Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets

BACKGROUND

Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the fecal microbiome of the female pig from early life to first parity are not well understood. Our objective was to describe microbiome and antimicrobial resistance dynamics of the fecal microbiome of breeding sows from early life through estrus, parturition and weaning of the first litter of piglets (i.e., from 3 to 53 weeks of age).

RESULTS

Our analysis revealed that fecal bacterial populations in developing gilts undergo changes consistent with major maturation milestones. As the pigs progressed towards first estrus, the fecal bacteriome shifted from Rikenellaceae RC9 gut group- and UCG-002-dominated enterotypes to Treponema- and Clostridium sensu stricto 1-dominated enterotypes. After first estrus, the fecal bacteriome stabilized, with minimal changes in enterotype transition and associated microbial diversity from estrus to parturition and subsequent weaning of first litter piglets. Unlike bacterial communities, fecal fungal communities exhibited low diversity with high inter- and intra-pig variability and an increased relative abundance of certain taxa at parturition, including Candida spp. Counts of resistant fecal bacteria also fluctuated over time, and were highest in early life and subsequently abated as the pigs progressed to adulthood.

CONCLUSIONS

This study provides insights into how the fecal microbial community and antimicrobial resistance in female pigs change from three weeks of age throughout their first breeding lifetime. The fecal bacteriome enterotypes and diversity are found to be age-driven and established by the time of first estrus, with minimal changes observed during subsequent physiological stages, such as parturition and lactation, when compared to the earlier age-related shifts. The use of pigs as a model for humans is well-established, however, further studies are needed to understand how our results compare to the human microbiome dynamics. Our findings suggest that the fecal microbiome exhibited consistent changes across individual pigs and became more diverse with age, which is a beneficial characteristic for an animal model system.

Evaluation of a Lactococcus lactis-based dried fermentation product administered through drinking water on nursery pig growth performance, fecal Escherichia coli virulence genes and pathotypes, antibiotic usage, and mortality

A total of 34,749 pigs were used in two experiments to evaluate the effects of a postbiotic dried fermentation product (DFP) administered through drinking water on nursery pig growth performance, antibiotic injection frequency, morbidity, mortality, fecal consistency, and characterization of fecal Escherichia coli. The DFP is composed of bioactive molecules derived from Lactococcus lactis. In Exp. 1, 350 barrows (DNA Line 200 × 400; initial body weight [BW] 6.1 ± 0.01 kg) were used in a 42-d study with five pigs per pen and 35 pens per treatment. The DFP was supplied for 14 d at a target dosage of 24 mg/kg BW using a water medicator at a 1:128 dilution. On days 7 and 14, fecal samples were collected for dry matter (DM) and to determine, by a multiplex polymerase chain reaction (PCR) assay, prevalence of 11 virulence genes characteristic of E. coli pathotypes. There was no evidence (P > 0.10) for differences for growth, incidence of diarrhea, number of antibiotic injections, removals, or fecal DM. On both fecal collection days, E. coli virulence genes were present with day 7 samples positive for genes that encode for hemolysins (hlyA, exhA), intimin (eae), and enteroaggregative heat-stable enterotoxin (astA). Prevalence of enterotoxin genes (elt, estA, estB, astA) increased on day 14, but DFP had no effects on the prevalence of any of the virulence genes. A total of 32 out of 72 E. coli isolates were identified as enterotoxigenic pathotype and all except one were from day 14 fecal samples. Fourteen isolates were positive for F4 fimbria and one isolate was positive for F4 and F18 fimbriae. In Exp. 2, 34,399 nursery pigs (initially 5.6 kg) were used in 20 nursery barns with 10 barns per treatment (control or DFP). The target dosage of the DFP for the first 14 d was 35 mg/kg BW. Following the 14-d supplementation period, pigs continued to be monitored for approximately 31 d. There was no evidence (P > 0.05) for the DFP to influence the overall percentage of pigs that died or growth performance. From days 0 to 14, providing the DFP reduced (P < 0.05) the percentage of pigs that were euthanized. However, providing the DFP increased (P < 0.05) the overall percentage of pigs that were euthanized and total mortality. For the number of antibiotic injections (treatment interventions), providing the DFP reduced the number of injections for the common period (P < 0.001) and overall (P = 0.002). These results indicate that the DFP did not influence growth performance but providing the DFP in Exp. 2 led to increased total nursery pig mortality.

Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs

BACKGROUND

The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AMR) in fecal bacteria change as the animal host ages, yet the temporal dynamics of AMR within communities of bacteria in pigs during a full production cycle remains largely unstudied.

RESULTS

A longitudinal study was performed to evaluate the dynamics of fecal microbiome and AMR in a cohort of pigs during a production cycle; from birth to market age. Our data showed that piglet fecal microbial communities assemble rapidly after birth and become more diverse with age. Individual piglet fecal microbiomes progressed along similar trajectories with age-specific community types/enterotypes and showed a clear shift from E. coli/Shigella-, Fusobacteria-, Bacteroides-dominant enterotypes to Prevotella-, Megaspheara-, and Lactobacillus-dominated enterotypes with aging. Even when the fecal microbiome was the least diverse, the richness of ARGs, quantities of AMR gene copies, and counts of AMR fecal bacteria were highest in piglets at 2 days of age; subsequently, these declined over time, likely due to age-related competitive changes in the underlying microbiome. ARGs conferring resistance to metals and multi-compound/biocides were detected predominately at the earliest sampled ages.

CONCLUSIONS

The fecal microbiome and resistome-along with evaluated descriptors of phenotypic antimicrobial susceptibility of fecal bacteria-among a cohort of pigs, demonstrated opposing trajectories in diversity primarily driven by the aging of pigs.

Short communication: evaluation of an endotoxin challenge and intraruminal bacterial inoculation model to induce liver abscesses in Holstein steers

Holstein steers (n = 40; initial body weight [BW] = 96.0 ± 10.5 kg) were individually housed in a climate-controlled barn to evaluate potential models for the genesis of liver abscesses (LA). In this 2 × 2 factorial, steers were balanced by BW and randomly assigned to one of two treatments: 1) intravenous saline injection followed by intraruminal bacterial inoculation with Fusobacterium necrophorum subsp. necrophorum (1 × 109 colony forming unit [CFU]/mL) and Salmonella enterica serovar Lubbock (1 × 106 CFU/mL; CON; n = 20 steers); or 2) intravenous injection with 0.25 µg/kg BW of lipopolysaccharide (LPS; Escherichia coli O111:B4) followed by intraruminal bacterial inoculation of F. necrophorum subsp. necrophorum (1 × 109 CFU/mL) and S. enterica serovar Lubbock (1 × 106 CFU/mL; LBI; n = 20 steers) and 1 of 2 harvest dates (3 or 10 d post LPS infusion). Body weights were recorded on days -4, -1, 3, and 10, and blood was collected for hematology on days -4, 3, and 10, relative to LPS infusion on day 0. Intraruminal bacterial inoculation occurred on day 1. Steers from each treatment group were harvested at two different time points on day 3 or 10 to perform gross pathological examination of the lung, rumen, liver, LA (if present), and colon. Feed disappearance was less for LBI than CON (P < 0.01); however, BW did not differ (P = 0.33) between treatments. Neither treatment nor time differed for hematology (P ≥ 0.13), and no gross pathological differences were noted in the lung, liver, LA, or colon (P ≥ 0.25). A treatment × harvest date interaction was noted for ruminal pathology in which LBI had an increased percentage of abnormal rumen scores on day 3 (P < 0.01). These results suggest that an LPS challenge in combination with intraruminal bacterial inoculation of pathogens commonly isolated from LA was not sufficient to induce LA in steers within 3 or 10 d (P = 0.95) when compared to CON. Further evaluation is needed to produce a viable model to investigate the genesis and prevention of LA in cattle.

