Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle.

Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuDNA coverages. Variant calling was performed from mtDNA, and 11 single nucleotide polymorphisms (SNP) were identified in the population. Samples were classified in taurine haplogroups. Haplogroup and mtDNA type were further classified based on the 11 segregating SNP. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Associations of mtDNA CN, mtDNA haplogroups, mtDNA types, and mtDNA SNP with growth and carcass traits were estimated with univariate animal models, and genetic correlations were estimated with a bivariate animal model based on pedigree. Mitochondrial DNA CN tended (P-value ≤0.08) to be associated with birth weight and weaning weight. There was no association (P-value >0.10) between mtDNA SNP, haplogroups, or types with growth and carcass traits. Genetic correlation estimates of mtDNA CN were -0.30 ± 0.16 with birth weight, -0.31 ± 0.16 with weaning weight, -0.15 ± 0.14 with post-weaning gain, -0.11 ± 0.19 with average daily dry-matter intake, -0.04 ± 0.22 with average daily gain, -0.29 ± 0.13 with mature cow weight, -0.11 ± 0.13 with slaughter weight, -0.14 ± 0.13 with carcass weight, -0.07 ± 0.14 with carcass backfat, 0.14 ± 0.14 with carcass marbling, and -0.06 ± 0.14 with ribeye area. In conclusion, mtDNA CN was negatively correlated with most traits investigated, and the genetic correlation was stronger with growth traits than with carcass traits.

This study investigated mitochondrial DNA copy number (mtDNA CN) as a potential genetic indicator of growth and carcass traits in a composite beef cattle population. Mitochondrial DNA CN was previously shown to be under genetic control. The current study estimated the genetic relationship of mtDNA CN with growth and carcass traits. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to whole-genome sequencing at a low depth that resulted in nuclear DNA and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuclear DNA coverages. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Genetic parameters were estimated from an animal model based on pedigree. Genetic correlation estimates of mtDNA CN with growth and carcass traits were low to moderate and mostly negative. These indicate that selection for lower mtDNA would be associated with an increase in birth weight, weaning weight, post-weaning gain, average daily dry-matter intake, mature cow weight, slaughter weight, and carcass weight. Therefore, the by-product of whole-genome sequencing at a low depth could be used as an indicator trait for growth and carcass traits in genetic evaluations, but the genetic relationships are not likely strong enough to prioritize mtDNA ahead of routinely used indicator traits.

Evaluating the Shelf Life and Sensory Properties of Beef Steaks from Cattle Raised on Different Grass Feeding Systems in the Western United States.

Consumer interest in grass-fed beef has been steadily rising due to consumer perception of its potential benefits. This interest has led to a growing demand for niche market beef, particularly in the western United States. Therefore, the objective of this study was to assess the impact of feeding systems on the change in microbial counts, color, and lipid oxidation of steaks during retail display, and on their sensory attributes. The systems included: conventional grain-fed (CON), 20 months-grass-fed (20GF), 25-months-grass-fed (25GF) and 20-months-grass-fed + 45-day-grain-fed (45GR). The results indicate that steaks in the 20GF group displayed a darker lean and fat color, and a lower oxidation state than those in the 25GF group. However, the feeding system did not have an impact on pH or objective tenderness of beef steaks. In addition, consumers and trained panelist did not detect a difference in taste or flavor between the 20GF or 25GF steaks but expressed a preference for the CON and 45GR steaks, indicating that an increased grazing period may improve the color and oxidative stability of beef, while a short supplementation with grain may improve eating quality.

Differences in carcass chilling rate underlie differences in sensory traits of pork chops from pigs with heavier carcass weights.

Pork hot carcass weights (HCW) have been increasing 0.6 kg per year, and if they continue to increase at this rate, they are projected to reach an average weight of 118 kg by the year 2050. This projection in weight is a concern for pork packers and processors given the challenges in product quality from heavier carcasses of broiler chickens. However, previous work demonstrated that pork chops from heavier carcasses were more tender than those from lighter carcasses. Therefore, the objective was to determine the effects of pork hot carcass weights, ranging from 90 to 145 kg with an average of 119 kg, on slice shear force and sensory traits of Longissimus dorsi chops when cooked to 63 or 71 °C, and to assess if differences in chilling rate can explain differences in sensory traits. Carcasses were categorized retrospectively into fast, medium, or slow chilling-rates based on their chilling rate during the first 17 h postmortem. Loin chops cut from 95 boneless loins were cooked to either 63 or 71 °C and evaluated for slice shear force and trained sensory panel traits (tenderness, juiciness, and flavor) using two different research laboratories. Slopes of regression lines and coefficients of determination between HCW and sensory traits were calculated using the REG procedure in SAS and considered different from 0 at P ≤ 0.05. As hot carcass weight increased, chops became more tender as evidenced by a decrease in SSF (63 °C ß = -0.0412, P = 0.01; 71 °C ß = -0.1005, P < 0.001). Furthermore, HCW explained 25% (R2 = 0.2536) of the variation in chilling rate during the first 5 h of chilling and 32% (R2 = 0.3205) of the variation in chilling rate from 5 to 13 h postmortem. Slow- and medium-rate chilling carcasses were approximately 12 kg heavier (P < 0.05) than fast chilling carcasses. Slice shear force of chops cooked to 63 and 71 °C was reduced in slow and medium chilling compared with fast chilling carcasses. Carcass temperature at 5 h postmortem explained the greatest portion of variation (R2 = 0.071) in slice shear force of chops cooked to 63 °C. These results suggest that carcasses tend to chill slower as weight increases, which resulted in slight improvements in sensory traits of boneless pork chops regardless of final degree of doneness cooking temperature.

