Determining the prevalence of Escherichia coli, Salmonella, and shiga toxin-producing Escherichia coli in manure of dairy lagoons.

AIM: The aim of this study was to determine the prevalence of microbial pathogens in manure of dairy lagoons in California. METHODS AND RESULTS: To determine pathogens in dairy manure stored in anaerobic lagoons of dairy farm, an extensive field study was conducted across California to sample manure from 20 dairy farms. Samples were analyzed to determine the prevalence of indicator E. coli, Shiga toxin producing E. coli (STEC), Salmonella, and E. coli O157:H7. To test the E. coli, STEC, and Salmonella, we used agar culture-based method followed by polymerase chain reaction (PCR) method. In addition, a real- time PCR based method was used to determine the presence of E coli O157:H7. Study demonstrated that the prevalence of Salmonella in manure sample is lower than E. coli. The presence of Salmonella was found in 2.26% of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, approximately 11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR. CONCLUSION: These findings demonstrate that indicator E. coli are abundantly present in anaerobic lagoons. However, the presence of STEC, and Salmonella is substantially low.

Impact of zinc supplementation on phenotypic antimicrobial resistance of fecal commensal bacteria from pre-weaned dairy calves.

The objective of this study was to evaluate the impact of dietary zinc supplementation in pre-weaned dairy calves on the phenotypic antimicrobial resistance (AMR) of fecal commensal bacteria. A repository of fecal specimens from a random sample of calves block-randomized into placebo (n = 39) and zinc sulfate (n = 28) groups collected over a zinc supplementation clinical trial at the onset of calf diarrhea, calf diarrheal cure, and the last day of 14 cumulative days of zinc or placebo treatment were analyzed. Antimicrobial susceptibility testing was conducted for Enterococcus spp. (n = 167) and E. coli (n = 44), with one representative isolate of each commensal bacteria tested per sample. Parametric survival interval regression models were constructed to evaluate the association between zinc treatment and phenotypic AMR, with exponentiated accelerated failure time (AFT) coefficients adapted for MIC instead of time representing the degree of change in AMR (MIC Ratio, MR). Findings from our study indicated that zinc supplementation did not significantly alter the MIC in Enterococcus spp. for 13 drugs: gentamicin, vancomycin, ciprofloxacin, erythromycin, penicillin, nitrofurantoin, linezolid, quinupristin/dalfopristin, tylosin tartrate, streptomycin, daptomycin, chloramphenicol, and tigecycline (MR = 0.96-2.94, p > 0.05). In E. coli, zinc supplementation was not associated with resistance to azithromycin (MR = 0.80, p > 0.05) and ceftriaxone (MR = 0.95, p > 0.05). However, a significant reduction in E. coli MIC values was observed for ciprofloxacin (MR = 0.17, 95% CI 0.03-0.97) and nalidixic acid (MR = 0.28, 95% CI 0.15-0.53) for zinc-treated compared to placebo-treated calves. Alongside predictions of MIC values generated from these 17 AFT models, findings from this study corroborate the influence of age and antimicrobial exposure on phenotypic AMR.

Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli.

BACKGROUND: Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18. RESULTS: Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q < 0.2 and fold change > 2.0). In addition, pigs in antibiotic had a reduced (P < 0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P < 0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI. CONCLUSIONS: The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.

Dietary butyrate and valerate glycerides impact diarrhea severity and immune response of weaned piglets under ETEC F4-ETEC F18 coinfection conditions.

Enterotoxigenic Escherichia coli (ETEC) causes post-weaning diarrhea in piglets, significantly impacting animal welfare and production efficiency. The two primary ETEC pathotypes associated with post-weaning diarrhea are ETEC F4 and ETEC F18. During the post-weaning period, piglets may be exposed to both ETEC F4 and ETEC F18. However, the effects of coinfection by both strains have not been studied. Short chain fatty acid feed additives, such as butyrate and valerate, are being investigated for their potential to improve animal performance and disease resistance. Therefore, this pilot experiment aimed to test the effects of butyrate glycerides or valerate glycerides on growth performance, diarrhea incidence, and immune responses of piglets under ETEC F4-ETEC F18 coinfection conditions. Twenty piglets were individually housed and assigned to one of the three dietary treatments immediately at weaning (21 to 24 d of age). The dietary treatments included control (basal diet formulation), control supplemented with 0.1% butyrate glycerides or 0.1% valerate glycerides. After a 7-d adaptation, all pigs were inoculated with ETEC F4 and ETEC F18 (0.5 × 109 CFU/1.5 mL dose for each strain) on three consecutive days. Pigs and feeders were weighed throughout the trial to measure growth performance. Fecal cultures were monitored for hemolytic coliforms, and blood samples were collected for whole blood and serum analysis. Pigs fed valerate glycerides tended (P = 0.095) to have higher final body weight compared with control. The overall severity of diarrhea was significantly (P < 0.05) lower in both treatment groups than control. Pigs fed valerate glycerides tended (P = 0.061) to have lower neutrophils and had significantly (P < 0.05) lower serum TNF-α on day 4 post-inoculation. This pilot experiment established an appropriate experimental dose for an ETEC F4-ETEC F18 coinfection disease model in weaned piglets. Results also suggest that butyrate glycerides and valerate glycerides alleviated diarrhea and regulated immune responses in piglets coinfected with ETEC F4 and ETEC F18.