Metabolome of purulent materials of liver abscesses from crossbred cattle and Holstein steers fed finishing diets with or without in-feed tylosin

Liver abscesses in feedlot cattle are a polymicrobial infection with Fusobacterium necrophorum and Trueperella pyogenes as the primary and secondary etiologic agents, respectively. Cattle with liver abscesses do not exhibit clinical signs and the abscesses are detected only at slaughter. The objective was to conduct metabolomics analysis of purulent materials of liver abscesses to identify biochemicals. Liver abscesses from crossbred cattle (n = 24) and Holstein steers (n = 24), each fed high-grain finishing diet with tylosin (n = 12) or no tylosin (n = 12), were included in the study. Abscess purulent materials were analyzed by ultrahigh-performance liquid chromatography-tandem mass spectroscopy. A total of 759 biochemicals were identified and were broadly categorized into carbohydrates, energy metabolism pathways intermediates, peptides, amino acids and their metabolites, lipids and their metabolites, nucleotides, vitamins and cofactors, xenobiotics, and partially characterized molecules. The top 50 biochemicals identified included amino acids, lipids, nucleotides, xenobiotics, peptides, and carbohydrates and their metabolites. Among the 15 amino acid metabolites in the top 50 biochemicals, four were tryptophan metabolites, indoleacrylate, indolepropionate, tryptamine, and anthranilate. The 3-phenylpropionate, a product of phenylalanine metabolism, was the predominant metabolite in purulent materials. Between the four treatment groups, a two-way ANOVA analysis identified biochemicals that exhibited significant main effects for cattle type and in-feed tylosin use and their interactions. A total of 59 and 85 biochemicals were different (P < 0.05) between the cattle type (crossbred vs. Holstein steers) and in-feed tylosin use (tylosin vs. no tylosin), respectively. Succinate, an intermediate of lactate fermentation by some bacterial species, was one of the top 30 biochemicals that differentiated the four treatment groups. A number of lysophospholipids, indicative of bacterial and host cell membrane lyses, were identified in the purulent materials. In conclusion, to our knowledge this is the first report on the metabolome of liver abscess purulent materials and several biochemicals identified were related to metabolic activities of the bacterial community, particularly F. necrophorum and T. pyogenes. Biochemicals unique to liver abscesses that appear in the blood may serve as biomarkers and be of diagnostic value to detect liver abscesses of cattle before slaughter.

Combined use of monensin and virginiamycin to improve rumen and liver health and performance of feedlot-finished steers

Monensin and virginiamycin are included in beef cattle finishing diets as prophylaxis to minimize the incidence of ruminal acidosis and liver abscesses. Due to different and probably complementary modes of action, this study aimed to determine the effects of a combination of monensin and virginiamycin, both included in the diet at recommended doses, on ruminal health, the occurrence of liver abscesses, and growth performance of feedlot-finished cattle. One hundred and forty-four steers (6 animals/pen) were fed 1 of 3 corn-based finishing diets containing 30 mg of monensin (MN), 25 mg of virginiamycin (VM), or 30 and 25 mg of monensin and virginiamycin (MN + VM), respectively, per kilogram of dry matter. Ruminal pH probes were inserted into two animals per pen and set to record pH every 10 min. On d 100, animals were slaughtered, and rumens and livers were recovered, on which occurrence and degree of ruminal damage, prevalence and number of liver abscesses, and liver scores (A-: livers with no more than two small abscesses; A+: livers with at least one large abscess or more than four medium abscesses; A: any other abscessed liver) were determined. Simultaneous inclusion of monensin and virginiamycin resulted in a 4.3% decrease (P < 0.04) in dry matter intake (DMI; 8.8, 9.2, and 9.2 ± 0.19 kg/d for MN + VM, MN, and VM-fed animals, respectively) and similar (P > 0.13) average daily body weight gain (ADG; 1.49 ± 0.021 kg/d) and hot carcass weight (HCW; 269 ± 1.7 kg), compared with feeding diets containing one additive or the other. Therefore, in terms of ADG, a 9.4% improvement (P < 0.01) in feed efficiency was observed in MN + VM-fed animals. Backfat thickness (5.6 ± 0.08 mm) and ribeye area (69.9 ± 0.53 cm²) remained unaffected (P ≥ 0.74), as well as the minimum (4.98 ± 0.047), mean (6.11 ± 0.037), and maximum ruminal pH (7.23 ± 0.033) values and the time (125 ± 22.3 min/d), area (57.67 ± 12.383 pH × h), and episodes (22 ± 3.8 bouts) of pH below 5.6 (P ≥ 0.12). Overall, prevalence (24 ± 3.4%) and the number of liver abscesses (1.6 ± 0.14 abscesses/abscessed liver), liver scores (20 ± 3.1% of A- and 4 ± 1.8% of A livers), and prevalence (67 ± 3.5%) and degree of damage to the ruminal epithelium (2.5 ± 0.22% affected surface) were similar (P ≥ 0.18) across treatments; however, the occurrence of ruminal lesions tended (P ≤ 0.07) to be associated with that of liver abscesses and reduced ADG when feeding monensin alone.

98 Gut Microbiome: Implications on gut Health

The rumen and the hindgut, which includes cecum and colon, of cattle are inhabited by a diverse microbial community, which is composed mainly of bacteria, but also includes archaea, protozoa, fungi and viruses. Most reside in the lumen, but also colonize the epithelial surface and their compositions are a critical component of the host health. Recent advances in sequencing techniques and biological computational tools have further underscored the complexity of the microbial community. The vast repertoire of the gut microbiome provides the host complementary genetic resources to harvest energy, provide proteins and vitamins, contribute to the development of gut epithelium and gut-associated lymphoid system, and to the overall gut health. The gut epithelium-vascular interface allows secretions, and absorption and metabolism of fermentation products and serves as a selective barrier to prevent translocation and systemic dissemination of microbes, microbial toxins, and immunogens. The barrier function includes protection form mechanical damage caused by feedstuffs, chemical damage from acidity, toxins and microbial invasion, especially pathogens. The mechanisms employed likely differ between the two fermentative regions of the gut, given the dramatic difference in epithelial structures. Rumen is lined by stratified squamous epithelium compared a single layer of columnar epithelium interspersed with mucus-producing goblet cells in the hindgut. The mucus layer is the first barrier the pathogen has to overcome for colonization and translocation. An imbalance in the composition of gut microbiota, called dysbiosis, leads to gut functional disorders. The dysbiosis can range from a change in one to a few species to the perturbation of entire microbial community. The assessment of gut microbial dysbiosis is a challenge because of the complexity and huge variations in the community composition, including animal-to-animal. The gut barrier function determines whether the dysbiotic changes are contained within the lumen or disseminated systemically to affect the health and productivity.