Pork carcass weights have increased year over year for at least the past 25 yr. The poultry industry has experienced similar increases in carcass weights in the recent past. The increases in broiler carcass weights have resulted in detrimental impacts on quality. Contrary to the poultry industry, increases in pork carcass weights have resulted in a general improvement in pork quality, including tenderness. The underlying cause of these improvements has not been explained. In the present study, chilling rate was associated with carcass weights, particularly during the first 5 h postmortem. In fact, carcass temperature measured in the Longissimus dorsi muscle at 5 h postmortem was the most predictive of instrumental tenderness values when boneless pork chops were cooked according to UDSA guidelines for whole-muscle pork products. The metabolic conversion of muscle to meat is most active during this initial chilling period. Therefore, chilling rate, which is associated with carcass weight, may be influencing the conversion of muscle to meat and provide some explanation as to why heavy carcasses result in more tender pork chops.

Seasonal Prevalence of Shiga Toxin-Producing Escherichia coli on Pork Carcasses for Three Steps of the Harvest Process at Two Commercial Processing Plants in the United States.

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen that has a significant impact on public health, with strains possessing the attachment factor intimin referred to as enterohemorrhagic E. coli (EHEC) and associated with life-threatening illnesses. Cattle and beef are considered typical sources of STEC, but their presence in pork products is a growing concern. Therefore, carcasses (n = 1,536) at two U.S. pork processors were sampled once per season at three stages of harvest (poststunning skins, postscald carcasses, and chilled carcasses) and then examined using PCR for Shiga toxin genes (stx), intimin genes (eae), aerobic plate count (APC), and Enterobacteriaceae counts (EBC). The prevalence of stx on skins, postscald, and chilled carcasses was 85.3, 17.5, and 5.4%, respectively, with 82.3, 7.8, and 1.7% of swabs, respectively, having stx and eae present. All stx-positive samples were subjected to culture isolation that resulted in 368 STEC and 46 EHEC isolates. The most frequently identified STEC were serogroups O121, O8, and O91 (63, 6.7, and 6.0% of total STEC, respectively). The most frequently isolated EHEC was serotype O157:H7 (63% of total EHEC). Results showed that scalding significantly reduced (P < 0.05) carcass APC and EBC by 3.00- and 2.50-log10 CFU/100 cm2, respectively. A seasonal effect was observed, with STEC prevalence lower (P < 0.05) in winter. The data from this study show significant (P < 0.05) reduction in the incidence of STEC (stx) from 85.3% to 5.4% and of EHEC (stx plus eae) from 82.3% to 1.7% within the slaughter-to-chilling continuum, respectively, and that potential EHEC can be confirmed present throughout using culture isolation.IMPORTANCE Seven serogroups of STEC are responsible for most (>75%) cases of severe illnesses caused by STEC and are considered adulterants of beef. However, some STEC outbreaks have been attributed to pork products, although the same E. coli are not considered adulterants in pork because little is known of their prevalence along the pork chain. The significance of the work presented here is that it identifies disease-causing STEC, EHEC, demonstrating that these same organisms are a food safety hazard in pork as well as beef. The results show that most STEC isolated from pork are not likely to cause severe disease in humans and that processes used in pork harvest, such as scalding, offer a significant control point to reduce contamination. The results will assist the pork processing industry and regulatory agencies to optimize interventions to improve the safety of pork products.

Effects of space allowance and marketing strategy on growth performance of pigs raised to 165 kg.