Piglets suffer from post-weaning diarrhea associated with Enterotoxigenic Escherichia coli (ETEC) F4 and F18, two prevalent strains on swine farms globally. Short chain fatty acids (SCFAs), such as butyrate and valerate, are natural, organic compounds that could potentially promote intestinal health when used as dietary supplements. During the post-weaning period, piglets are vulnerable to simultaneous infection by ETEC F4 and F18. Therefore, this experiment aimed to develop an experimental disease model for coinfection with ETEC F4 and F18, employing a dose of 0.5 × 109 CFU/1.5 mL of each strain, administered over three consecutive days. In addition, the experiment evaluated treatment diets supplemented with 0.1% butyrate or valerate glycerides compared with the control diet. Results from this experiment revealed that the inoculation dose incited infection and diarrhea in piglets, implying its suitability for use in a disease challenge model. Moreover, the results indicated that the inclusion of butyrate and valerate glycerides to pig's diet reduced the severity of diarrhea. Furthermore, pigs fed SCFA glycerides exhibited lowered levels of inflammatory blood markers. In conclusion, the experimental dose induced diarrhea in piglets, and dietary supplementation of butyrate and valerate glycerides alleviated the severity of diarrhea while augmenting inflammatory status.

Prevalence and antimicrobial resistance profiles of Vibrio spp. and Enterococcus spp. in retail shrimp in Northern California.

Shrimp is one of the most consumed seafood products globally. Antimicrobial drugs play an integral role in disease mitigation in aquaculture settings, but their prevalent use raises public health concerns on the emergence and spread of antimicrobial resistant microorganisms. Vibrio spp., as the most common causative agents of seafood-borne infections in humans, and Enterococcus spp., as an indicator organism, are focal bacteria of interest for the monitoring of antimicrobial resistance (AMR) in seafood. In this study, 400 samples of retail shrimp were collected from randomly selected grocery stores in the Greater Sacramento, California, area between September 2019 and June 2020. The prevalence of Vibrio spp. and Enterococcus spp. was 60.25% (241/400) and 89.75% (359/400), respectively. Subsamples of Vibrio (n = 110) and Enterococcus (n = 110) isolates were subjected to antimicrobial susceptibility testing (AST). Vibrio isolates had high phenotypic resistance to ampicillin (52/110, 47.27%) and cefoxitin (39/110, 35.45%). Enterococcus were most frequently resistant to lincomycin (106/110, 96.36%), quinupristin-dalfopristin (96/110, 87.27%), ciprofloxacin (93/110, 84.55%), linezolid (86/110, 78.18%), and erythromycin (58/110, 52.73%). For both Vibrio and Enterococcus, no significant associations were observed between multidrug resistance (MDR, resistance to ≥3 drug classes) in isolates from farm raised and wild caught shrimp (p > 0.05) and in isolates of domestic and imported origin (p > 0.05). Whole genome sequencing (WGS) of a subset of Vibrio isolates (n = 42) speciated isolates as primarily V. metschnikovii (24/42; 57.14%) and V. parahaemolyticus (12/42; 28.57%), and detected 27 unique antimicrobial resistance genes (ARGs) across these isolates, most commonly qnrVC6 (19.05%, 8/42), dfrA31 (11.90%, 5/42), dfrA6 (9.5%, 4/42), qnrVC1 (9.5%, 4/42). Additionally, WGS predicted phenotypic resistance in Vibrio isolates with an overall sensitivity of 11.54% and specificity of 96.05%. This study provides insights on the prevalence and distribution of AMR in Vibrio spp. and Enterococcus spp. from retail shrimp in California which are important for food safety and public health and exemplifies the value of surveillance in monitoring the spread of AMR and its genetic determinants.

Effects of supplementation of Bacillus amyloliquefaciens on performance, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with a pathogenic enterotoxigenic E. coli F18.