333 Development of a 4-Plex Quantitative PCR Assay for the Detection and Quantification of Species and Subspecies of Fusobacterium Necrophorum and Fusobacterium Varium in Bovine Rumen Fluid

The Fusobacterium genus contains Gram-negative, rod-shaped anaerobic bacteria. Fusobacterium necrophorum and its two subspecies, necrophorum and funduliforme, are normal ruminal inhabitants of cattle. Subsp. necrophorum is the primary causative agent of liver abscesses in feedlot cattle. Fusobacterium varium is also a normal rumen inhabitant, but its role in ruminal fermentation and involvement in liver abscesses is unknown. Currently, no PCR assays exist to quantify F. varium and both subspecies of F. necrophorum. Therefore, our objective was to develop, validate, and determine the applicability of a quantitative PCR assay for quantification of F. varium and the two subspecies of F. necrophorum. Assay targets were the species-specific hgdA gene, encoding for (R)-2-hydroxyglutarylCoA dehydratase subunit alpha, and the subspecies-specific promoter sequence of the leukotoxin gene, lktA. Assay specificity was validated with different species and strains of Fusobacterium, and other bacterial species. Assay sensitivity was determined using pure cultures. Applicability of the assay for quantification of F. necrophorum and F. varium was determined using ruminal fluid from slaughtered cattle. Species and subspecies-level specificity was confirmed. Pure culture quantification limits (CFU/ml) were 2.1x103 for the F. necrophorum species, 5.6x102 for subsp. necrophorum, 1.5x103 for subsp. funduliforme, and 1.8x103 for F. varium. Analysis of ruminal fluid collected from cattle with healthy livers (n=83) and abscessed livers (n=68) indicated that 97% of samples contained F. funduliforme, with mean concentrations of 7.8 x103, and 8.1x103, respectively. Additionally, subsp. necrophorum and F. varium were more prevalent in ruminal fluid from cattle with abscessed livers (41% and 59%) compared with samples from cattle with healthy livers (31% and 41%). In conclusion, subsp. funduliforme appears to be the normal inhabitant of the rumen, while subsp. necrophorum and F. varium are more prevalent in the rumen of cattle with abscessed livers than those with healthy livers.

Association between Tulathromycin Treatment for Bovine Respiratory Disease and Antimicrobial Resistance Profiles among Gut Commensals and Foodborne Bacterial Pathogens Isolated from Feces of Beef Steers

ABSTRACT

This study was conducted to evaluate the association between a therapeutic dose of tulathromycin for bovine respiratory disease in beef steers and the antimicrobial and multidrug resistance profiles of the gastrointestinal tract commensals Escherichia coli and Enterococcus spp. and the foodborne pathogens Salmonella enterica and Campylobacter spp. isolated from fecal samples. Individual fecal samples were collected on days 0, 14, and 28 from 70 beef steers that were housed in a single pen and had been treated or not treated with tulathromycin. Samples were cultured for bacterial isolation, and isolates were tested for antimicrobial susceptibility with the broth microdilution method to determine the MICs of clinically relevant antimicrobials used in both human and veterinary medicine. Generalized linear mixed effects models were fitted to estimate the prevalence of the bacterial species and the prevalence of resistant isolates over time and between treated and nontreated cattle and of multidrug-resistant isolates. Model-adjusted mean prevalences of E. coli, Enterococcus spp., S. enterica, and Campylobacter spp. were 99.5, 85.9, 1.5, and 17.7%, respectively. The prevalence of erythromycin-resistant Enterococcus spp. was significantly higher on day 14 (59.7%) than on day 28 (22.2%). A higher prevalence of erythromycin-resistant Enterococcus spp. was found in samples from treated (59.3%) than in samples from nontreated (27.6%) animals. Multidrug resistance (three or more antimicrobial classes) was observed in 8.4% of E. coli isolates and 62.7% of Enterococcus isolates. The administration of tulathromycin was significantly associated with an increased prevalence of erythromycin-resistant Enterococcus spp. isolates.

HIGHLIGHTS

A Longitudinal Investigation of the Effects of Age, Dietary Fiber Type and Level and Injectable Antimicrobials on the Fecal Microbiome and Antimicrobial Resistance of Finisher Pigs

Age and diet are among the factors that influence the community composition of the fecal microbiome. Additionally, antimicrobial use can alter the composition of bacterial communities. An 86-d study with finisher pigs aimed to evaluate age-related dynamics (d 98-177 of age), effects of types and levels of dietary fiber, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance (AMR) was conducted. A total of 287 pigs, housed in 36 pens, with 7 to 8 pigs per pen, fed a corn grain and soybean meal-based basal diet, formulated to contain 8.7% neutral detergent fiber (NDF), were randomly assigned to one of three treatments: 1. basal diet with no supplement, 2. basal diet supplemented with 20% distillers dried grains with solubles (DDGS) formulated to contain 13.6% NDF, or 3. basal diet supplemented with 14.5% sugar beet pulp (SBP) formulated to contain 13.6% NDF. Five finisher pigs from each treatment group were selected randomly, and fecal samples were collected on d 98, 110, 144, and 177 of age. In addition, fecal samples were collected from pigs that were injected intramuscularly ceftiofur hydrochloride or penicillin G on d 1 and 3 along with pen-mate untreated controls on d 1. Fecal samples were subjected to 16S rRNA amplicon-based microbiome analysis and culture methods to quantify the abundance of total and AMR coliforms and enterococci populations. The alpha diversity, such as species richness, increased with age, and the overall bacterial composition changed with age (P =0.001) and diet (P = 0.001). Diet-associated shifts in the specific bacterial taxa were observed. The richness, diversity, and evenness of bacterial taxa did not differ between pigs that were injected with ceftiofur versus their untreated pen mates or by dietary treatments, but differed in pigs that received penicillin G injection. Both antimicrobial treatments contributed to changes in the overall fecal bacterial composition at the genus level. Collectively, the data demonstrate that both age and the diet (control vs. DDGS-, control vs. SBP- or DDGS- vs. SBP-based diets) were associated with overall bacterial community composition and the impact of age on variations in fecal microbiome composition was greater than the diet. Antibiotic treatment had minimal effect on bacterial diversity and relative abundance of taxa. Further, diets and antimicrobial treatment had minimal impact on the overall counts of AMR coliforms and enterococci populations in feces.

