Impact of added copper, alone or in combination with chlortetracycline, on growth performance and antimicrobial resistance of fecal enterococci of weaned piglets

Studies suggest a link between added copper (Cu) and co-selection of antimicrobial resistance (AMR) in Enterococcus spp., but data are inconsistent. This study aimed to assess the impact of added Cu, alone or with a feed-grade antimicrobial, on growth performance, transferable Cu resistance gene (tcrB) prevalence, abundance of tcrB in fecal community DNA, and AMR in fecal enterococci in weaned piglets. A total of 320 barrows (DNA 200 × 400, DNA Genetics) weaned at approximately 21 d of age with 7.4 kg (7.4 ± 0.06 kg) BW were used in a 28-d study. Piglets were fed a common non-medicated diet for 7 d of acclimation. Treatments were arranged in a 2 × 2 factorial design with main effects of added Cu (0 vs. 200 mg/kg Cu from Cu sulfate) and chlortetracycline (0 vs. 440 mg/kg CTC). Growth performance and fecal samples were obtained on days 0, 14, and 28. There was no evidence (P > 0.05) for Cu and CTC interaction in growth performance. Pigs fed diets with added Cu had increased (P < 0.05) ADG and ADFI from days 0 to 14, with no evidence for differences (P > 0.05) from days 15 to 28 and 0 to 28. Pigs fed diets with CTC had improved (P < 0.01) ADG, ADFI, and G:F from days 0 to 28. Prevalence of tcrB-positive enterococci was not affected by the addition of Cu and/or CTC (P > 0.05). Prevalence of tcrB-positive enterococci was higher on day 14 than other sampling days (P = 0.002). Prevalence of tetracycline resistance gene [tet(M)]-positive enterococci was not affected by treatments or day (P > 0.05). Prevalence of macrolide resistance gene [erm(B)]-positive enterococci had a significant treatment and sampling day interaction (P = 0.021). The abundance of the tcrB gene in feces, quantified by PCR, was not affected by Cu treatment. The median Cu minimum inhibitory concentrations (MIC) of tcrB-negative and -positive isolates were 3 and 20 mM, respectively (P < 0.001). For day 0 and day 28, all Enterococcus isolates were susceptible to gentamicin, kanamycin, streptomycin, daptomycin, and tigecycline, with a majority of isolates resistant to chloramphenicol, erythromycin, lincomycin, linezolid, tetracycline, tylosin tartrate, and Synercid. In conclusion, 200 mg/kg added Cu or 440 mg/kg CTC in nursery diets improved growth performance of nursery pigs. Added Cu, with or without a selection pressure of CTC, did not increase Cu-resistant enterococci and did not co-select resistance to antibiotics.

449 Late-Breaking: Impact of feeding a propriety yeast-based synbiotic product on fecal shedding of top-7 Shiga toxin-producing Escherichia coli in feedlot cattle

Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O111, O103, O121, O145, and O157, called ‘top-7’, are major foodborne pathogens. Cattle are a major reservoir, in which STEC colonize the hindgut and are shed in the feces, which is a major source of contamination of food. Our objective was to evaluate the impact of a proprietary yeast-based synbiotic product (prebiotic and probiotic; Alltech, Inc., Nicholasville, KY) on fecal shedding of top-7 STEC in feedlot cattle. Twenty existing pens, housing 40–112 steers per pen, with an estimated 60 to 90 days to slaughter, were randomly assigned to a control group or a treatment group that received 22 g of the synbiotic product per steer per day, as a top dress, in a finishing diet. Twenty pen-floor fecal samples were collected from each pen on days 0, 21, 42, and 54. Fecal samples were enriched and subjected to a multiplex PCR assay targeting serogroup-specific genes for the top-7 STEC and three major virulence genes, stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), and eae (intimin). Bivariate descriptive statistics for the major serogroups and virulence genes were assessed prior to multivariable analysis using mixed effects logistic regression. The overall prevalence of the top-7 serogroups were 44.5% of O26, 41.3% of O157, 15.1% of O103, 13.7% of O45, 7.8% of O121, and 0.6% of O111. The overall prevalence of stx1, stx2, and eae were 43.9%, 70.8%, and 49%, respectively. E. coli O26, O157, and O45 had a significant treatment and sampling day interaction (P &lt; 0.0001). On d 42, fecal samples from treated group had lower prevalence (P &lt; 0.01) of O26, O103, and O45 compared to the control group. In conclusion, the in-feed administration of the synbiotic product appears to reduce fecal shedding of certain top-7 STEC serogroups in the feedlot cattle.