The objective of this study was to investigate the effects of dietary supplementation of Bacillus (B.) amyloliquefaciens on growth performance, diarrhea, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with F18 enterotoxigenic Escherichia coli (ETEC). A total of 50 weaned pigs (7.41 ± 1.35 kg BW) were individually housed and randomly allotted to one of the following five treatments: sham control (CON-), sham B. amyloliquefaciens (BAM-), challenged control (CON+), challenged B. amyloliquefaciens (BAM+), and challenged carbadox (AGP+). The experiment lasted 28 days, with 7 days of adaptation and 21 days after the first ETEC inoculation. ETEC challenge reduced (P < 0.05) average daily gain (ADG) of pigs. Compared with CON+, AGP+ enhanced (P < 0.05) ADG, while B. amyloliquefaciens supplementation tended (P < 0.10) to increase ADG in pigs from days 0 to 21 post-inoculation (PI). The ETEC challenge increased (P < 0.05) white blood cell (WBC) count on days 7 and 21 PI, while BAM+ pigs tended (P < 0.10) to have low WBC on day 7 PI and had lower (P < 0.05) WBC on day 21 PI compared with CON+. In comparison to AGP+ fecal microbiota, BAM+ had a lower (P < 0.05) relative abundance of Lachnospiraceae on day 0 and Clostridiaceae on day 21 PI, but a higher (P < 0.05) relative abundance of Enterobacyeriaceae on day 0. In ileal digesta, the Shannon index was higher (P < 0.05) in BAM+ than in AGP+. Bray-Curtis PCoA displayed a difference in bacterial community composition in ileal digesta collected from sham pigs vs. ETEC-infected pigs on day 21 PI. Pigs in BAM+ had a greater (P < 0.05) relative abundance of Firmicutes, but a lower (P < 0.05) relative abundance of Actinomycetota and Bacteroidota in ileal digesta than pigs in AGP+. Ileal digesta from AGP+ had a greater (P < 0.05) abundance of Clostridium sensu stricto 1 but lower (P < 0.05) Bifidobacterium than pigs in BAM+. In conclusion, supplementation of B. amyloliquefaciens tended to increase ADG and had limited effects on the diarrhea of ETEC-infected pigs. However, pigs fed with B. amyloliquefaciens exhibit milder systemic inflammation than controls. B. amyloliquefaciens differently modified the intestinal microbiota of weaned pigs compared with carbadox.

Assessment of Prevalence and Diversity of Antimicrobial Resistant Escherichia coli from Retail Meats in Southern California.

Retail meat products may serve as reservoirs and conduits for antimicrobial resistance, which is frequently monitored using Escherichia coli as indicator bacteria. In this study, E. coli isolation was conducted on 221 retail meat samples (56 chicken, 54 ground turkey, 55 ground beef, and 56 pork chops) collected over a one-year period from grocery stores in southern California. The overall prevalence of E. coli in retail meat samples was 47.51% (105/221), with E. coli contamination found to be significantly associated with meat type and season of sampling. From antimicrobial susceptibility testing, 51 isolates (48.57%) were susceptible to all antimicrobials tested, 54 (51.34%) were resistant to at least 1 drug, 39 (37.14%) to 2 or more drugs, and 21 (20.00%) to 3 or more drugs. Resistance to ampicillin, gentamicin, streptomycin, and tetracycline were significantly associated with meat type, with poultry counterparts (chicken or ground turkey) exhibiting higher odds for resistance to these drugs compared to non-poultry meats (beef and pork). From the 52 E. coli isolates selected to undergo whole-genome sequencing (WGS), 27 antimicrobial resistance genes (ARGs) were identified and predicted phenotypic AMR profiles with an overall sensitivity and specificity of 93.33% and 99.84%, respectively. Clustering assessment and co-occurrence networks revealed that the genomic AMR determinants of E. coli from retail meat were highly heterogeneous, with a sparsity of shared gene networks.

Dietary supplementation of botanical blends enhanced performance and disease resistance of weaned pigs experimentally infected with enterotoxigenic Escherichia coli F18.