218 Evaluation of a Direct-Fed Microbial Product (DIRECTä) on Fecal Shedding of Shiga Toxin-Producing Escherichia Coli in Finishing Cattle in a Commercial Feedlot

Shiga toxin-producing Escherichia coli (STEC), particularly seven serogroups O26, O45, O103, O111, O121, O145, and O157, are major food borne pathogens. Cattle are a major reservoir in which STEC colonize the hindgut and are shed in the feces. Most cattle shed the organisms at low concentrations and a small proportion, called super shedders, shed at high concentrations (≥ 104 per g). Our objective was to evaluate the effect of a commercial DFM product containing lactic acid and propionic acid bacteria (Microbios Direct LA = 1 x 107 CFU and Direct PRO = 5 x 107 CFU/animal/d). The study was conducted in a commercial feedlot and a total of 16 pens were randomly assigned to control or DFM-treated group. Twenty pen-floor fecal samples were collected from each pen on 3 occasions, at 2-week intervals, approximately 100 d after DFM supplementation. Fecal samples were subjected to culture and PCR methods to quantify E. coli O157 and determine prevalence of the 6 non-O157 serogroups and 4 major virulence genes, Shiga toxins 1 and 2, intimin (an adhesin) and enterohemolysin. Data were analyzed using PROC MIXED procedure with pen as the experimental unit. The treatment means comparison within sampling day were carried out for variables that showed significant treatment and sampling day interaction. The overall fecal shedding of E. coli O157 was higher in the control group than in the DFM group, and the difference was significant in the third sampling day. Among the top-6 STEC, O26 and O103 were the dominant serogroups. The prevalence of the 4 major STEC virulence genes and the non-O157 STEC serogroups were not affected by inclusion of the DFM in the diet. In conclusion, DFM supplementation appeared to reduce fecal shedding E. coli O157, but prevalence of the 6 non-O157 serogroups and virulence genes were not affected.

Coliform and Escherichia coli Contamination on External and Internal Surfaces of Beef Carcasses with and without Tissue Adhesion Excision

ABSTRACT

Following removal of hides and viscera during beef processing, carcasses are inspected for tissue adhesions that can affect meat quality or harbor bacteria. Carcasses with pleural or abdominal adhesions may be diverted from the production line for manual excision and then returned to the line. No published data indicate whether adhesion excision is associated with bacterial contamination. Therefore, our objective was to determine the presence and concentration of generic Escherichia coli and non-E. coli coliforms from the internal and external surfaces of carcasses that were, or were not, diverted for adhesion excision. During 9 processing days over a 4-month period in a large commercial beef processing facility, 1,738 carcass sponge samples from 2,730 cm2 areas on both the internal and the external surfaces of carcasses with and without tissue adhesions were collected. Coliforms and E. coli were cultured and enumerated using Petrifilm procedures, and data were analyzed with mixed models. Coliforms were present at higher concentrations than E. coli, and prevalence and mean log concentrations of both coliforms and E. coli were significantly higher for samples from the external than from the internal surfaces of carcasses. However, differences in prevalence and concentration of coliforms between external and internal surfaces varied significantly based on whether carcasses had adhesions excised. The difference was greatest for coliforms present on the external (2.06 log CFU/100 cm2) versus the internal (0.93 log CFU/100 cm2) carcass surfaces without adhesions, whereas the difference in concentrations from the external (1.80 log CFU/100 cm2) and the internal (1.31 log CFU/100 cm2) surfaces of carcasses with adhesions was not as large. These results indicate that surveillance of carcass bacteria may be affected by whether the external versus the internal surfaces are sampled and whether carcasses are diverted for excision of adhesions.

HIGHLIGHTS

Whole genome sequence analyses-based assessment of virulence potential and antimicrobial susceptibilities and resistance of Enterococcus faecium strains isolated from commercial swine and cattle probiotic products

Enterococcus faecium is one of the more commonly used bacterial species as a probiotic in animals. The organism, a common inhabitant of the gut of animals and humans, is a major nosocomial pathogen responsible for a variety infections in humans and sporadic infections in animals. In swine and cattle, E. faecium-based probiotic products are used for growth promotion and gut functional and health benefits. The objective of this study was to utilize whole genome sequence-based analysis to assess virulence potential, detect antimicrobial resistance genes, and analyze phylogenetic relationships of E. faecium strains from commercial swine and cattle probiotics. Genomic DNA extracted from E. faecium strains, isolated from commercial probiotic products of swine (n = 9) and cattle (n = 13), were sequenced in an Illumina MiSeq platform and analyzed. Seven of the nine swine strains and seven of the 13 cattle strains were identified as Enterococcus lactis, and not as E. faecium. None of the 22 probiotic strains carried major virulence genes required to initiate infections, but many carried genes involved in adhesion to host cells, which may benefit the probiotic strains to colonize and persist in the gut. Strains also carried genes encoding resistance to a few medically important antibiotics, which included aminoglycosides [aac(6')-Ii, aph(3')-III, ant(6)-Ia], macrolide, lincosamide and streptogramin B (msrC), tetracyclines [tet(L) and tet(M)], and phenicols [cat-(pc194)]. The comparison of the genotypic to phentypic AMR data showed presence of both related and unrelated genes in the probiotic strains. Swine and cattle probiotic E. faecium strains belonged to diverse sequence types. Phylogenetic analysis of the probiotic strains, and strains of human (n = 29), swine (n = 4), and cattle (n = 4) origin, downloaded from GenBank, indicated close clustering of strains belonging to the same species and source, but a few swine and cattle probiotic strains clustered closely with other cattle and human fecal strains. In conclusion, the absence of major virulence genes characteristic of the clinical E. faecium strains suggests that these probiotic strains are unlikely to initiate opportunistic infection. However, the carriage of AMR genes to medically important antibiotics and close clustering of the probiotic strains with other human and cattle fecal strains suggests that probiotic strains may pose risk to serve as a source of transmitting AMR genes to other gut bacteria.

38 Evaluation of Sorghum Phenolic Compounds for Their Antimicrobial Activities Against Liver Abscess Causing Pathogens in Feedlot Cattle

Liver abscesses occur in finishing cattle fed high-grain, low-roughage diets. Cattle with abscessed livers seldom show any clinical signs and are detected only at the time of slaughter. Liver abscesses are of significant economic concern to the feedlot industry. Liver abscesses comprise, on average, 67% of all liver abnormalities in cattle slaughtered in the United States with a prevalence of 10–20% and may reduce the value of the beef carcass up to $38 per animal with the most severe abscesses. There are four causative agents of the disease including the two subspecies of Fusobacterium necrophorum, ssp. necrophorum and ssp. funduliforme, Trueperella pyogenes, and Salmonella enterica. Tylosin, supplemented in the feed, is the most commonly used antibiotic in the feedlot industry to prevent liver abscesses. Because of the concerns about antimicrobial resistance, there is a need to find an effective alternative to this antibiotic, and sorghum grain extracts, which are high in phenolic compounds, may have the potential to be used as natural antibiotic alternatives. Our objectives were to investigate the efficacy of phenolic extracts from black, sumac, brown, and burgundy sorghums on liver abscess pathogens. The sorghum phenolics were extracted using 75% aqueous acetone and total phenolic content was determined by spectrophotometrically. Bacterial strains were cultured in Mueller-Hinton broth (Salmonella and Trueperella pyogenes) or anaerobic brain-heart infusion broth (Fusobacterium) with and without sorghum extracts (1 mg/ml) at 12, 24, and 48 hours and bacterial concentrations were determined. If the compound was inhibitory, a micro-broth dilution method was used to quantify the inhibitory activity. Both black and sumac sorghum phenolics inhibited growth of all four bacterial species. Further studies are ongoing to investigate different concentrations and phenolic compounds from varieties of sorghum grains on the liver abscess pathogens.