A total of 976 pigs (PIC 327 × Camborough; PIC, Hendersonville, TN; initially 22.0 ± 1.53 kg body weight [BW]) were used in a 160-d growth study to evaluate the effects of increasing space allowance and varying marketing strategies on growth performance of pigs raised to market weights of ~165 kg. Pens of pigs were blocked by location within the barn and allotted to one of six treatments. Pen served as the experimental unit, and there were eight replicate pens per treatment. The first four treatments consisted of increased initial stocking density and did not utilize topping strategies: (1) 14 pigs/pen (1.17 m2/pig), (2) 17 pigs/pen (0.97 m2/pig), (3) 20 pigs/pen (0.82 m2/pig), and (4) 23 pigs/pen (0.71 m2/pig). The fifth treatment began with 25 pigs/pen (0.66 m2/pig) and had four marketing events with the heaviest 3 pigs/pen removed on day 93, and additional pigs removed to a common inventory of 20 pigs/pen on day 122 and 17 pigs/pen on day 147 with final marketing on day 160. The final treatment began the experiment with 23 pigs/pen (0.71 m2/pig) with three marketing events to achieve a common inventory of 20 pigs/pen on day 108 and 17 pigs/pen on day 147. Pens of pigs were weighed and feed disappearance measured on days 0, 55, 93, 108, 122, 135, 147, and 160. As space allowance decreased from 1.17 to 0.71 m2/pig via increased initial pen inventory (treatments 1 to 4), overall average daily gain (ADG) and average daily feed intake (ADFI) decreased (linear, P < 0.001), while gain:feed ratio (G:F) did not differ (P > 0.05). The treatments with multiple marketing events were compared with each other and with the treatment that began with 0.71 m2/pig and only marketed once at the end of the study. Overall ADG and ADFI were not different (P > 0.05) among these three treatments. Marketing pigs three or four times improved (P < 0.05) G:F compared with the treatment that began the study with 0.71 m2/pig and marketed only once. Reducing floor space allowance for heavy weight pigs decreased intake, which resulted in lower growth rate and final BW, with these reductions occurring before the critical k-value was reached. Total weight gain per pen was maximized with the lowest space allowance and the multiple marketing treatments. Thus, strategic use of pig removals prior to final marketing may allow producers to maximize both number of pigs and total weight marketed through a barn when feeding to heavy weights.

Comparison of Machine Learning Algorithms for Predictive Modeling of Beef Attributes Using Rapid Evaporative Ionization Mass Spectrometry (REIMS) Data.

Ambient mass spectrometry is an analytical approach that enables ionization of molecules under open-air conditions with no sample preparation and very fast sampling times. Rapid evaporative ionization mass spectrometry (REIMS) is a relatively new type of ambient mass spectrometry that has demonstrated applications in both human health and food science. Here, we present an evaluation of REIMS as a tool to generate molecular scale information as an objective measure for the assessment of beef quality attributes. Eight different machine learning algorithms were compared to generate predictive models using REIMS data to classify beef quality attributes based on the United States Department of Agriculture (USDA) quality grade, production background, breed type and muscle tenderness. The results revealed that the optimal machine learning algorithm, as assessed by predictive accuracy, was different depending on the classification problem, suggesting that a "one size fits all" approach to developing predictive models from REIMS data is not appropriate. The highest performing models for each classification achieved prediction accuracies between 81.5-99%, indicating the potential of the approach to complement current methods for classifying quality attributes in beef.

Effect of hot carcass weight on the rate of temperature decline of pork hams and loins in a blast-chilled commercial abattoir123.

Adequate carcass chilling is required to optimize pork quality and food safety. The rate at which carcasses chill is dependent on their mass. Hot carcass weight has increased steadily over the years, certainly affecting the chilling rate of the average carcass in contemporary abattoirs. Therefore, the objective was to model the effect of HCW on temperature decline of a contemporary population of pork carcasses slaughtered at a commercial abattoir that used a blast-chilling method. In addition, carcasses were sorted into HCW classes, and the effect of HCW group was tested on the rate of temperature decline of the longissimus dorsi and semimembranosus. Hot carcass weight, internal temperature of the loin muscle (at the 10th rib) and ham, as well as ambient temperature, were recorded from 40 to 1,320 min postmortem (45 time points) on 754 pork carcasses. An exponential decay model based on Newton's law of cooling,  T(t)=Ta+(T0-Ta)e-kt, was fit to temperature decline of the ham and loin of the whole population using PROC MODEL of SAS. The initial models for the decline of both ham and loin temperature displayed significant autocorrelation of errors based on evaluation of the autocorrelation function plots and Durbin-Watson test (P < 0.0001). Therefore, second- and third-order autocorrelation parameters were tested. Based on Durbin-Watson test, the use of second-order autocorrelation model with lags of 1 and 2 was deemed adequate and was therefore included in all subsequent models. This base model and its respective parameter estimates were all significant (P < 0.01) for the whole population. Carcasses approximating 85, 90, 95, 100, and 105 kg (± 1 kg) were selected and binned into their respective weight classes. Dummy variables were used to compare the effect of HCW class on parameter estimate of ham and loin models. The developed model significantly fit all weight classes (P < 0.01) for both ham and loin temperature decline. For both loin and ham models, estimates of the rate constant (k) generally decreased as HCW increased. For loin temperature, k estimate for 105-kg carcasses was 0.00124 less (P = 0.02) than 85-kg carcasses, with the intermediate HCW classes not differing from the 85-kg class. For ham temperature, estimates of k for 90, 95, 100, and 105 kg HCW were all significantly and successively less than the k estimate for 85 kg class. For perspective, loins of 95-kg carcasses were estimated to reach 2 °C in 17 h, whereas loins from 105-kg carcasses would not reach 2 °C until 27 h. For hams, 95-kg carcasses were projected to reach 2 °C in 21 h, whereas those from 105-kg carcasses would take 28 h. Overall, HCW significantly affects the rate of temperature decline of pork hams, but not loins from pork carcasses weighing between 85 and 100 kg.

Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and µ-calpain genes.

The objective of this study was to enhance estimates of additive, dominance, and epistatic effects of marker polymorphisms on beef carcass and quality traits. Myostatin (MSTN) F94L SNP and the µ-calpain (CAPN1) 316 and 4751 SNP haplotype have previously been associated with fat and muscle traits in beef cattle. Multiyear selection in a composite population segregating these polymorphisms increased minor allele (F94L L) and chosen haplotype (CAPN1 CC and GT) frequencies to intermediate levels resulting in more precise estimates of additive and nonadditive genetic effects. During the 3 yr after selection, 176 steers were evaluated for growth, carcass, meat quality, tenderness (n = 103), and meat color traits. The statistical model included year, age of dam, age of the steer, and genotype in a random animal model. The 9 genotypes (3 CAPN1 diplotypes × 3 F94L genotypes) affected marbling score, ribeye area, adjusted fat thickness, vision yield grade (all P < 0.001), slice shear force (P = 0.03), and CIE L* reflectance (P = 0.01). Linear contrasts of the 9 genotypes estimated additive, recessive, and epistatic genetic effects. Significant additive effects of the F94L L allele decreased marbling score, adjusted fat thickness, vision yield grade, and slice shear force; and increased ribeye area and CIE L* reflectance. The homozygous F94L FF and LL genotypes differed by 1.3 to 1.9 phenotypic SD for most carcass traits and by 0.8 to 0.9 SD for slice shear force and CIE L* reflectance but carcass weight differed by only 3 kg (0.1 SD). The L allele was partially recessive to F for ribeye area (P = 0.02) and the heterozygous FL means tended to be closer to the FF genotype than the LL genotype for other carcass traits but differences from additive were not significant. The CAPN1 additive × F94L additive effect on slice shear force was the only significant epistatic estimate. The F94L L allele is prevalent in Limousin but nearly absent in other U.S. purebreds. This allele had about half of the effects on birth weight, muscle, and fat traits reported for severe MSTN mutations in Belgian Blue and Piedmontese breeds. The interaction between MSTN and CAPN1 genotypes may reflect the strong additive effects of MSTN F94L L allele on fat and muscle traits interfering with the phenotypic effect of CAPN1 genotype on meat tenderness.

Surface pH of Fresh Beef as a Parameter To Validate Effectiveness of Lactic Acid Treatment against Escherichia coli O157:H7 and Salmonella.

The U.S. beef industry must provide documentation to the U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) that the antimicrobial interventions implemented or any subsequent changes in the process are effective under the actual conditions that apply in its operation. The main objective of this study was to determine whether surface pH after application of diluted lactic acid solution on surfaces of fresh meat can be used as a control measure indicator for the reduction of E. coli O157:H7 and Salmonella. Samples (240 each) of lean and adipose beef tissues were inoculated with cocktail mixtures of Escherichia coli O157:H7 and Salmonella. Application parameters were varied such that lean and adipose tissues were spray treated with either 2 or 4.5% lactic acid solution at either 38 or 60°C for 1 to 10 s. Lean and adipose tissues were collected before and after spray treatments for enumeration of the pathogens. Based on the conditions of this study, there was no difference between spray treatments at 38 or 60°C, but 4.5% lactic acid solution reduced pathogens more effectively ( P ≤ 0.05) than did 2% lactic acid solution. Spray treatment with lactic acid solution for 1 to 10 s reduced surface pH values of lean tissues (3 to 3.8) and adipose tissues (2.75 to 3.65). At surface pH values of 3.0 and 2.75, lactic acid reduced E. coli O157:H7 on surfaces of lean and adipose tissues by approximately 1.60 and 1.54 log CFU/cm2, respectively. At surface pH values of 3.8 and 3.65, lactic acid reduced E. coli O157:H7 on lean and adipose tissues by approximately 0.3 and 0.42 log CFU/cm2, respectively. The surface pH values after lactic acid treatment and the reductions of both pathogens showed a strong linear relationship; this indicates that a surface pH of 3.1 would provide at least 1-log reduction of E. coli O157:H7 and Salmonella, regardless of lactic acid application parameters. Therefore, surface pH after spray treatment with lactic acid could be used to validate pathogen reduction.