Botanicals exhibit promising impacts on intestinal health, immune-regulation, and growth promotion in weaned pigs. However, these benefits may vary depending on major active components in the final feed additive products. Therefore, this study aimed to investigate two types of botanical blends (BB) that were comprised of 0.3% capsicum oleoresin and 12% garlic extracts from different sources on performance, diarrhea, and health of weaned piglets experimentally infected with a pathogenic Escherichia coli F18. Sixty weanling pigs (7.17 ± 0.97 kg body weight (BW)) blocked by weight and gender were assigned to one of five dietary treatments: negative control (NC), positive control (PC), or dietary supplementation with 100 mg/kg of BB1, 50 mg/kg or 100 mg/kg of BB2. This study lasted 28 d with 7 d before and 21 d after the first E. coli inoculation (day 0). All pigs, except negative control, were orally inoculated with 1010 cfu E. coli F18/3-mL dose for 3 consecutive days. Blood samples were collected periodically to analyze systemic immunity. Intestinal tissues and mucosa were collected on days 5 and 21 PI for analyzing histology and gene expression. All data, except for frequency of diarrhea, were analyzed by ANOVA using the PROC MIXED of SAS. The Chi-square test was used for analyzing frequency of diarrhea. Escherichia coli infection reduced (P < 0.05) growth rate and feed intake and increased (P < 0.05) frequency of diarrhea of weaned pigs throughout the experiment. Supplementation of 100 mg/kg BB1 or BB2 alleviated (P < 0.05) frequency of diarrhea of E. coli challenged pigs during the entire experiment. Escherichia coli infection also enhanced (P < 0.05) serum TNF-α and haptoglobin concentrations on day 4 post-inoculation (PI) but reduced (P < 0.05) duodenal villi height and area on day 5 PI, while pigs supplemented with 100 mg/kg BB1 or BB2 had lower (P < 0.05) serum TNF-α than pigs in PC on day 4 PI. Pigs fed with 100 mg/kg BB2 had higher (P < 0.05) jejunal villi height than pigs in PC on day 5 PI. Pigs fed with 100 mg/kg BB2 had reduced (P < 0.05) gene expression of IL1B, PTGS2, and TNFA in ileal mucosa than pigs in PC on day 21 PI. In conclusion, dietary supplementation of botanical blends at 100 mg/kg could enhance disease resistance of weaned pigs infected with E. coli F18 by enhancing intestinal morphology and regulating local and systemic immunity of pigs.

This experiment aimed to investigate two botanical blends consisting of 0.3% capsicum oleoresin and 12% garlic extracts on performance, diarrhea, and health of weaned piglets experimentally infected with a pathogenic Escherichia coli F18. The two botanical blends have the same formulation, except that different garlic oils were used. A total of 60 weaned pigs were randomly allotted to one of five experimental treatments: 1) a complex control diet without E. coli F18 challenge; 2) control diet with E. coli F18 challenge; 3) supplementing 100 mg/kg of botanical blend type 1 to pigs challenged with E. coli F18; 4) and 5) supplementing 50 or 100 mg/kg of botanical blend type 2 to pigs challenged with E. coli F18. The experiment lasted 28 d with 7 d adaptation and 21 d after the first F18 E. coli inoculation. Results of this experiment demonstrate that supplementation of 100 mg/kg of botanical blend enhanced disease resistance and tended to improve growth of weaned pigs, regardless of garlic oil variety. An improved intestinal morphology and reduced systemic inflammation was also observed in pigs supplemented with 100 mg/kg of botanical blends. In conclusion, supplementation of 100 mg/kg of botanical blends could reduce diarrhea of E. coli infected pigs and modify local or systemic immunity of pigs.

Diverse Genotypes of Cryptosporidium in Sheep in California, USA.

Cryptosporidium spp. is a parasite that can infect a wide variety of vertebrate species. The parasite has been detected in sheep worldwide with diverse species and genotypes of various levels of zoonotic potential and public health concern. The purpose of this study was to determine the distribution of genotypes of Cryptosporidium in sheep in California, USA. Microscopic positive samples from individual sheep from central and northern California ranches were genotyped by sequencing a fragment of the 18S rRNA gene and BLAST analysis. Eighty-eight (63.8%) of the microscopic positive samples were genotyped, and multiple genotypes of Cryptosporidium were identified from sheep in the enrolled ranches. Approximately 89% of isolates (n = 78) were C. xiaoi or C. bovis, 10% of isolates (n = 9) were C. ubiquitum, and 1% of isolates (n = 1) were C. parvum. The C. parvum and C. ubiquitum isolates were detected only from lambs and limited to four farms. Given that the majority of Cryptosporidium species (i.e., C. xiaoi and C. bovis) were of minor zoonotic concern, the results of this study suggest that sheep are not a reservoir of major zoonotic Cryptosporidium in California ranches.

Prevalence of Antimicrobial Resistance in Select Bacteria From Retail Seafood-United States, 2019.

In 2019, the United States National Antimicrobial Resistance Monitoring System (NARMS) surveyed raw salmon, shrimp, and tilapia from retail grocery outlets in eight states to assess the prevalence of bacterial contamination and antimicrobial resistance (AMR) in the isolates. Prevalence of the targeted bacterial genera ranged among the commodities: Salmonella (0%-0.4%), Aeromonas (19%-26%), Vibrio (7%-43%), Pseudomonas aeruginosa (0.8%-2.3%), Staphylococcus (23%-30%), and Enterococcus (39%-66%). Shrimp had the highest odds (OR: 2.8, CI: 2.0-3.9) of being contaminated with at least one species of these bacteria, as were seafood sourced from Asia vs. North America (OR: 2.7; CI: 1.8-4.7) and Latin America and the Caribbean vs. North America (OR: 1.6; CI: 1.1-2.3) and seafood sold at the counter vs. sold frozen (OR: 2.1; CI: 1.6-2.9). Isolates exhibited pan-susceptibility (Salmonella and P. aeruginosa) or low prevalence of resistance (<10%) to most antimicrobials tested, with few exceptions. Seafood marketed as farm-raised had lower odds of contamination with antimicrobial resistant bacteria compared to wild-caught seafood (OR: 0.4, CI: 0.2-0.7). Antimicrobial resistance genes (ARGs) were detected for various classes of medically important antimicrobials. Clinically relevant ARGs included carbapenemases (bla IMI-2, bla NDM-1) and extended spectrum ß-lactamases (ESBLs; bla CTX-M-55). This population-scale study of AMR in seafood sold in the United States provided the basis for NARMS seafood monitoring, which began in 2020.

Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line.

BACKGROUND: Microbiota play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth, and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy farm are still lacking. We used 16S rRNA gene sequencing to evaluate the fecal bacterial communities of 90 dairy cattle housed in 12 distinctly defined management units on a modern dairy farm. RESULTS: We found that cattle from management units 5, 6, 8, and 9 had similar bacterial communities while the other units showed varying levels of differences. Hutch calves had a dramatically different bacterial community than adult cattle, with at least 10 genera exclusively detected in their samples but not in non-neonatal cattle. Moreover, we compared fecal bacteria of cattle from every pair of the management units and detailed the number and relative abundance of the significantly differential genera. Lastly, we identified 181 pairs of strongly correlated taxa in the community, showing possible synergistic or antagonistic relationships. CONCLUSIONS: This study assesses the fecal microbiota of cattle from 12 distinctly defined management units along the production line on a California dairy farm. The results highlight the similarities and differences of fecal microbiota between cattle from each pair of the management units. Especially, the data indicate that the newborn calves host very different gut bacterial communities than non-neonatal cattle, while non-neonatal cattle adopt one of the two distinct types of gut bacterial communities with subtle differences among the management units. The gut microbial communities of dairy cattle change dramatically in bacterial abundances at different taxonomic levels along the production line. The findings provide a reference for research and practice in modern dairy farm management.

Antimicrobial Resistance Profiles of Non-typhoidal Salmonella From Retail Meat Products in California, 2018.

Non-typhoidal Salmonella remains a leading cause of foodborne illness in the United States, with food animal products serving as a key conduit for transmission. The emergence of antimicrobial resistance (AMR) poses an additional public health concern warranting better understanding of its epidemiology. In this study, 958 retail meat samples collected from January to December 2018 in California were tested for Salmonella. From multivariable logistic regression, there was a 6.47 (90% CI 2.29-18.27), 3.81 (90% CI 1.29-11.27), and 3.12 (90% CI 1.03-9.45) higher odds of contamination in samples purchased in the fall, spring, and summer than in winter months, respectively, and a 3.70 (90% CI 1.05-13.07) higher odds in ground turkey compared to pork samples. Fourteen distinct serotypes and 17 multilocus sequence types were identified among the 43 isolates recovered, with S. Kentucky (25.58%), S. Reading (18.60%), S. Infantis (11.63%), and S. Typhimurium (9.30%) comprising the top serotypes. High prevalence of resistance was observed in retail chicken isolates for streptomycin (12/23, 52.17%) and tetracycline (12/23, 52.17%), in ground turkey isolates for ampicillin (8/15, 53.34%), and in ground beef isolates for nalidixic acid (2/3, 66.67%). Fourteen (32.56%) were susceptible to all antimicrobials tested, 11 (25.58%) were resistant to one drug, and 12 (27.91%) were resistant to two drugs. The remaining six isolates (13.95%) were multidrug-resistant (MDR, ≥3 drug classes) S. Infantis (n = 4), S. Reading (n = 1), and S. Kentucky (n = 1). Whole-genome sequencing (WGS) identified 16 AMR genes and 17 plasmid replicons, including bla CTX-M-65 encoding ceftriaxone resistance and a D87Y mutation in gyrA conferring resistance to nalidixic acid and reduced susceptibility to ciprofloxacin. The IncFIB(pN55391) replicon previously identified in connection to the worldwide dissemination of pESI-like mega plasmid carriage in an emerged S. Infantis clone was detected in four of the six MDR isolates. Genotypes from WGS showed high concordance with phenotype with overall sensitivity and specificity of 95.31% and 100%, respectively. This study provides insight into the AMR profiles of a diversity of Salmonella serotypes isolated from retail meat products in California and highlights the value of routine retail food surveillance for the detection and characterization of AMR in foodborne pathogens.

Supplementation of oligosaccharide-based polymer enhanced growth and disease resistance of weaned pigs by modulating intestinal integrity and systemic immunity.