Quantification of Bacteria Indicative of Fecal and Environmental Contamination from Hides to Carcasses

Fecal bacteria, which reside in the gastrointestinal tract of cattle, can contaminate beef carcasses during processing. In beef cattle slaughter plants, the presence and concentrations of generic Escherichia coli, coliforms, Enterobacteriaceae (EB), and total aerobic bacteria are monitored as indicator organisms of fecal and environmental contamination. The objectives of this study were as follows: (1) to determine the concentrations of generic E. coli, coliforms, EB, and aerobic bacteria on beef carcasses at different processing points in Midwestern commercial beef slaughter plants during the summer, spring, and fall seasons; and (2) to estimate bacterial transfer on carcasses during the hide removal and evisceration processes. Hide and carcass surface sample swabs were collected from slaughtered cattle at four large commercial processing plants. At each plant visit (3 visits to each of the 4 plants) and during 3 seasons, 20 samples were collected at 5 points: hide-on (hide of animal near exsanguination pit), hide-off carcass, pre-evisceration carcass, postevisceration carcass, and postintervention carcass, for a total of 3600 samples. Bacterial concentrations were determined using 3M^™ Petrifilm^™ plates. Associations between season and processing plant with concentrations of E. coli, coliforms, EB, and total aerobic bacteria, overall, between hide-on and hide-off, and between pre- and post-evisceration, were evaluated using multilevel mixed-effects linear regression models. Bacterial concentrations on beef carcasses significantly decreased throughout processing. Moreover, hide removal was an important source of carcass contamination, given bacterial concentrations detected on hide-off carcass samples were the highest, and bearing in mind that carcass muscle surfaces should be sterile. Results from this study indicate that the interventions applied by the processing plants were effective, as they probably contributed to the significant reduction of bacterial concentrations of carcasses.

PSVII-8 Efficacy of corn dried distillers grains with solubles as a replacement for soybean meal in a Boer goat diet

Due to increased use of dried distillers grains with solubles (DDGS) in animal feed and accessibility of ethanol plants in the Midwest, this study evaluated the effect of feeding DDGS in place of soybean meal (SBM) on the fecal microbiome of Boer goats. Twenty-four Boer goat kids (apx. 70 d of age; 28.21 ± 0.96 kg) were blocked by BW and randomly assigned to 1 of 2 treatment diets for 47 d. Treatments were 0% (0DDGS) and 100% (30DDGS) DDGS in place of SBM. Goats were placed in 8 pens (4 pens/treatment; 3 goats/pen) with ad libitum access to feed and water. Fecal pellets were collected on d 47 via rectal grab and stored at -80°C until microbiome sequencing was performed. The V4 region of the 16S rRNA gene was sequenced by MR DNA (MR DNA, Shallowater, TX) on the Illumina HiSeq 2500 platform (Illumina, Inc., San Diego, CA). Data were analyzed using ANOVA with Tukey’s test for pairwise comparisons. Genera impacted by DDGS inclusion with individual relative abundances greater than 1% included increased Ruminococcus (P = 0.01) and Methanobrevibacter (P = 0.009) and decreased Lachnoclostridium (P = 0.02). Ruminococcus and Methanobrevibacter most likely increased in 30DDGS due to greater amounts of soluble fiber passing through the rumen, thus being fermented in the hindgut. The overall percentage of the phyla Bacteroidetes (P = 0.36) and Firmicutes (P = 0.12) did not differ between treatments; however, Firmicutes:Bacteroidetes increased (P = 0.05) in the 30DDGS diet. Treatment did not impact β-diversity (P = 0.47) although species richness increased (P = 0.09) in DDGS-fed goats as more soluble fiber was available for fermentation in the hindgut. In all, results of this study found replacing SBM with DDGS did not greatly alter the fecal microbiome of Boer goats.

DNA Microarray-Based Genomic Characterization of the Pathotypes of Escherichia coli O26, O45, O103, O111, and O145 Isolated from Feces of Feedlot Cattle †

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, referred to as the top six non-O157 serogroups, are responsible for more than 70% of human non-O157 STEC infections in North America. Cattle harbor non-O157 strains in the hindgut and shed them in the feces. The objective of this study was to use the U.S. Food and Drug Administration (FDA) E. coli identification (ECID) DNA microarray to identify the serotype, assess the virulence potential of each, and determine the phylogenetic relationships among five of the six non-O157 E. coli serogroups isolated from feedlot cattle feces. Forty-four strains of STEC, enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), or putative nonpathotype E. coli (NPEC) of cattle origin and five human clinical strains of EHEC were assayed with the FDA-ECID DNA microarray. The cattle strains harbored diverse flagellar genes. The bovine and human strains belonging to serogroups O26, O45, and O103 carried stx₁ only, O111 carried both stx₁ and stx₂, and O145 carried either stx₁ or stx₂. The strains were also positive for various subtypes of intimin and other adhesins (IrgA homologue adhesin, long polar fimbriae, mannose-specific adhesin, and curli). Both human and cattle strains were positive for LEE-encoded type III secretory system genes and non-LEE-encoded effector genes. SplitsTree4, a program used to determine the phylogenetic relationship among the strains, revealed that the strains within each serogroup clustered according to their pathotype. In addition to genes encoding Shiga toxins, bovine non-O157 E. coli strains possessed other major virulence genes, including those for adhesins, type III secretory system proteins, and plasmid-borne virulence genes, similar to human clinical strains. Because virulence factors encoded by these genes are involved in the pathogenesis of various pathotypes of E. coli, the bovine non-O157 strains could cause human illness. The FDA-ECID DNA microarray assay rapidly provided a profile of the virulence genes for assessment of the virulence potential of each strain.