48 Evaluation of Antimicrobial Activities of Phytophenols Against Bacterial Pathogens That Cause Liver Abscesses in Feedlot Cattle

Liver abscesses occur in finishing cattle fed high-grain, low-roughage diets. Cattle with abscessed livers do not show any clinical signs and are detected only at slaughter. Liver abscesses, which account for 67% of all liver abnormalities in cattle slaughtered in the United States, are of major economic concern to the beef industry. Fusobacterium necrophorum, Trueperella pyogenes, and Salmonella enterica, particularly the serotype Lubbock, are the main etiologic agents. Currently, the control of liver abscesses is based on in-feed use of antibiotics. The emergence and dissemination of antimicrobial resistance to antibiotics use in animals is a public health concern. Plant-based phenolic compounds, called phytophenols, are known to have antimicrobial properties. Our objectives were to evaluate antimicrobial activities of phytophenols on the liver abscess bacterial pathogens. Phytophenols extracted from rosemary, green tea, grapeseed, organic goji berry, and green coffee were selected for testing. The phytophenols were extracted using 75% aqueous acetone and total phenolic content was determined by a spectrophotometric analysis. Bacteria were cultured in Mueller-Hinton broth (S. Lubbock and T. pyogenes) or anaerobic brain-heart infusion broth (F. necrophorum with and without phytophenols, at 6, 12, 24, and 48 hours and bacterial concentrations were determined. If phytophenol was inhibitory, a micro-broth dilution method was used to quantify the inhibition. Phytophenols from green tea, grape seed, and rosemary inhibited T. pyogenes. Further studies are ongoing to investigate different concentrations of phenolic compounds on the pathogens. Phytophenols that inhibit the pathogens may have the potential to be used as feed additives to prevent liver abscesses.

28 In-feed or In-water Antibiotic Administration Did Not Influence the Fecal Prevalence and Antimicrobial Susceptibility Profiles of Salmonella in Piglets

A total of 1,296 weaned piglets were used in a 35-d study to assess the impact of in-feed vs in-water administrations of chlortetracycline (CTC) and or tiamulin on prevalence and antimicrobial resistance (AMR) profiles of Salmonella enterica. Piglets were allocated to 48 pens (27 pigs per pen) and pens were assigned randomly to six treatment groups: control (no antibiotic), in-feed CTC, in-water CTC, in-feed tiamulin, in-water tiamulin, and in feed CTC and tiamulin. Fresh fecal samples were collected randomly from 5 of 27 piglets from each pen on days -7, 0 (pre-treatment), 7, 14 (treatment), 21, and 28 (post-treatment). Salmonella isolation and identification were done by enrichment, plating on selective medium, and species confirmation of putative colonies by PCR. Antimicrobial susceptibility and resistance of the isolates were determined using premade antibiotic panel (SensititreTM CMV3AGNF and BOPO7F) and results were interpreted based on the Clinical and Laboratory Standards Institute guidelines. All Salmonella isolates were identified as serotype Typhimurium. The overall prevalence of Salmonella was 3.0% (43/1,440) with no treatment effect (P &gt; 0.05). All isolates were resistant (100%) to tetracycline and tiamulin. Additionally, the isolates were resistant to ampicillin (100%), streptomycin (100%), sulfisoxazole (100), ciprofloxacin (95.4%) and nalidixic acid (74.4%). Only a few isolates were resistant to trimethoprim/sulphamethoxazole (4.7%), ceftriaxone (7.0%), and ceftiofur (7.0%). PCR assays indicated the presence of tetB gene in all isolates, while 11 (25.6%) and 4 (9.3%) isolates were positive for tetD and tetA genes, respectively. Neither in-feed nor in-water administration of CTC or tiamulin impacted the fecal prevalence and antimicrobial susceptibility of Salmonella in nursery piglets.

29 Live Yeast and Yeast Extracts with and Without Pharmacological Levels of Zinc on Nursery Pig Growth Performance and Fecal Escherichia coli Antimicrobial Resistance

A total of 360 barrows (DNA 200×400; initially 5.6 kg) were used to evaluate yeast-based probiotics (Phileo by Lesaffre, Milwaukee, WI) in diets with or without pharmacological levels of Zn on growth and fecal Escherichia coli antimicrobial resistance (AMR). There were 5 pigs/pen and 18 pens/treatment. Dietary treatments were arranged in a 2×2 factorial with main effects of yeast pre- and probiotics (0 vs. 0.10% Actisaf Sc 47 HR+, 0.05% SafMannan, and 0.05% Nucleosaf in phase 1 then concentrations were lowered by 50% in phase 2) and pharmacological levels of Zn (110 vs. 3,000 mg/kg in phase 1 and 2,000 mg/kg in phase 2 provided by zinc oxide). Treatments were fed in two phases from d 0 to 7 and 7 to 21 with a common diet fed from d 21 to 42 post-weaning. There were no probiotics×Zn interactions. From d 0 to 21, pigs fed pharmacological Zn had increased (P &lt; 0.001) ADG and ADFI; however, there were no effects of added pre- and probiotics. Fecal samples were collected on d 4, 21, and 42 from the same three pigs/pen for AMR profiles and fecal dry matter (DM). On d 4, pigs fed pharmacological Zn had greater fecal DM (P = 0.043); however, no differences were observed on d 21 or 42. E. coli was isolated from fecal samples and species confirmation was accomplished by PCR detection of uidA and clpB genes. Microbroth dilution method using SensititreTM CMV3AGNF panel was used to determine antimicrobial susceptibilities of E. coli isolates to 14 different antimicrobials. There was no evidence for differences in AMR of fecal E. coli isolates to antibiotics by added pre- and probiotics or Zn. Results suggest that pharmacological levels of Zn stimulate intake and growth and improve fecal consistency in the nursery with no statistical response from added pre- and probiotics.

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Whole-genome sequencing analysis of uncommon Shiga toxin-producing Escherichia coli from cattle: Virulence gene profiles, antimicrobial resistance predictions, and identification of novel O-serogroups

Shiga toxin-producing E. coli (STEC) are major foodborne pathogens. While many studies have focused on the "top-7 STEC", little is known for minor serogroups. A total of 284 non-top-7 STEC strains isolated from cattle feces were subjected to whole-genome sequencing (WGS) to determine the serotypes, the presence of virulence genes and antimicrobial resistance (AMR) determinants. Nineteen typeable and three non-typeable serotypes with novel O-antigen loci were identified. Twenty-one AMR genes and point mutations in another six genes that conferred resistance to 10 antimicrobial classes were detected, as well as 46 virulence genes. The distribution of 33 virulence genes and 15 AMR determinants exhibited significant differences among serotypes (p < 0.05). Among all strains, 81.7% (n = 232) and 14.1% (n = 40) carried stx2 and stx1 only, respectively; only 4.2% (n = 12) carried both. Subtypes stx1a, stx1c, stx2a, stx2c, stx2d, and stx2g were identified. Forty-six strains carried eae and stx2a and therefore had the potential cause severe diseases; 47 strains were genetically related to human clinical strains inferred from a pan-genome phylogenetic tree. We were able to demonstrate the utility of WGS as a surveillance tool to characterize the novel serotypes, as well as AMR and virulence profiles of uncommon STEC that could potentially cause human illness.