BACKGROUND: There is a great demand for antibiotic alternatives to maintain animal health and productivity. The objective of this experiment was to determine the efficacy of dietary supplementation of a blood group A6 type 1 antigen oligosaccharides-based polymer (Coligo) on growth performance, diarrhea severity, intestinal health, and systemic immunity of weaned pigs experimentally infected with an enterotoxigenic Escherichia coli (ETEC), when compared with antibiotics. RESULTS: Pigs in antibiotic carbadox or Coligo treatment groups had greater (P < 0.05) body weight on d 5 or d 11 post-inoculation (PI) than pigs in the control group, respectively. Supplementation of antibiotics or Coligo enhanced (P < 0.05) feed efficiency from d 0 to 5 PI and reduced (P < 0.05) frequency of diarrhea throughout the experiment, compared with pigs in the control group. Supplementation of antibiotics reduced (P < 0.05) fecal ß-hemolytic coliforms on d 2, 5, and 8 PI. Pigs in antibiotics or Coligo groups had reduced (P < 0.05) neutrophil counts and serum haptoglobin concentration compared to pigs in the control group on d 2 and 5 PI. Pigs in Coligo had reduced (P < 0.05) total coliforms in mesenteric lymph nodes on d 5 and 11 PI, whereas pigs in antibiotics or Coligo groups had reduced (P < 0.05) total coliforms in spleen on d 11 PI compared with pigs in the control group. On d 5 PI, pigs in the Coligo group had greater (P < 0.05) gene expression of ZO1 in jejunal mucosa, but less (P < 0.05) mRNA expression of IL1B, IL6, and TNF in ileal mucosa, in comparison with pigs in the control group. Supplementation of antibiotics enhanced (P < 0.05) the gene expression of OCLN in jejunal mucosa but decreased (P < 0.05) IL1B and IL6 gene expression in ileal mucosa, compared with the control. On d 11 PI, supplementation of antibiotics or Coligo up-regulated (P < 0.05) gene expression of CLDN1 in jejunal mucosa, but Coligo reduced (P < 0.05) IL6 gene expression in ileal mucosa compared to pigs in the control group. CONCLUSIONS: Supplementation of Coligo improved growth performance, alleviated diarrhea severity, and enhanced gut health in weaned pigs infected with ETEC F18 in a manner similar to in-feed antibiotics.

Dietary supplementation of Bacillus subtilis or antibiotics modified intestinal microbiome of weaned pigs under enterotoxigenic Escherichia coli infection.

Our previous research reported that supplementation of Bacillus subtilis DSM 25841 promoted growth and disease resistance of weaned pigs under enterotoxigenic Escherichia coli (ETEC) challenge and its efficacy is comparable to carbadox. This follow-up study aimed to characterize the effects of ETEC infection, supplementing B. subtilis DSM 25841 or carbadox on intestinal microbiota of pigs. Forty-eight weaned pigs (6.17 ± 0.36 kg BW) were randomly allotted to one of four treatments: negative control (NC), positive control (PC), antibiotics (AGP, 50 mg/kg of carbadox), and direct fed microbials (DFM, 2.56 × 109 CFU/kg of B. subtilis). The experiment lasted 28 days with 7 days before and 21 days after first E. coli inoculation (day 0). Pigs in the PC, AGP, and DFM groups were orally inoculated with F18 ETEC for 3 consecutive days with 1010 CFU per dose per day. Fecal samples were collected on day -7, and day 7 and day 21 post inoculation, digesta samples were collected from jejunum, ileum, and distal colon on day 21 post inoculation to perform 16S rRNA sequencing. Sampling days and locations influenced (p < 0.05) Chao1 index and beta-diversity. Age increased (p < 0.05) the relative abundance of Firmicutes but decreased (p < 0.05) the relative abundance of Bacteroidetes in feces. ETEC infection increased (p < 0.05) the relative abundance of Proteobacteria in feces on day 7 post inoculation. AGP reduced (p < 0.05) relative abundance of Firmicutes and Lactobacillaceae in feces compared with PC and DFM. AGP reduced (p < 0.05) relative abundance of Bifidobacteriaceae in jejunum and ileum, while DFM reduced (p < 0.05) relative abundance of Actinomycetaceae in jejunum and Lachnospiraceae in ileum, compared with PC. Pigs fed with DFM had greater (p < 0.05) relative abundance of Ruminococcaceae, Veillonellaceae, Bifidobacteriaceae in jejunum, Lactobacillaceae in ileum and colon, and Bifidobacteriaceae in colon than pigs in AGP. Current results indicate that carbadox or B. subtilis had stronger influences on microbial diversity and composition in ileum than other intestinal segments and feces. Supplementation of B. subtilis could increase or maintain the relative abundance of beneficial bacteria in ileum compared with carbadox.

Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California.