Effects of Tylosin Administration Routes on the Prevalence of Antimicrobial Resistance Among Fecal Enterococci of Finishing Swine

Antibiotics can be administered orally or parenterally in swine production, which may influence antimicrobial resistance (AMR) development in gut bacteria. A total of 40 barrows and 40 gilts were used to determine the effects of tylosin administration route on growth performance and fecal enterococcal AMR. The antibiotic treatments followed Food and Drug Administration label directions and were as follows: (1) no antibiotic (CON), (2) 110 mg tylosin per kg feed for 21 d (IN-FEED), (3) 8.82 mg tylosin per kg body weight through intramuscular injection twice daily for the first 3 d of each week for 3 weeks (IM), and (4) 66 mg tylosin per liter of drinking water (IN-WATER). Antibiotics were administered during d 0 to 21 and all pigs were then fed the CON diet from d 21 to 35. Fecal samples were collected on d 0, 21, and 35. Antimicrobial susceptibility was determined by microbroth dilution method. No evidence of route × sex interaction (p > 0.55) was observed for growth performance. From d 0 to 21, pigs receiving CON and IN-FEED had greater (p < 0.05) average daily gain (ADG) than those receiving IM, with the IN-WATER group showing intermediate ADG. Pigs receiving CON had greater (p < 0.05) gain-to-feed ratio (G:F) than IM and IN-WATER, but were not different from pigs receiving IN-FEED. Overall, enterococcal isolates collected from pigs receiving IN-FEED or IM were more resistant (p < 0.05) to erythromycin and tylosin than CON and IN-WATER groups. Regardless of administration route, the estimated probability of AMR to these two antibiotics was greater on d 21 and 35 than on d 0. In summary, IM tylosin decreased ADG and G:F in finishing pigs, which may be because of a response to the handling during injection administration. Tylosin administration through injection and feed resulted in greater probability of enterococcal AMR to erythromycin and tylosin compared with in-water treatment.

Effects of chlortetracycline alone or in combination with direct fed microbials on nursery pig growth performance and antimicrobial resistance of fecal Escherichia coli

A total of 300 nursery pigs (initially 5.9 ± 0.05 kg BW) were used in a 42-d growth trial to evaluate the effects of feeding a therapeutic level of chlortetracycline (CTC) with or without direct fed microbials (DFM) on growth performance and antimicrobial resistance (AMR) of fecal Escherichia coli. CTC is a broad-spectrum in-feed antibiotic commonly used in the swine industry. Weaned pigs (~21 d of age) were allotted to pens based on initial BW and fed a common starter diet for 4 d. Pens were then blocked by BW and allotted to dietary treatments in a completely randomized block design. Dietary treatments were arranged in a 2 × 3 factorial consisting of combinations of CTC (none vs. 400 mg/kg from days 0 to 42) and DFM (0 vs. 0.05% DFM 1 vs. 0.05% DFM 2). Fecal samples were collected from three randomly selected pigs from each pen on days 0, 21, and 42 for E. coli isolation and AMR determination. Overall, pigs fed diets containing CTC had improved (P < 0.001) ADG, ADFI, and BW compared to those not fed CTC with no evidence for any effect of either DFM 1 or DFM 2. Regardless of CTC, inclusion of DFM 2 in diets improved (P < 0.05) ADFI from days 0 to 14 and on day 14 BW compared to diets that did not include DFM 2. The addition of CTC with or without DFMs to nursery pig diets increased (P < 0.05) the probability of AMR to tetracycline and ceftiofur of fecal E. coli isolates, but this resistance generally decreased (P < 0.05) over time. A decrease (P < 0.05) in AMR to ampicillin and tetracycline (TET) throughout the trial was observed, while resistance to ceftriaxone decreased (P < 0.020) from days 0 to 21 and increased from days 21 to 42 amongst dietary treatments regardless of CTC or DFM inclusion in the diet. A CTC × DFM × day interaction (P < 0.015) was observed for streptomycin, whereby from days 21 to 42 AMR increased in diets containing either CTC or DFM 1 alone, but the combination decreased resistance. There was no evidence for any effect of DFMs on AMR of fecal E. coli isolates to any other antibiotics evaluated. In conclusion, therapeutic levels of added CTC with or without DFM inclusion improved nursery pig performance, but increased AMR of fecal E. coli isolates to TET and ceftiofur. A moderate improvement in intake and day 14 BW was observed when DFM 2 was included in the diet with or without CTC, but, except for streptomycin, there was no evidence that added dietary DFMs affected resistance of fecal E. coli to antibiotics.

Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces

Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC, O26, O45, O103, O111, O121, and O145) are foodborne pathogens of public health importance. Culture and PCR-based methods have been developed for the detection of these serogroups in cattle feces. The objectives of this study were to evaluate diagnostic sensitivity and specificity of PCR- and culture-based methods for the detection of the six non-O157 serogroups, and to estimate their true prevalence in cattle feces, using a Bayesian latent class modeling approach that accounts for conditional dependence among the three methods. A total of 576 fecal samples collected from the floor of pens of finishing feedlot cattle during summer 2013 were used. Fecal samples, suspended in E. coli broth, were enriched and subjected to three detection methods: culture (involving immunomagnetic separation with serogroup specific beads and plating on a selective medium), conventional (cPCR), and multiplex quantitative PCR (mqPCR) assays. Samples were considered serogroup positive if the sample or the recovered isolate tested positive by PCR for an O gene of interest; neither Shiga toxin (stx) nor intimin (eae) genes were assessed. Prior information on the performance of the three methods was elicited from three subject experts. Culture was generally the least sensitive and most specific of the 3 tests across serogroups, mqPCR was generally the most sensitive test and cPCR more specific than mqPCR. Sensitivity analysis indicated that posterior inferences on test performance and prevalence were susceptible to prior specification in cases where few or no detections present in the data for selected combinations of diagnostic methods (i.e. extreme category problem). Our results characterize performance of detection methods and true prevalence of non-O157 serogroups, thus informing necessary adjustments for test bias in risk modeling.

Distribution of the pco Gene Cluster and Associated Genetic Determinants among Swine Escherichia coli from a Controlled Feeding Trial

Copper is used as an alternative to antibiotics for growth promotion and disease prevention. However, bacteria developed tolerance mechanisms for elevated copper concentrations, including those encoded by the pco operon in Gram-negative bacteria. Using cohorts of weaned piglets, this study showed that the supplementation of feed with copper concentrations as used in the field did not result in a significant short-term increase in the proportion of pco-positive fecal Escherichia coli. The pco and sil (silver resistance) operons were found concurrently in all screened isolates, and whole-genome sequencing showed that they were distributed among a diversity of unrelated E. coli strains. The presence of pco/sil in E. coli was not associated with elevated copper minimal inhibitory concentrations (MICs) under a variety of conditions. As found in previous studies, the pco/sil operons were part of a Tn7-like structure found both on the chromosome or on plasmids in the E. coli strains investigated. Transfer of a pco/sil IncHI2 plasmid from E. coli to Salmonella enterica resulted in elevated copper MICs in the latter. Escherichia coli may represent a reservoir of pco/sil genes transferable to other organisms such as S. enterica, for which it may represent an advantage in the presence of copper. This, in turn, has the potential for co-selection of resistance to antibiotics.

Effects of dietary energy level and intake of corn by-product-based diets on newly received growing cattle: antibody production, acute phase protein response, stress, and immunocompetency of healthy and morbid animals

