) remodeling, including collagens, MMP14, and TIMP4. Accordingly, enrichment analysis revealed an activation of PPARG signaling pathways and fatty acid metabolism in SCAT vs. IMAT, which are key for lipogenesis and adipogenesis (Figure 2). IMAT showed activation of pathways for thermogenesis and oxidative phosphorylation compared with both SCAT and VIAT, indicating that IMAT utilization may be more directed towards muscle function and development (Figure 2 and 3). Top VIAT DEG were primarily associated with immune cell adhesion, and immune response (CDHR1, TENM2, and TNFRSF9), suggesting a pro-inflammatory profile of visceral adiposity. Notably, enrichment analysis showed an activation of the immune function in VIAT compared with IMAT and SCAT (Figures 3 and 4). In agreement with transcriptome analysis, adipocyte size was increased in SCAT vs. IMAT and VIAT, implying higher lipid accumulation (Figure 5). SCAT was also stiffer and had increased collagen fibrillogenesis compared with IMAT, suggesting a key role for ECM in mechanisms of AT adipogenesis and lipogenesis (Figure 5). In summary, these results indicate that AT anatomical location impacts AT transcriptome, which may translate into functional differences in adipogenesis and ECM remodeling. Understanding transcriptional and functional differences among IMAT, SCAT and VIAT can help on the identification of target genes to modulate AT deposition in distinct areas of the body, therefore, improving quality of beef carcasses and industry profitability. [ABSTRACT FROM AUTHOR]

Our objective was to evaluate the use of a novel direct-fed microbial as an alternative to antimicrobials to decrease liver abscesses in feedlot cattle. Angus beef steers (n = 240; initial BW = 263 ± 18.0 kg) were used in a randomized complete block design comprised of 3 BW blocks and 3 pen replications per treatment. Experimental treatments were randomly assigned to pen within BW block and consisted of: 1) negative control, dietary supplement contained no tylosin phosphate (NCON); 2) positive control, dietary supplement contained tylosin phosphate (PCON); 3) positive control with tylosin phosphate removed the last 65 d of the feeding period (PCONW); and 4) novel direct-fed microbial fed at 1 g mixture/animal with 1 × 1011 CFU/g (DFM). By design, initial BW did not differ (P = 0.79) among treatments, and at the end of the 59-d receiving period, there were no differences in final BW (P = 0.25). From d 0 to d 30, ADG, DMI, DMI as a percentage of BW, and G:F did not differ (P = 0.21). Likewise, ADG, DMI, DMI as a percentage of BW, and G:F, from d 31 to d 59, were not different (P = 0.30). From d 0 to d 59, there were no differences in ADG, DMI, DMI as a percentage of BW, nor G:F (P = 0.20). During the finishing period, live- and carcassadjusted final BW did not differ (P = 0.57) among treatments. During the finishing period, there were also no differences in ADG, DMI, DMI as a percentage of BW, or G:F (P = 0.17). Carcass-adjusted ADG, DMI as a percentage of BW, and G:F also did not differ (P = 0.16). Across treatments, no differences in HCW were noted (P = 0.84). Dressing percentage, marbling score, longissimus dorsi (LM) area, 12th-rib fat thickness, and calculated yield grade (YG) were not different among dietary treatments (P = 0.32). Liver abscess incidence and severity were not affected by dietary treatments (P = 0.13). The inclusion of a novel direct-fed microbial in finishing cattle diets did not affect growth performance, carcass characteristics, nor the prevalence of liver abscesses. However, the removal of tylosin phosphate 65 d before harvest numerically resulted in the lowest frequency of severe liver abscesses when compared with steers not fed tylosin phosphate. [ABSTRACT FROM AUTHOR]

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 β-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, β-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. [ABSTRACT FROM AUTHOR]

The effects of dietary inclusion of live bacteria on feedlot beef cattle growth performance and carcass characteristics were evaluated. Crossbred-Angus yearling steers (n = 192; initial BW = 409 kg ± 8 kg) were blocked by body weight (BW) and randomly assigned into 48 pens (4 steers/pen; 16 pens/treatment) following a randomized complete block design. A steam-flaked corn-based fishing diet was offered ad libitum once daily containing the following treatments: 1) Control, in which no direct fed microbial (DFM) was offered (lactose as carrier only); 2 and 3) Probiotic mixtures at distinct concentrations [Mixture A and B, at 2g/animal-daily (lactose used as carrier)]. Orts DM were quantified daily and subtracted from total dietary DM offered to calculate DM intake. Two-day consecutive unshrunk BW were recorded before feeding on d 0, 30, 60, 90, 121, and 153 (prior to shipment to a federally inspected slaughter facility). Data were analyzed using the GLIMMIX procedure of SAS and pen was considered the experimental unit, in which F-test protected pre-planned contrasts comparing control versus DFM mixture-A and control versus DFM mixture-B were used. Steers offered mixture-A increased carcass-adjusted ADG (P = 0.03) by 6.7%, gain efficiency (P < 0.01) by 6%, tended to increase carcass-adjusted final BW (P = 0.07) by 15kg and hot carcass weight (P = 0.07) by 10kg. The overall (d 0 to end) DM intake (P = 0.36) was not affected by treatment; however, a subtle (1.2%) decrease (P < 0.01) during the initial 30 days for steers offered DFM mixture-B was observed. Carcass variables (dressing percentage, 12th rib fat, longissimus muscle area, marbling, yield grade, and liver scores) were not affected (P = 0.13) by treatments. Growth performance was improved with DFM mixture-A which seemed to positively affect carcass weight without inducing deleterious effects on other carcass characteristics. [ABSTRACT FROM AUTHOR]

Treatment of food-producing animals with antimicrobial drugs (AMD) is controversial because of concerns regarding promotion of antimicrobial resistance (AMR). To investigate this concern, resistance genes in metagenomic bovine fecal samples during a clinical trial were analyzed to assess the impacts of treatment on beef feedlot cattle resistomes. Four groups of cattle were exposed, using a 2-by-2 factorial design, to different regimens of antimicrobial treatment. Injections of ceftiofur crystalline- free acid (a third-generation cephalosporin) were used to treat all cattle in treatment pens or only a single animal, and either chlortetracycline was included in the feed of all cattle in a pen or the feed was untreated. On days 0 and 26, respectively, pre- and posttrial fecal samples were collected, and resistance genes were characterized using shotgun metagenomics. Treatment with ceftiofur was not associated with changes to β-lactam resistance genes. However, cattle fed chlortetracycline had a significant increase in relative abundance of tetracycline resistance genes. There was also an increase of an AMR class not administered during the study, which is a possible indicator of coselection of resistance genes. Samples analyzed in this study had previously been evaluated by culture characterization (Escherichia coli and Salmonella) and quantitative PCR (qPCR) of metagenomic fecal DNA, which allowed comparison of results with this study. In the majority of samples, genes that were selectively enriched through culture and qPCR were not identified through shotgun metagenomic sequencing in this study, suggesting that changes previously documented did not reflect changes affecting the majority of bacterial genetic elements found in the predominant fecal resistome. IMPORTANCE Despite significant concerns about public health implications of AMR in relation to use of AMD in food animals, there are many unknowns about the long- and short-term impact of common uses of AMD for treatment, control, and prevention of disease. Additionally, questions commonly arise regarding how to best measure and quantify AMR genes in relation to public health risks and how to determine which genes are most important. These data provide an introductory view of the utility of using shotgun metagenomic sequencing data as an outcome for clinical trials evaluating the impact of using AMD in food animals. [ABSTRACT FROM AUTHOR]