The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal Escherichia coli and Enterococcus spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested E. coli isolates (n = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for Enterococcus spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in E. coli was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in Enterococcus spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all E. coli and 77.6% in Enterococcus spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for E. coli but much less so for isolates of Enterococcus. Consistent with prior work, fecal E. coli and Enterococcus spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.

Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach.

BACKGROUND: Understanding the effects of herd management practices on the prevalence of multidrug-resistant pathogenic Salmonella and commensals Enterococcus spp. and Escherichia coli in dairy cattle is key in reducing antibacterial resistant infections in humans originating from food animals. Our objective was to explore the herd and cow level features associated with the multi-drug resistant, and resistance phenotypes shared between Salmonella, E. coli and Enterococcus spp. using machine learning algorithms. METHODS: Randomly collected fecal samples from cull dairy cows from six dairy farms in central California were tested for multi-drug resistance phenotypes of Salmonella, E. coli and Enterococcus spp. Using data on herd management practices collected from a questionnaire, we built three machine learning algorithms (decision tree classifier, random forest, and gradient boosting decision trees) to predict the cows shedding multidrug-resistant Salmonella and commensal bacteria. RESULTS: The decision tree classifier identified rolling herd average milk production as an important feature for predicting fecal shedding of multi-drug resistance in Salmonella or commensal bacteria. The number of culled animals, monthly culling frequency and percentage, herd size, and proportion of Holstein cows in the herd were found to be influential herd characteristics predicting fecal shedding of multidrug-resistant phenotypes based on random forest models for Salmonella and commensal bacteria. Gradient boosting models showed that higher culling frequency and monthly culling percentages were associated with fecal shedding of multidrug resistant Salmonella or commensal bacteria. In contrast, an overall increase in the number of culled animals on a culling day showed a negative trend with classifying a cow as shedding multidrug-resistant bacteria. Increasing rolling herd average milk production and spring season were positively associated with fecal shedding of multidrug- resistant Salmonella. Only six individual cows were detected sharing tetracycline resistance phenotypes between Salmonella and either of the commensal bacteria. DISCUSSION: Percent culled and culling rate reflect the increase in culling over time adjusting for herd size and were associated with shedding multidrug resistant bacteria. In contrast, number culled was negatively associated with shedding multidrug resistant bacteria which may reflect producer decisions to prioritize the culling of otherwise healthy but low-producing cows based on milk or beef prices (with respect to dairy beef), amongst other factors. Using a data-driven suite of machine learning algorithms we identified generalizable and distant associations between antimicrobial resistance in Salmonella and fecal commensal bacteria, that can help develop a producer-friendly and data-informed risk assessment tool to reduce shedding of multidrug-resistant bacteria in cull dairy cows.

Diverse Genotypes and Species of Cryptosporidium in Wild Rodent Species from the West Coast of the USA and Implications for Raw Produce Safety and Microbial Water Quality.

Cryptosporidium spp. are protozoan parasites that infect perhaps all vertebrate animals, with a subset of species and genotypes that function as food- and waterborne pathogens. The objective of this work was to collate the Cryptosporidium species and genotypes from common wild rodents on the west coast of the USA and update the information regarding the zoonotic potential of Cryptosporidium from these ubiquitous wild species. Representative sequences of the 18S rRNA gene for a unique set of Cryptosporidium isolates obtained from deer mice, house mice, mountain beavers, yellow-bellied marmot, long-tailed vole, California ground squirrels, Belding's ground squirrels, and a golden-mantled ground squirrel in GenBank were selected for phylogenetic analysis. Phylogenetic and BLAST analysis indicated that 4 (18%) of the 22 unique Cryptosporidium sequences from these wild rodent species were 99.75% to 100% identical to known zoonotic species (C. parvum, C. ubiquitum, C. xiaoi), suggesting that a minority of these representative Cryptosporidium isolates could have a public health impact through food and waterborne routes of human exposure. These zoonotic isolates were shed by deer mice and a yellow-bellied marmot from California, and from a mountain beaver trapped in Oregon. In addition, the group of unique Cryptosporidium isolates from deer mice and ground dwelling squirrels exhibited considerable DNA diversity, with multiple isolates appearing to be either host-limited or distributed throughout the various clades within the phylogenetic tree representing the various Cryptosporidium species from host mammals. These results indicate that only a subset of the unique Cryptosporidium genotypes and species obtained from wild rodents on the US west coast are of public health concern; nevertheless, given the geographic ubiquity of many of these host species and often high density at critical locations like municipal watersheds or produce production fields, prudent pest control practices are warranted to minimize the risks of water- and foodborne transmission to humans.

Trace amounts of antibiotic exacerbated diarrhea and systemic inflammation of weaned pigs infected with a pathogenic Escherichia coli.