Determining the relationship between early postmortem loin quality attributes and aged loin quality attributes using meta-analyses techniques.

Meta-analyses techniques using 11 independent datasets were used to determine correlations between pork loin quality evaluated at 1-d postmortem and quality evaluated at 12- to 28-d postmortem. Datasets encompassed approximately 3,957 loins. The effects of aging on ventral loin surface quality were determined using a paired-T test. Ventral loin surfaces become 8% lighter (P < 0.0001), 44.5% redder (P < 0.0001), and 46% more yellow (P < 0.0001) during the aging period. Therefore, it is apparent that loin quality changes during postmortem aging. Because of this, it becomes necessary to determine the correlation between early and aged pork quality parameters. Pearson correlation coefficients within original datasets were calculated, and then sample-weighted mean correlations r¯ and variances [Var(r)] were calculated across datasets. Early postmortem ventral instrumental lightness (L*) was moderately correlated with aged ventral L* r¯ = 0.50), aged ventral visual color r¯ = -0.38), aged chop face (freshly cut) L* r¯ = 0.44), and aged chop face visual color r¯ = -0.38). Early postmortem ventral instrumental redness (a*) was moderately correlated with aged ventral a* r¯ = 0.49) and aged chop face a* r¯ = 0.46). Early postmortem ventral visual color was moderately correlated with aged ventral L* r¯ = -0.51), aged ventral color (r¯ = 0.50), aged chop face L* r¯ = -0.43), and aged chop face visual color r¯ = 0.43). However, no instrumental or visual color parameters were moderately or strongly correlated with instrumental tenderness or sensory panel ratings of tenderness and juiciness (|r¯| ≤ 0.36). Early postmortem ventral visual marbling was moderately correlated with aged ventral marbling r¯ = 0.63) and aged chop face visual marbling r¯ = 0.56). Visual marbling was not (|r¯| ≤ 0.12) correlated with instrumental tenderness or sensory panel ratings of tenderness and juiciness. Stepwise regression, using a holo-analysis approach, was used to determine the predictive ability of early postmortem ventral color, marbling, firmness, and pH on sensory panels ratings of tenderness (R2 = 0.13), juiciness (R2 = 0.09), and flavor (R2 = 0.28). Early postmortem color and marbling are important pork quality traits in consumers purchasing decisions, but are poorly related to traits associated with eating experience. Still, they may be predicative of traits associated with purchasing intent.

Effects and interactions of myostatin and callipyge mutations: I. Growth and carcass traits.

Objectives were to document effects of the Texel myostatin mutation (MSTN) on growth and carcass traits and also test whether or not interactions with the callipyge mutation (CLPG) could be detected. Twelve rams heterozygous at both loci on the two different chromosomes were mated to 215 terminal-sire type composite crossbred ewes genotyped as non-carriers for both loci. A total of 365 lambs were born, 362 of those were genotyped and 236 lambs contributed carcass data to estimate effects and interactions among the four genotype combinations produced. The four genotype combinations were defined as follows: ++/++ for wild-type at both loci; ++/C+ for wild-type at MSTN and heterozygous at CLPG; M+/++ for heterozygous at MSTN and wild-type at CLPG; and M+/C+ for heterozygous at both loci. The two independently segregating sire-derived alleles represent different breed-of-origin contrasts at each locus (Texel vs. composite origin for MSTN and Dorset vs. Texel origin for CLPG). Birth weight was recorded on all lambs, and subsequent body weights were adjusted to 56 (weaning), 70, and 140 d of age. Within sire-sex-genotype subgroups, naturally reared lambs were assigned to one of eight slaughter groups accounting for variation in birth date. Lambs were serially slaughtered at weekly intervals, 30 lambs per group, from roughly 26 to 33 wk of age. In addition to standard carcass traits, subjective leg scores were assigned and widths of carcasses were measured at the widest points of the shoulder and rump. Differences in birth weight were detected (P < 0.01) for the combination of the two loci and birth type, with single-born differences among genotypes exceeding differences among twin born progeny. Those interaction differences among genotypes were not as important at weaning (P = 0.36). Impact on growth rate differences among the genotypes during the post-weaning period were variable and dependent on sex of the lamb (P < 0.01). A synergistic interaction between MSTN and CLPG was observed for leg muscling scores (P < 0.05) but no other measures of carcass shape were affected. One copy of MSTN had a more modest impact on fat deposition and muscle conformation than did CLPG and did not interact (all values P > 0.20). Although some non-additive interactions that vary by trait and sex were detected, in general the data are consistent with the two mutations acting on muscle growth through independent pathways.