Bacterial community analysis of purulent material from liver abscesses of crossbred cattle and Holstein steers fed finishing diets with or without tylosin

Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n = 24) and Holstein steers (n = 24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced, and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top 3 genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family, and genera did not differ (P > 0.05) between the 4 treatment groups. Generic richness and evenness, determined by Shannon-Weiner and Simpson's diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.

Leukotoxin production by Fusobacterium necrophorum strains in relation to severity of liver abscesses in cattle

Fusobacterium necrophorum, a Gram-negative anaerobe, is the primary etiologic agent of liver abscesses of beef cattle. The bacterium, a member of the microbial community of the rumen, travels to the liver via portal circulation to cause abscesses. The severity of liver abscesses vary from mild with one or two small abscesses to severe with medium to large multiple abscesses. Leukotoxin, a secreted protein, is the critical virulence factor involved in the infection. Our objective was to compare leukotoxin production between strains of F. necrophorum isolated from mild and severe liver abscesses collected from slaughtered cattle. The quantification of leukotoxin was based on assays to measure cytotoxicity and protein antigen concentration. One-hundred strains, 50 from mild and 50 from severe abscesses, were utilized in the study. Cell-free supernatants were prepared from cultures grown in anaerobic broth at 9 and 24 h incubations. The leukotoxic activity was quantified by measuring cytotoxicity based on the release of lactic dehydrogenase from bovine lymphocyte cells, BL3, treated with the culture supernatant. Leukotoxin protein concentration was quantified by a sandwich ELISA assay with a leukotoxin-specific monoclonal antibody as the capture antibody. The leukotoxin activity and concentration were highly variable among the strains within each severity of liver abscesses. Although the leukotoxic activity was unaffected by incubation time, leukotoxin protein concentration was consistently higher at 24 h compared to 9 h incubation. Strains from severe liver abscesses had significantly higher leukotoxic activity and higher protein concentration compared to strains from mild liver abscesses (P < 0.0001) at both 9 and 24 h culture supernatants. Across all strains, the correlation coefficients between leukotoxic activity and leukotoxin concentration at 9 and 24 h were 0.14 (P = 0.17) and 0.47 (P < 0.0001), respectively. In conclusion, strains isolated from severe liver abscesses had significantly higher leukotoxic activities and leukotoxin protein concentrations compared to strains isolated from mild liver abscesses.

Age Dependence of Antimicrobial Resistance Among Fecal Bacteria in Animals: A Scoping Review

Introduction: A phenomenon of decreasing antimicrobial resistance (AMR) among fecal bacteria as food animals age has been noted in multiple field studies. We conducted a scoping review to summarize the extent, range, and nature of research activity and the data for the following question: "does AMR among enteric/fecal bacteria predictably shift as animals get older?". Methods: This review followed a scoping review methodology framework. Pertinent literature published up until November 2018 for all animals (except humans) was retrieved using keyword searches in two online databases, namely, PubMed® and the Web of Science™ Core Collection, without filtering publication date, geographic location, or language. Data were extracted from the included studies, summarized, and plotted. Study quality was also assessed using the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) guidelines for all included papers. Results: The publications with detailed relevant data (n = 62) in food animals, poultry, and dogs were identified. These included longitudinal studies (n = 32), cross-sectional studies of different age groups within one food animal production system or small-animal catchment area (n = 16), and experimental or diet trials (n = 14). A decline in host-level prevalence and/or within-host abundance of AMR among fecal bacteria in production beef, dairy cattle, and swine was reported in nearly two-thirds (65%) of the identified studies in different geographic locations from the 1970's to 2018. Mixed results, with AMR abundance among fecal bacteria either increasing or decreasing with age, have been reported in poultry (broiler chicken, layer, and grow-out turkey) and dogs. Conclusions: Quantitative synthesis of the data suggests that the age-dependent AMR phenomenon in cattle and swine is observed irrespective of geographic location and specific production practices. It is unclear whether the phenomenon predates or is related to antimicrobial drug use. However, almost 50% of the identified studies predate recent changes in antimicrobial drug use policy and regulations in food animals in the United States and elsewhere.

Shiga Toxin-Producing Escherichia coli in Feces of Finisher Pigs: Isolation, Identification, and Public Health Implications of Major and Minor Serogroups†

ABSTRACT

Shiga toxin-producing Escherichia coli (STEC) are major foodborne human pathogens that cause mild to hemorrhagic colitis, which could lead to complications of hemolytic uremic syndrome. Seven serogroups, O26, O45, O103, O111, O121, O145, and O157, account for the majority of the STEC illnesses in the United States. Shiga toxins 1 and 2, encoded by stx1 and stx2, respectively, and intimin, encoded by eae gene, are major virulence factors. Cattle are a major reservoir of STEC, but swine also harbor them in the hindgut and shed STEC in the feces. Our objectives were to use a culture method to isolate and identify major and minor serogroups of STEC in finisher pig feces. Shiga toxin genes were subtyped to assess public health implications of STEC. Fecal samples (n = 598) from finisher pigs, collected from 10 pig flows, were enriched in E. coli broth and tested for stx1, stx2, and eae by a multiplex PCR (mPCR) assay. Samples positive for stx1 or stx2 gene were subjected to culture methods, with or without immunomagnetic separation and plating on selective or nonselective media, for isolation and identification of stx-positive isolates. The culture method yielded a total of 178 isolates belonging to 23 serogroups. The three predominant serogroups were O8, O86, and O121. The 178 STEC strains included 26 strains with stx1a and 152 strains with stx2e subtypes. Strains with stx1a, particularly in association with eae (O26 and O103), have the potential to cause severe human infections. All stx2-positive isolates carried the subtype stx2e, a subtype that causes edema disease in swine, but is rarely involved in human infections. Several strains were also positive for genes that encode for enterotoxins, which are involved in neonatal and postweaning diarrhea in swine. In conclusion, our study showed that healthy finisher pigs harbored and shed several serogroups of E. coli carrying virulence genes involved in neonatal diarrhea, postweaning diarrhea, and edema disease, but prevalence of STEC of public health importance was low.