Effects of dietary energy level and intake of corn by-product-based diets on antibody production, acute phase protein response, stress, and immunocompetency of healthy and morbid newly received growing cattle were evaluated. Four dietary treatments were formulated to supply 0.99, 1.10, 1.21, and 1.32 Mcal NEg/ kg DM and were offered at 100%, 95%, 90%, and 85% of ad libitum based on 0.99/100 treatment intake, respectively. Thirty-two pens were utilized with approximately 12 animals/pen. Four animals from each pen (32/dietary treatment) were randomly selected and used to serve as a subset to monitor immune function and acute phase proteins following a split-plot design. In addition, two animals were randomly and independently selected from each pen (16/dietary treatment) and used to measure fecal cortisol metabolite. Additionally, animals removed from the pen one (M1), two (M2), or three (M3) times and classified as morbid were bled in conjunction with a healthy control (H) removed at the same time and the serum analyzed for the same parameters. A quadratic response to time (P < 0.01) was detected for haptoglobin concentrations and for antibody titers for bovine viral diarrhea type 1 (BVD-I) and infectious bovine rhinotracheitis (IBR; P < 0.01). Haptoglobin was lowest on arrival, highest on day 14, and similar to baseline levels by day 27. Titer levels for BVD-I and IBR were lowest on arrival, higher on day 14, and significantly higher on day 27. Titers for bovine viral diarrhea type 2 (BVD-II) responded linearly (P < 0.05) with lower levels on arrival and highest levels on day 27. Haptoglobin was elevated in morbid animals compared to healthy pen mates (P < 0.05). Titer levels for BVD-I and IBR were also higher in healthy animals compared to animals pulled for morbidity (P < 0.01). Fecal cortisol was higher on arrival than on day 14 (P < 0.05). Dietary treatment had no effect on any of the parameters investigated. In summary, high-energy receiving diets based on fermentable fiber from by-products can be fed to newly received growing cattle without negative effects on antibody production toward vaccines, inflammation, or overall stress. In addition, haptoglobin concentrations and titer levels for BVD-I and IBR viruses are higher in healthy animals compared to sick animals.

Antimicrobial resistance of Enterococcus faecium strains isolated from commercial probiotic products used in cattle and swine

Probiotics, an antibiotic alternative, are widely used as feed additives for performance benefits in cattle and swine production systems. Among bacterial species contained in probiotics, Enterococcus faecium is common. Antimicrobial resistance (AMR), particularly multidrug resistance, is a common trait among enterococci because of their propensity to acquire resistance and horizontally transfer AMR genes. Also, E. faecium is an opportunistic pathogen, and in the United States, it is the second most common nosocomial pathogen. There has been no published study on AMR and virulence potential in E. faecium contained in probiotic products used in cattle and swine in the United States. Therefore, our objectives were to determine phenotypic susceptibilities or resistance to antimicrobials, virulence genes (asa1, gelE, cylA, esp, and hyl) and assess genetic diversity of E. faecium isolated from commercial products. Twenty-two commercially available E. faecium-based probiotic products used in cattle (n = 13) and swine (n = 9) were procured and E. faecium was isolated and species confirmed. Antimicrobial susceptibility testing to determine minimum inhibitory concentrations was done by micro-broth dilution method using National Antimicrobial Resistance Monitoring Systems Gram-positive Sensititre panel plate (CMV3AGPF), and categorization of strains as susceptible or resistant was as per Clinical Laboratory and Standards Institute's guidelines. E. faecium strains from 7 products (3 for swine and 4 for cattle) were pan-susceptible to the 16 antimicrobials tested. Strains from 15 products (6 for swine and 9 for cattle) exhibited resistance to at least one antimicrobial and a high proportion of strains was resistant to lincomycin (10/22), followed by tetracycline (4/22), daptomycin (4/22), ciprofloxacin (4/22), kanamycin (3/22), and penicillin (2/22). Four strains were multidrug resistant, with resistant phenotypes ranging from 3 to 6 antimicrobials or class. None of the E. faecium strains were positive for any of the virulence genes tested. The clonal relationships among the 22 E. faecium strains were determined by pulsed-field gel electrophoresis (PFGE) typing. A total of 10 PFGE patterns were observed with 22 strains and a few of the strains from different probiotic products had identical (100% Dice similarity) PFGE patterns. In conclusion, the E. faecium strains in a few commercial probiotics exhibited AMR to medically-important antimicrobials, but none contained virulence genes.

Detection and Quantification of Seven Major Serogroups of Shiga Toxin-Producing Escherichia coli on Hides of Cull Dairy, Cull Beef, and Fed Beef Cattle at Slaughter†

Dehiding during beef cattle processing can introduce fecal contaminants, including Shiga toxin-producing Escherichia coli (STEC), from hides onto carcass surfaces, creating the potential for contaminated beef. Fecal shedding of major STEC serogroups (O26, O45, O103, O111, O121, O145, and O157; STEC-7) may differ among cattle populations, yet no study has been conducted to isolate STEC-7 on hides of multiple cattle types on the same production days at the same processing plant. Our objective was to estimate and compare prevalence and concentrations of STEC-7 on hides of cull dairy, cull beef, and fed beef cattle from the same date and processing plant. Overall, 1,500 cattle hides were sponge sampled from cull dairy ( n = 500), cull beef ( n = 500) and fed beef cattle ( n = 500) over 10 processing days. To determine prevalence, samples were subjected to an immunomagnetic separation culture method, and presumptive STEC isolates were tested by PCR for serogroup and major virulence genes. A spiral plate method was used to enumerate STEC-7 from hide samples. Data were analyzed with linear mixed models. All STEC-7 serogroups except O121 were detected and quantified on cattle hides in this study population. Slightly more fed beef hides (77 of 500; 15.4%) and cull beef hides (76 of 500; 15.2%) were positive for at least one STEC-7 strain compared with cull dairy hides (57 of 500; 11.4%), but cattle type was not significantly associated ( P = 0.19) with STEC-7 prevalence. Fed beef hides had a significantly higher prevalence ( P < 0.05) of STEC O103, O145, and O157 serogroups than did either of the other cattle types. The highest proportions of quantifiable samples were for STEC O145 (32 of 1,500 samples; 2.1%) and O157 (31 of 1,500 samples; 2.1%) serogroups, with the majority of concentrations at 3 to 5 and 2 to 4 log CFU/100 cm² of hide, respectively. Results indicate that hide contamination with some major STEC serogroups differs significantly among cattle types at harvest, even within the same day and location.

Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces†

Several real-time quantitative PCR (qPCR) assays have been developed for detection and quantification of Escherichia coli O157:H7 in complex matrices by targeting genes for serogroup-specific O-antigen ( rfbE_O157), H7 antigen, and one or more major virulence factors (Shiga toxin and intimin). A major limitation of such assays is that coamplification of H7 and virulence genes in a sample does not signal association of those genes with the O157 serogroup. Clusters of regularly interspaced short palindromic repeats (CRISPR) polymorphisms are highly correlated with certain enterohemorrhagic E. coli (EHEC) serotypes, including O157:H7, and the presence of genes for Shiga toxin ( stx₁ and stx₂) and intimin ( eae). Our objectives were to develop and validate a qPCR assay targeting the CRISPR array for the detection and quantification of EHEC O157:H7 in cattle feces and to evaluate the applicability of the assay for detection of and comparison with a four-plex qPCR assay targeting rfbE_O157, stx₁, stx₂, and eae genes and a culture method. Detection limits of the CRISPR_O157:H7 qPCR assay for cattle feces spiked with pure cultures were 2.1 × 10³ and 2.3 × 10⁰ CFU/g before and after enrichment, respectively. Detection of E. coli O157 in feedlot cattle fecal samples ( n = 576) was compared among the CRISPR_O157:H7 qPCR assay, culture method, and four-plex qPCR assay. The CRISPR_O157:H7 qPCR detected 42.2% of the samples (243 of 576 samples) as positive for E. coli O157:H7, compared with 30.4% (175 samples) by the culture method. Nearly all samples (97.2%; 560 samples) were positive for rfbE_O157 by the four-plex PCR, but 21.8% (122 of 560 samples) were negative for the stx and/or eae genes, making it unlikely that EHEC O157:H7 was present in these samples. Cohen's kappa statistic indicated a fair and poor agreement beyond that due to chance between the CRISPR assay and the culture method and four-plex assay, respectively. This novel qPCR assay can detect the EHEC O157:H7 serotype in cattle feces by targeting CRISPR polymorphisms.

Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes

A real-time PCR (qPCR) assay targeting on invA and pagC genes was developed and validated for the detection and quantification of Salmonella enterica strains (Bai et al., 2018) [1]. A host gene, normally an endogenous housekeeping gene (Beer-Davidson et al., 2018; Poon et al., 2004) [2,3], or an irrelevant exogenous gene (Cheng et al., 2015; Sedlak et al., 2014) [4,5] has been widely used as an internal control to monitor nucleic acid extraction efficiencies and potential PCR inhibitions in PCR-based detection assays. An endogenous internal control designed based on the 18S rRNA gene was used in the above-mentioned qPCR assay. This 18S rRNA internal control amplifies the target gene in multiple species including bovine, swine, ovine, caprine and cervine. Data was generated by the duplex qPCR assay on 138 enriched cattle lymph node samples without the internal control, and compared with data on the same samples tested by the triplex qPCR assay that has the 18S rRNA gene as internal control. Threshold cycle (Ct) data for the duplex and the triplex qPCR on the 138 samples were similar, and are presented in this brief report.