Salmonella in Peripheral Lymph Nodes of Healthy Cattle at Slaughter.

To more fully characterize the burden of Salmonella enterica in bovine peripheral lymph nodes (PLN), PLN (n = 5,450) were collected from healthy cattle at slaughter in 12 commercial abattoirs that slaughtered feedlot-fattened (FF) cattle exclusively (n = 7), cattle removed (or culled) from breeding herds (n = 3), or both FF and cull cattle (n = 2). Qualitative and quantitative methods were used to estimate prevalence and concentration of Salmonella in PLN. Isolates were subjected to a variety of phenotypic, serological, and molecular assays. Overall, Salmonella prevalence in PLN from FF and cull cattle was 7.1 and 1.8%. However, burden varied by season in that observed prevalence in PLN collected in cooler or warmer seasons was 2.4 and 8.2%, respectively. Prevalence in PLN from cull cattle in the southwest region of the US was 2.1 and 1.1% for cool and warm seasons, respectively; however, prevalence in FF PLN was far greater in that it was 6.5 and 31.1%, respectively. Salmonella was recovered from 289 (5.6%) PLN and 2.9% (n = 160) of all PLN tested had quantifiable concentrations that varied from 1.6 to 4.9 log10 colony forming units/PLN. The most common serotypes isolated from PLN were Montevideo (26.9%), Lille (14.9%), Cerro (13.0%), Anatum (12.8%), and Dublin (6.9%). In all, 376 unique isolates were collected from the 289 Salmonella-positive PLN. Antimicrobial susceptibility testing revealed the majority (80.6%) of these isolates were pansusceptible; however, 10.7% of isolates were found to be resistant to two or more antimicrobial classes. We were able to document an observed increased in prevalence of Salmonella in PLN during the warmer season, particularly in FF cattle from the southwest region of the US. The mechanisms underlying the observed association between season, region, and production source have yet to be elucidated. Nevertheless, these findings increase our understanding of the sources of contamination of beef products and shed light on transmission dynamics that may be useful in targeting these sources.

Evaluation of Commercial ß-Agonists, Dietary Protein, and Shade on Fecal Shedding of Escherichia coli O157:H7 from Feedlot Cattle.

Escherichia coli O157:H7 is a foodborne pathogen commonly associated with cattle feces. Diet, including dietary supplements such as ß-agonists, may impact fecal shedding of this pathogen. A series of three experiments were conducted to determine if the ß-agonists ractopamine hydrochloride (RAC) or zilpaterol hydrochloride (ZH) would impact the level or prevalence of fecal E. coli O157:H7 shedding. In Experiment 1, dietary RAC did not impact fecal shedding of E. coli O157:H7 based on the level or prevalence, but the addition of dietary soybean meal (SBM) in the study did reduce E. coli O157:H7 shedding. In Experiments 2 and 3, dietary ZH did not affect fecal E. coli O157:H7 shedding as determined by enumeration or prevalence, but in Experiment 2 the addition of 30% (dry matter basis) wet distillers grains with solubles (WDGS) in the diet tended to increase E. coli O157:H7 shedding. Shade is a potential management tool to reduce heat stress in cattle, and in Experiment 3 the presence of shade over the feedlot pens did not affect E. coli O157:H7 shedding. The use of ß-agonists in cattle diets did not significantly affect fecal shedding of E. coli O157:H7, and in particular the percentage of animals shedding enumerable levels of the pathogen did not change, indicating that there was not a change in colonization. As has been reported previously and indicated again in this study, the use of WDGS in the diet may increase E. coli O157:H7 shedding. In contrast, the addition of SBM to cattle diets, to increase the dietary crude protein, appeared to reduce E. coli O157:H7 shedding, but this potential dietary intervention needs to be confirmed with additional research.

Mitochondrial abundance and efficiency contribute to lean color of dark cutting beef.

Beef carcasses exhibiting four levels of dark cutting severity (DCS): Severe, Moderate, Mild, and Shady were compared to Control carcasses to investigate biochemical traits contributing to the dark cutting condition. Color attributes of Longissimus lumborum (LL) were measured after grading and during simulated retail display. Mitochondrial abundance and efficiency, bloomed oxymyoglobin, reducing ability, glycolytic potential, myoglobin concentration, and protein solubility and oxidation were determined. Glycolytic potential and lactate concentrations decreased (P<0.05) as DCS increased. Residual glycogen was greater (P<0.05) in steaks from Control carcasses compared to DCS classes. Generally, as DCS increased, LL steaks were darker and less red in color (P<0.05). Increased (P<0.05) oxygen consumption and reducing ability coincided with greater myoglobin concentration and greater abundance of less efficient mitochondria as DCS increased (P<0.05). These data suggest the dark cutting condition is associated with greater oxidative metabolism coupled with less efficient mitochondria resulting in depletion of glycogen during stress.