HIGHLIGHTS

388 Nutrition and the Ruminal Microbiome: Emerging Frontiers from an Old Friend

Rumen, a pregastric anaerobic gut ecosystem, inhabits arguably the most diverse and complex microbial community, with a mutualistic relationship with the host. The relationship is best exemplified in the utilization of lignocellulosic material and non-protein nitrogen to provide energy and protein to the host. The microbial community of the rumen is composed of bacteria, archaea, protozoa, fungi and bacteriophages. Culture- or microscopy-based procedures have identified over 200 species of bacteria, methanogens, ciliated protozoa and zoosporic fungi. The community analysis based on the genetic material of all microbial cells, called microbiome, has vastly expanded our understanding of the ruminal ecosystem. Microbiome analysis is based on sequencing of the targeted amplicons (16S rDNA variable regions for bacteria and archaea, 18S rDNA for protozoa or Internal Transcribed Regions for fungi) or whole genome shotgun metagenomics analysis. Rapid advancements in nucleic acid sequencing technologies and bioinformatics pipelines have provided unprecedented opportunities to delineate the diversity and complexity of the microbial community in relation ruminal function and dysfunctions and link ruminal microbes to host nutrition and productivity. Culture-independent methods have identified thousands of microbial species in the rumen, suggesting that a major fraction of the microbiome has not been cultured and functionally identified. A core microbiome in bacterial and archaeal populations of the rumen has been identified across a wide geographical regions, but significant variations in diversity, abundance, and individual taxa do exist because of diet and host genetics. However, there is evidence of signature microbiome among individual animals on the same diet and environment. Microbiome-wide association studies in relation to dietary changes, ruminal function and dysfunctions have begun to link and define the complexity of the host-microbe relationships. Translation of the potential of the microbiome analysis is supported by emerging evidences that specific microbiota can be linked to ruminal activity and productivity.

265 Evaluating the route of antibiotic administration and its effect on nursery pig growth performance

A total of 2,592 pigs (L337×1050, PIC, Hendersonville, TN; initially 5.58 kg BW) were used in a 28-d study to evaluate the route of antibiotic administration (in-feed vs in-water) on pig performance. Pigs were weaned at 21 d of age and placed in a commercial research facility with 27 pigs per pen. After a 7-d pre-trial period, pens of pigs were assigned to weight blocks in a randomized complete block design. There were 12 replications per treatment with pen as experimental unit for in-feed medication treatments and a pairs of pens as the experimental unit for water medication treatments. Treatments included a control (no medication), chlortetracycline (CTC) provided via feed or water to achieve 22 mg/kg BW, tiamulin in feed (5 to10 mg/kg BW) or water (23 mg/kg BW), or a combination of CTC and tiamulin in feed. Experimental treatments were provided for 14-d followed by a 14-d period without medication. Data were analyzed using R Studio (Version 3.5.2). From d 0 to 14, there was an antibiotic×route of administration interaction for ADG and G:F. For ADG, pigs fed diets containing CTC had increased (P&lt; 0.05) ADG compared with those fed tiamulin in feed, with pigs provided CTC or tiamulin in the water intermediate. For G:F, pigs provided tiamulin in feed had decreased G:F compared to pigs fed CTC in feed or CTC or tiamulin supplied in water. Pigs fed CTC in the diet had increased ADFI compared to the control with pigs provided antibiotics in the water or tiamulin in feed intermediate (P&lt; 0.05). Pigs provided the combination of CTC and tiamulin in feed were not different than those provided CTC in feed. There was no evidence of difference among treatments in subsequent performance. In summary, providing CTC in feed with or without tiamulin improved nursery pig growth performance.

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18 Impact of in-feed vs. in-water antibiotic administrations on the fecal prevalence and antimicrobial susceptibilities of Campylobacter and Salmonella in piglets

Campylobacter and Salmonella are common food borne pathogens in the gut of pigs and are shed in the feces. The control of these bacteria in pigs is of importance in reducing the potential for transmission to humans. In swine, oral route, either in-feed or in-water, is by far the most common route of administration of antibiotics. Because the distribution of the antibiotic in the gut and the dosage are different, the impact of in-feed vs. in-water administration of antibiotics on the fecal shedding of food borne pathogens, Campylobacter and Salmonella, and on the development of antimicrobial resistance (AMR) in gut bacteria is a largely unexplored area. Therefore, a study was conducted to compare the effects of in-feed and in-water antibiotic administration on fecal prevalence of Campylobacter and Salmonella and AMR development in nursery piglets. A total of 1,296 weaned piglets were allocated into pens (48 pens; 27 pigs per pen) distributed in a single room. Pens were assigned randomly to six treatment groups; Control (No antibiotic), In-feed chlortetracycline (CTC), In-water CTC, In-feed tiamulin, In-water tiamulin, and a combination of CTC and tiamulin (In-feed). Fresh fecal samples were collected randomly from 5 of 27 piglets from each pen on pre-treatment (days -7, 0), treatment (days 7, 14) and post-treatment (days 21, 28) phases. Bacterial isolations and identifications were done by culture method and PCR, respectively. Overall prevalence of Campylobacter and Salmonella were 18.2% (262/1,440) and 3.9% (56/1,440) respectively. Speciation of Campylobacter isolates indicated C. hyointestinalis (17.9%; 258/1,440) and C. coli (0.3%; 4/1,440). Pigs from control group had a higher prevalence (P&lt; 0.05) of both Campylobacter and Salmonella when compared to other treatment groups. Both treatment and post-treatment phases had a significant effect on the prevalence of Campylobacter and Salmonella (P&lt; 0.05).

Effectiveness of a Direct-Fed Microbial Product Containing Lactobacillus acidophilus and Lactobacillus casei in Reducing Fecal Shedding of Escherichia coli O157:H7 in Commercial Feedlot Cattle

The objective of this study was to evaluate the effectiveness of a direct-fed microbial (DFM) product in reducing fecal shedding of Escherichia coli O157:H7 in finishing commercial feedlot cattle in Kansas (KS) and Nebraska (NE). Utilizing a randomized complete block design within the feedlot (KS, n = 1; NE, n = 1), cattle were randomly allocated to 20 pens, grouped in blocks of two based on allocation date, and then, within the block, randomly assigned to a treatment group (DFM or negative control). The DFM product was included in the diet at a targeted daily dose of 1 × 10⁹ colony-forming units (CFU) of the Lactobacillus acidophilus and Lactobacillus casei combination per animal for at least 60 d before sampling. Feedlots were sampled for four consecutive weeks; weekly sampling consisted of collecting 20 pen floor fecal samples per pen. Fecal samples were subjected to culture-based methods for detection and isolation of E. coli O157, and positive samples were quantified using real-time polymerase chain reaction. Primary outcomes of interest were fecal prevalence of E. coli O157:H7 and E. coli O157 supershedding (≥10⁴ CFU/g of feces) prevalence. Data for each feedlot were analyzed at the pen level using mixed models accounting for the study design features. Model-adjusted mean E. coli O157:H7 fecal prevalence estimates (standard error of the mean [SEM]) for DFM and control groups were 8.2% (SEM = 2.2%) and 9.9% (SEM = 2.5%) in KS and 14.6% (SEM = 2.8%) versus 14.3% (SEM = 2.6%) in NE; prevalence did not differ significantly between treatment groups at either site (KS, p = 0.51; NE, p = 0.92). Mean E. coli O157 supershedding prevalence estimates for DFM and control groups were 2.2% (SEM = 0.7%) versus 1.8% (SEM = 0.7%) in KS (p = 0.66) and 6.7% (SEM = 1.5%) versus 3.2% (SEM = 1.0%) in NE (p = 0.04). In conclusion, administering the DFM product in the finishing diet of feedlot cattle did not significantly reduce E. coli O157:H7 fecal prevalence or supershedding prevalence in study pens at either commercial feedlot.