A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes

Cattle lymph nodes can harbor Salmonella and potentially contaminate beef products. We have developed and validated a new real-time PCR (qPCR) assay for the detection and quantification of Salmonella enterica in cattle lymph nodes. The assay targets both the invA and pagC genes, the most conserved molecular targets in Salmonella enterica. An 18S rRNA gene assay that amplifies from cattle and other animal species was also included as an internal control. Available DNA sequences for invA, pagC and 18S rRNA genes were used for primer and probe selections. Three Salmonella serotypes, S. Typhimurium, S. Anatum, and S. Montevideo, were used to assess the assay's analytical sensitivity. Correlation coefficients of standard curves generated for each target and for all three serotypes were >99% and qPCR amplification efficiencies were between 93% and 110%. Assay sensitivity was also determined using standard curve data generated from Salmonella-negative cattle lymph nodes spiked with 10-fold dilutions of the three Salmonella serotypes. Assay specificity was determined using Salmonella culture method, and qPCR testing on 36 Salmonella strains representing 33 serotypes, 38 Salmonella strains of unknown serotypes, 252 E. coli strains representing 40 serogroups, and 31 other bacterial strains representing 18 different species. A collection of 647 cattle lymph node samples from steers procured from the Midwest region of the US were tested by the qPCR, and compared to culture-method of detection. Salmonella prevalence by qPCR for pre-enriched and enriched lymph nodes was 19.8% (128/647) and 94.9% (614/647), respectively. A majority of qPCR positive pre-enriched samples (105/128) were at concentrations between 10⁴ and 10⁵ CFU/mL. Culture method detected Salmonella in 7.7% (50/647) and 80.7% (522/647) of pre- and post-enriched samples, respectively; 96.0% (48/50) of pre-enriched and 99.4% (519/522) of post-enriched culture-positive samples were also positive by qPCR. More samples tested positive by qPCR than by culture method, indicating that the real-time PCR assay was more sensitive. Our data indicate that this triplex qPCR can be used to accurately detect and quantify Salmonella enterica strains from cattle lymph node samples. The assay may serve as a useful tool to monitor the prevalence of Salmonella in beef production systems.

Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated From Cattle Feces Using Whole Genome Sequencing

Escherichia coli O104:H4, a Shiga toxin-producing hybrid pathotype that was implicated in a major foodborne outbreak in Germany in 2011, has not been detected in cattle. However, serotypes of O104, other than O104:H4, have been isolated from cattle feces, with O104:H7 being the most predominant. In this study, we investigated, based on whole genome sequence analyses, the virulence potential of E. coli O104 strains isolated from cattle feces, since cattle are asymptomatic carriers of E. coli O104. The genomes of ten bovine E. coli O104 strains (six O104:H7, one O104:H8, one O104:H12, and two O104:H23) and five O104:H7 isolated from human clinical cases were sequenced. Of all the bovine O104 serotypes (H7, H8, H12, and H23) that were included in the study, only E. coli O104:H7 serotype possessed Shiga toxins. Four of the six bovine O104:H7 strains and one of the five human strains carried stx1c. Three human O104 strains carried stx2, two were of subtype 2a, and one was 2d. Genomes of stx carrying bovine O104:H7 strains were larger than the stx-negative strains of O104:H7 or other serotypes. The genome sizes were proportional to the number of genes carried on the mobile genetic elements (phages, prophages, transposable elements and plasmids). Both bovine and human strains were negative for intimin and other genes associated with the type III secretory system and non-LEE encoded effectors. Plasmid-encoded virulence genes (ehxA, epeA, espP, katP) were also present in bovine and human strains. All O104 strains were negative for antimicrobial resistance genes, except one human strain. Phylogenetic analysis indicated that bovine E. coli O104 strains carrying the same flagellar antigen clustered together and STEC strains clustered separately from non-STEC strains. One of the human O104:H7 strains was phylogenetically closely related to and belonged to the same sequence type (ST-1817) as the bovine O104:H7 STEC strains. This suggests that the bovine feces could be a source of human illness caused by E. coli O104:H7 serotype. Because bovine O104:H7 strains carried virulence genes similar to human clinical strains and one of the human clinical strains was phylogenetically related to bovine strains, the serotype has the potential to be a diarrheagenic pathogen in humans.

Effects of high condensed-tannin substrate, prior dietary tannin exposure, antimicrobial inclusion, and animal species on fermentation parameters following a 48 h in vitro incubation

Condensed tannins (CT), prior dietary CT exposure, animal species, and antimicrobial inclusion effects on 48 h extent of in vitro fermentation were measured in an experiment with a 3 × 2 × 2 × 3 factorial arrangement of treatments. Treatments included species of inoculum donor (Bos taurus, Ovis aries, or Capra hircus; n = 3/species), prior adaptation to dietary CT (not adapted or adapted), culture substrate (low-CT or high-CT), and antimicrobial additive (none, bacterial suppression with penicillin + streptomycin, or fungal suppression with cycloheximide). Low-CT or high-CT substrates were incubated in vitro using inoculum from animals either not exposed (period 1) or previously exposed to dietary CT (period 2). The extent of IVDMD after 48 h of incubation was greater (P < 0.001) for cultures with low-CT substrate (21.5%) than for cultures with high-CT substrate (16.5%). Cultures with high-CT substrate or with suppressed bacterial activity had less (P < 0.001) gas pressure than cultures with low-CT substrate or cultures with suppressed fungal activity. Total VFA concentrations were greater (P < 0.001) in low-CT cultures when inoculum donors were without prior CT exposure (83.7 mM) than when inoculum was from CT-exposed animals (79.6 mM). Conversely, total VFA concentrations were greater (P < 0.001) in high-CT cultures with tannin-exposed inoculum (59.4 mM) than with nonexposed inoculum (52.6 mM). As expected, CT and suppression of bacterial fermentative activities had strong negative effects on fermentation; however, prior exposure to dietary CT attenuated some negative effects of dietary CT on fermentation. In our experiment, the magnitude of inoculum-donor species effects on fermentation was minor.