Differential abundance of sarcoplasmic proteome explains animal effect on beef Longissimus lumborum color stability.

The sarcoplasmic proteome of beef Longissimus lumborum demonstrating animal-to-animal variation in color stability was examined to correlate proteome profile with color. Longissimus lumborum (36 h post-mortem) muscles were obtained from 73 beef carcasses, aged for 13 days, and fabricated to 2.5-cm steaks. One steak was allotted to retail display, and another was immediately vacuum packaged and frozen at -80°C. Aerobically packaged steaks were stored under display, and color was evaluated on days 0 and 11. The steaks were ranked based on redness and color stability on day 11, and ten color-stable and ten color-labile carcasses were identified. Sarcoplasmic proteome of frozen steaks from the selected carcasses was analyzed. Nine proteins were differentially abundant in color-stable and color-labile steaks. Three glycolytic enzymes (phosphoglucomutase-1, glyceraldehyde-3-phosphate dehydrogenase, and pyruvate kinase M2) were over-abundant in color-stable steaks and positively correlated (P<0.05) to redness and color stability. These results indicated that animal variations in proteome contribute to differences in beef color.

Occurrence of Antimicrobial-Resistant Escherichia coli and Salmonella enterica in the Beef Cattle Production and Processing Continuum.

Specific concerns have been raised that third-generation cephalosporin-resistant (3GC(r)) Escherichia coli, trimethoprim-sulfamethoxazole-resistant (COT(r)) E. coli, 3GC(r) Salmonella enterica, and nalidixic acid-resistant (NAL(r)) S. enterica may be present in cattle production environments, persist through beef processing, and contaminate final products. The prevalences and concentrations of these organisms were determined in feces and hides (at feedlot and processing plant), pre-evisceration carcasses, and final carcasses from three lots of fed cattle (n = 184). The prevalences and concentrations were further determined for strip loins from 103 of the carcasses. 3GC(r) Salmonella was detected on 7.6% of hides during processing and was not detected on the final carcasses or strip loins. NAL(r) S. enterica was detected on only one hide. 3GC(r) E. coli and COT(r) E. coli were detected on 100.0% of hides during processing. Concentrations of 3GC(r) E. coli and COT(r) E. coli on hides were correlated with pre-evisceration carcass contamination. 3GC(r) E. coli and COT(r) E. coli were each detected on only 0.5% of final carcasses and were not detected on strip loins. Five hundred and 42 isolates were screened for extraintestinal pathogenic E. coli (ExPEC) virulence-associated markers. Only two COT(r) E. coli isolates from hides were ExPEC, indicating that fed cattle products are not a significant source of ExPEC causing human urinary tract infections. The very low prevalences of these organisms on final carcasses and their absence on strip loins demonstrate that current sanitary dressing procedures and processing interventions are effective against antimicrobial-resistant bacteria.

Cross-sectional study examining Salmonella enterica carriage in subiliac lymph nodes of cull and feedlot cattle at harvest.

Bovine peripheral lymph nodes (LNs), including subiliac LNs, have been identified as a potential source of human exposure to Salmonella enterica, when adipose trim containing these nodes is incorporated into ground beef. In order to gain a better understanding of the burden of S. enterica in peripheral LNs of feedlot and cull cattle, a cross-sectional study was undertaken in which 3327 subiliac LNs were collected from cattle at harvest in seven plants, located in three geographically distinct regions of the United States. Samples were collected in three seasons: Fall 2010, Winter/Spring 2011, and Summer/Fall 2011. A convenience sample of 76 LNs per day, 2 days per season (approximately 1 month apart), was collected per plant, from carcasses held in the cooler for no less than 24 h. Every 10(th) carcass half on a rail was sampled, in an attempt to avoid oversampling any single cohort of cattle. Median point estimates of S. enterica contamination were generally low (1.3%); however, median Salmonella prevalence was found to be greater in subiliac LNs of feedlot cattle (11.8%) compared to those of cull cattle (0.65%). Enumeration analysis of a subset of 618 feedlot cattle LNs showed that 67% of those harboring S. enterica (97 of 144) did so at concentrations ranging from <0.1 to 1.8 log10 CFU/g, while 33% carried a higher burden of S. enterica, with levels ranging from 1.9 to >3.8 log10 CFU/g. Serotyping of S. enterica isolated identified 24 serotypes, with the majority being Montevideo (44.0%) and Anatum (24.8%). Antimicrobial susceptibility phenotypes were determined for all isolates, and the majority (86.1%) were pansusceptible; however, multidrug-resistant isolates (8.3%) were also occasionally observed. As Salmonella contained within LNs are protected from carcass interventions, research is needed to define opportunities for mitigating the risk of Salmonella contamination in LNs of apparently healthy cattle.

Isolation and characterization of Clostridium difficile associated with beef cattle and commercially produced ground beef.