Multiplex PCR Assays for the Detection of One Hundred and Thirty Seven Serogroups of Shiga Toxin-Producing Escherichia coli Associated With Cattle

Escherichia coli carrying prophage with genes that encode for Shiga toxins are categorized as Shiga toxin-producing E. coli (STEC) pathotype. Illnesses caused by STEC in humans, which are often foodborne, range from mild to bloody diarrhea with life-threatening complications of renal failure and hemolytic uremic syndrome and even death, particularly in children. As many as 158 of the total 187 serogroups of E. coli are known to carry Shiga toxin genes, which makes STEC a major pathotype of E. coli. Seven STEC serogroups, called top-7, which include O26, O45, O103, O111, O121, O145, and O157, are responsible for the majority of the STEC-associated human illnesses. The STEC serogroups, other than the top-7, called “non-top-7” have also been associated with human illnesses, more often as sporadic infections. Ruminants, particularly cattle, are principal reservoirs of STEC and harbor the organisms in the hindgut and shed in the feces, which serves as a major source of food and water contaminations. A number of studies have reported on the fecal prevalence of top-7 STEC in cattle feces. However, there is paucity of data on the prevalence of non-top-7 STEC serogroups in cattle feces, generally because of lack of validated detection methods. The objective of our study was to develop and validate 14 sets of multiplex PCR (mPCR) assays targeting serogroup-specific genes to detect 137 non-top-7 STEC serogroups previously reported to be present in cattle feces. Each assay included 7–12 serogroups and primers were designed to amplify the target genes with distinct amplicon sizes for each serogroup that can be readily identified within each assay. The assays were validated with 460 strains of known serogroups. The multiplex PCR assays designed in our study can be readily adapted by most laboratories for rapid identification of strains belonging to the non-top-7 STEC serogroups associated with cattle.

Potential risk-factors affecting Salmonella sp. and Escherichia coli occurrence and distribution in Midwestern United States swine feed mills

AIM

This study aimed to evaluate the patterns and potential risk factors associated with the occurrence of Salmonella sp. and Escherichia coli in selected United States swine feed mills.

METHODS AND RESULTS

A total of 405 samples were collected during fall 2018, spring and summer 2019 from selected sites including floors, equipment, shoes and feed in six feed mills in the US Midwest region. Each sample was analysed for the presence of Salmonella and E. coli with culture methods and confirmed by PCR. A survey regarding production volumes, hygiene practices and microbial testing capabilities was conducted in each facility All mills had at least one sampling site positive for either Salmonella or E. coli. Of the 405 samples, 4·7, and 14·1% were positive for Salmonella sp., and E. coli respectively. Sites with higher percentages of positive samples were the receiving, manufacturing, and control area floors. The survey responses indicated that the age of the mill might be a risk factor for bacterial contamination: the older the facility, the higher the number of positive samples. Other risk factors evaluated, such as the production capacity, did not appear to relate to bacterial prevalence.

CONCLUSION

The data documents the presence of E. coli and Salmonella in selected US swine feed mills, and an association between E. coli occurrence and number of ingredient suppliers to feed mill.

SIGNIFICANCE AND IMPACT OF THE STUDY

This information could be used to understand risk factors affecting the occurrence of Salmonella sp. and E. coli in feed mills and help implement monitoring and mitigation strategies for public health.

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.

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.

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.

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.

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.

Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin

Escherichia coli O103, harbored in the hindgut and shed in the feces of cattle, can be enterohemorrhagic (EHEC), enteropathogenic (EPEC), or putative non-pathotype. The genetic diversity particularly that of virulence gene profiles within O103 serogroup is likely to be broad, considering the wide range in severity of illness. However, virulence descriptions of the E. coli O103 strains isolated from cattle feces have been primarily limited to major genes, such as Shiga toxin and intimin genes. Less is known about the frequency at which other virulence genes exist or about genes associated with the mobile genetic elements of E. coli O103 pathotypes. Our objective was to utilize whole genome sequencing (WGS) to identify and compare major and putative virulence genes of EHEC O103 (positive for Shiga toxin gene, stx1, and intimin gene, eae; n = 43), EPEC O103 (negative for stx1 and positive for eae; n = 13) and putative non-pathotype O103 strains (negative for stx and eae; n = 13) isolated from cattle feces. Six strains of EHEC O103 from human clinical cases were also included. All bovine EHEC strains (43/43) and a majority of EPEC (12/13) and putative non-pathotype strains (12/13) were O103:H2 serotype. Both bovine and human EHEC strains had significantly larger average genome sizes (P < 0.0001) and were positive for a higher number of adherence and toxin-based virulence genes and genes on mobile elements (prophages, transposable elements, and plasmids) than EPEC or putative non-pathotype strains. The genome size of the three pathotypes positively correlated (R² = 0.7) with the number of genes carried on mobile genetic elements. Bovine strains clustered phylogenetically by pathotypes, which differed in several key virulence genes. The diversity of E. coli O103 pathotypes shed in cattle feces is likely reflective of the acquisition or loss of virulence genes carried on mobile genetic elements.

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.

Effects of limonene on ruminal concentrations, fermentation, and lysine degradation in cattle

Previous in vitro data showed that was inhibited by limonene. We further evaluated effects of limonene on growth of in vitro as well as on ruminal concentrations of in vivo. With in vitro cultivation in anaerobic brain-heart infusion broth, limonene decreased growth of . Thymol also reduced growth of , but it was less effective than limonene. Tylosin effectively reduced growth of in vitro. Although the response over fermentation times and concentrations of antimicrobials differed somewhat between tylosin and limonene, the 2 antimicrobial agents yielded similar inhibitory effects on growth of at concentrations ranging from 6 to 24 mg/L. The effects of limonene on ruminal concentration in vivo were tested in 7 ruminally cannulated heifers (225 kg initial BW) used in a 7 × 4 Youden square design. Treatments included: 1) control, 2) limonene at 10 mg/kg diet DM, 3) limonene at 20 mg/kg diet DM, 4) limonene at 40 mg/kg diet DM, 5) limonene at 80 mg/kg diet DM, 6) CRINA-L (a blend of essential oil components) at 180 mg/kg diet DM, and 7) tylosin at 12 mg/kg diet DM. Each period included 11 d with 10 d washouts between periods. Samples of ruminal contents were collected before treatment initiation and after 4, 7, and 10 d of treatment for measuring by the most probable number method using selective culture medium. Limonene linearly decreased ( = 0.03) ruminal concentration, with the lowest concentration achieved with 40 mg of limonene/kg dietary DM. Limonene tended ( ≤ 0.07) to linearly reduce ruminal molar proportions of propionate and valerate while tending to linearly increase ( ≤ 0.10) those of butyrate and 2-methyl butyrate. Limonene did not affect ruminal NH concentrations or degradation rates of lysine. Neither CRINA-L ( = 0.52) nor tylosin ( = 0.19) affected ruminal concentrations. CRINA-L significantly decreased ruminal concentrations of NH and molar proportions of 3-methyl butyrate, whereas tylosin significantly decreased molar proportions of propionate while increasing those of butyrate and tending to increase those of acetate. Limonene supplementation reduced ruminal concentrations of suggesting that it may have the potential to reduce the prevalence of liver abscesses, although further research is needed to assess the effect of limonene in feedlot cattle.