Bacterial flora of liver abscesses in crossbred beef cattle and Holstein steers fed finishing diets with or without tylosin

Holstein steers raised for beef production consistently have a higher prevalence and more severe form of liver abscesses than cattle of beef breeds. A study was conducted to compare bacterial flora of liver abscesses collected from multiple abattoirs from 4 groups of cattle, arranged in a 2 × 2 factorial design, consisting of crossbred cattle and Holstein steers, and each group fed a finishing diet supplemented with or without tylosin. A total of 383 liver abscess samples, consisting of 94 and 81 from crossbred cattle and 89 and 119 from Holstein steers fed finishing diets with or without tylosin, respectively, were subjected for anaerobic and aerobic bacterial isolations. The minimum inhibitory concentrations (MIC) of tylosin to the predominant bacterial species were determined. The likelihood chi-square test was performed to assess unadjusted differences in bacterial prevalence proportions between the 2 types of cattle (crossbred and Holstein steers) and feed type (tylosin or no tylosin). There was no interaction between cattle type and tylosin inclusion on the prevalence of any of the bacterial species isolated. Liver abscesses from Holstein steers yielded a higher total number of isolates compared to liver abscesses from crossbred cattle (1060 vs. 788). subsp. was isolated from all abscesses. The prevalence of subsp. was 19.1% and was not affected by the cattle type or tylosin. The prevalence of was higher ( < 0.01) in crossbred cattle (73.7%) compared to Holstein steers (29.8%). Also, the prevalence of was higher in abscesses from tylosin-fed (66.1%) cattle than no tylosin-fed cattle (35%). The overall prevalence of was 25.3% and was similar ( = 0.58) between cattle type, but the prevalence was lower ( < 0.01) in tylosin-fed (16.9%) compared to no tylosin-fed group (33%). Mean MIC of tylosin for and were similar across both cattle types and tylosin inclusion. Although bacterial flora of liver abscesses from Holstein steers appeared to be more diverse than that of crossbred cattle, there was no difference in the prevalence of the and and in fact, prevalence of was higher in crossbred than Holstein steers. Therefore, the difference in bacterial flora is not the likely reason for higher prevalence and severity of liver abscesses in Holstein steers than crossbred beef cattle.

Spiral Plating Method To Quantify the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces

Cattle are a major reservoir of the six major Shiga toxin-producing non-O157 Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) responsible for foodborne illnesses in humans. Besides prevalence in feces, the concentrations of STEC in cattle feces play a major role in their transmission dynamics. A subset of cattle, referred to as super shedders, shed E. coli O157 at high concentrations (≥4 log CFU/g of feces). It is not known whether a similar pattern of fecal shedding exists for non-O157. Our objectives were to initially validate the spiral plating method to quantify the six non-O157 E. coli serogroups with pure cultures and culture-spiked fecal samples and then determine the applicability of the method and compare it with multiplex quantitative PCR (mqPCR) assays for the quantification of the six non-O157 E. coli serogroups in cattle fecal samples collected from commercial feedlots. Quantification limits of the spiral plating method were 3 log, 3 to 4 log, and 3 to 5 log CFU/mL or CFU/g for individual cultures, pooled pure cultures, and cattle fecal samples spiked with pooled pure cultures, respectively. Of the 1,152 cattle fecal samples tested from eight commercial feedlots, 122 (10.6%) and 320 (27.8%) harbored concentrations ≥4 log CFU/g of one or more of the six serogroups of non-O157 by spiral plating and mqPCR methods, respectively. A majority of quantifiable samples, detected by either spiral plating (135 of 137, 98.5%) or mqPCR (239 of 320, 74.7%), were shedding only one serogroup. Only one of the quantifiable samples was positive for a serogroup carrying Shiga toxin (stx1) and intimin (eae) genes; 38 samples were positive for serogroups carrying the intimin gene. In conclusion, the spiral plating method can be used to quantify non-O157 serogroups in cattle feces, and our study identified a subset of cattle that was super shedders of non-O157 E. coli. The method has the advantage of quantifying non-O157 STEC, unlike mqPCR that quantifies serogroups only.