The incidence of Clostridium difficile infection has recently increased in North American and European countries. This pathogen has been isolated from retail pork, turkey, and beef products and reported associated with human illness. This increase in infections has been attributed to the emergence of a toxigenic strain designated North America pulsed-field gel electrophoresis type 1 (NAP1). The NAP1 strain has been isolated from calves as well as ground meat products, leading to speculation of illness from consumption of contaminated meat products. However, information on C. difficile associated with beef cattle during processing and commercially produced ground beef is limited. To address this data gap, samples from various steps during beef production were collected. Samples from hides (n = 525), preevisceration carcasses (n = 475), postintervention carcasses (n = 471), and 956 commercial ground beef samples were collected from across the United States. The prevalence of C. difficile spores on hides was 3.2%. C. difficile spores were not detected on preevisceration and postintervention carcasses or in commercially produced ground beef. Phenotypic and genetic characterizations were carried out for all 18 isolates collected from hide samples. Twenty-two percent of the isolates were nontoxigenic strains, while 78% of the isolates were toxigenic. Toxinotyping and PCR ribotyping patterns revealed that 6 and 33% of the isolates were identified as NAP1 and NAP7 strains, respectively. This article evidences that the prevalence of C. difficile, specifically pathogenic strains, in the U.S. beef production chain is low.

Evaluation of commonly used antimicrobial interventions for fresh beef inoculated with Shiga toxin-producing Escherichia coli serotypes O26, O45, O103, O111, O121, O145, and O157:H7.

Although numerous antimicrobial interventions targeting Escherichia coli O157:H7 have been developed and implemented to decontaminate meat and meat products during the harvesting process, the information on efficacy of these interventions against the so-called Big Six non-O157 Shiga toxin-producing E. coli (STEC) strains is limited. Prerigor beef flanks (160) were inoculated to determine if antimicrobial interventions currently used by the meat industry have a similar effect in reducing non-O157 STEC serogroups O26, O45, O103, O111, O121, and O145 compared with E. coli O157:H7. A high (10(4) CFU/cm(2)) or a low (10(1) CFU/cm(2)) inoculation of two cocktail mixtures was applied to surfaces of fresh beef. Cocktail mixture 1 was composed of O26, O103, O111, O145, and O157, while cocktail mixture 2 was composed of O45, O121, and O157. The inoculated fresh beef flanks were subjected to spray treatments by the following four antimicrobial compounds: acidified sodium chlorite, peroxyacetic acid, lactic acid, and hot water. High-level inoculation samples were enumerated for the remaining bacteria populations after each treatment and compared with the untreated controls, while low-level inoculation samples were chilled for 48 h at 4°C before enrichment, immunomagnetic separation, and isolation. Spray treatments with hot water were the most effective, resulting in mean pathogen reductions of 3.2 to 4.2 log CFU/cm(2), followed by lactic acid. Hot water and lactic acid also were the most effective interventions with the low-level inoculation on surfaces of fresh beef flanks after chilling. Peroxyacetic acid had an intermediate effect, while acidified sodium chlorite was the least effective in reducing STEC levels immediately after treatment. Results indicate that the reduction of non-O157 STEC by antimicrobial interventions on fresh beef surfaces were at least as great as for E. coli O157:H7. However, the recovery of these low inoculation levels of pathogens indicated that there is no single intervention to eliminate them.

Microbiological analysis of bovine lymph nodes for the detection of Salmonella enterica.

Bovine peripheral lymph nodes (LNs) have been identified as a potential source of Salmonella when trim containing these nodes is incorporated into ground beef. Studies examining the prevalence of Salmonella in peripheral LNs of cattle are few in number, and the microbiological methods used for these analyses have not been validated. Given that Salmonella contamination may be found on postintervention carcasses, it is important to understand the extent to which Salmonella contamination from surrounding adipose tissue is transferred to LN samples during sample preparation. To better understand the potential for crosscontamination, 906 LN samples were collected from postintervention carcasses and these, along with the corresponding adipose trim (AT), were analyzed for the presence of Salmonella. The results showed that the Salmonella prevalence in LNs and on AT was 0.8 and 5 % , respectively, but that it was possible to find AT positive for Salmonella contamination while the corresponding LNs were negative and vice versa. In order to examine the dynamics of cross-contamination between surface adipose tissue and LNs in the trimming process, inoculation studies were performed. The efficacy of LN submersion in boiling water as a means of surface sterilization and the effect of boiling on the viability of Salmonella contained within LN samples were also examined. The results showed that, on average, 23 to 43 % of the inoculated LN samples in this study were cross-contaminated by Salmonella on surrounding adipose tissue when present in the range of 10(1) to 10(2) CFU per sample; however, surface decontamination methods were very effective at removing Salmonella cross-contaminants in this range.