The experiment was conducted to investigate the effects of trace amounts of antibiotic on growth performance, diarrhea, systemic immunity, and intestinal health of weaned pigs experimentally infected with an enterotoxigenic Escherichia coli. Weaned pigs (n = 34, 6.88 ± 1.03 kg body weight [BW]) were individually housed in disease containment rooms and randomly allotted to one of the three dietary treatments: nursery basal diet (CON) and two additional diets supplemented with 0.5 or 50 mg/kg carbadox to the nursery basal diet (TRA or REC), respectively. The experiment lasted 18 d with 7 d before and 11 d after the first E. coli inoculation. The E. coli F18 inoculum was orally provided to all pigs with a dose of 1010 colony-forming unit (CFU)/3 mL for three consecutive days. Fecal and blood samples were collected on day 0 before inoculation and days 2, 5, 8, and 11 postinoculation (PI) to test the percentage of ß-hemolytic coliforms in total coliforms and complete blood cell count, respectively. Sixteen pigs were euthanized on day 5 PI, whereas the remaining pigs were euthanized at the end of the experiment to collect the jejunal and ileal mucosa and mesenteric lymph node for gene expression and bacterial translocation, respectively. Pigs in REC had greater (P < 0.05) final BW and lower (P < 0.05) overall frequency of diarrhea compared with pigs in the CON and TRA groups. Pigs in TRA had the lowest (P < 0.05) average daily gain and feed efficiency from day 0 to 5 PI, highest (P < 0.05) percentage of ß-hemolytic coliforms in fecal samples on days 2 and 5 PI, and greatest (P < 0.05) bacterial colonies in mesenteric lymph nodes on day 11 PI compared with pigs in the CON and REC groups. Pigs in TRA had the greatest (P < 0.05) neutrophils on day 5 PI and higher (P < 0.05) white blood cell counts and lymphocytes than other groups on day 11 PI. Pigs in TRA had the greatest (P < 0.05) serum C-reactive protein on days 2 and 5 PI and serum tumor necrosis factor-α on day 5 PI, compared with pigs in the CON and REC groups. Pigs fed REC had increased (P < 0.05) mRNA expression of zona occludens-1 (ZO-1) and occludin (OCDN) and reduced (P < 0.05) interleukin-1 beta (IL1B), interleukin-6 (IL6), and tumor necrosis factor-alpha (TNFA) in ileal mucosa on day 5 PI, compared with the CON, whereas TRA upregulated (P < 0.05) mRNA expression of IL1B, IL6, and cyclooxygenase-2 (COX2) in the ileal mucosa on day 11 PI, compared with the REC. In conclusion, trace amounts of antibiotic may exacerbate the detrimental effects of E. coli infection on pig performance by increasing diarrhea and systemic inflammation of weanling pigs.

Understanding the transmission dynamics of Escherichia coli O157:H7 super-shedding infections in feedlot cattle.

BACKGROUND: The presence of Escherichia coli O157:H7 (E. coli O157:H7) super-shedding cattle in feedlots has the potential to increase the overall number (bio-burden) of E. coli O157:H7 in the environment. It is important to identify factors to reduce the bio-burden of E. coli O157 in feedlots by clarifying practices associated with the occurrence of super-shedders in feedlot cattle. METHODS: The objective of this study is to (1) identify host, pathogen, and management risk factors associated with naturally infected feedlot cattle excreting high concentrations of E. coli O157:H7 in their feces and (2) to determine whether the ingested dose or the specific strain of E. coli O157:H7 influences a super-shedder infection within experimentally inoculated feedlot cattle. To address this, (1) pen floor fecal samples and herd parameters were collected from four feedlots over a 9-month period, then (2) 6 strains of E. coli O157:H7, 3 strains isolated from normal shedder steers and 3 strains isolated from super-shedder steers, were inoculated into 30 one-year-old feedlot steers. Five steers were assigned to each E. coli O157:H7 strain group and inoculated with targeted numbers of 102, 104, 106, 108, and 1010 CFU of bacteria respectively. RESULTS: In the feedlots, prevalence of infection with E. coli O157:H7 for the 890 fecal samples collected was 22.4%, with individual pen prevalence ranging from 0% to 90% and individual feedlot prevalence ranging from 8.4% to 30.2%. Three samples had E. coli O157:H7 levels greater than 104 MPN/g feces, thereby meeting the definition of super-shedder. Lower body weight at entry to the feedlot and higher daily maximum ambient temperature were associated with increased odds of a sample testing positive for E. coli O157:H7. In the experimental inoculation trial, the duration and total environmental shedding load of E. coli O157:H7 suggests that the time post-inoculation and the dose of inoculated E. coli O157:H7 are important while the E. coli O157:H7 strain and shedding characteristic (normal or super-shedder) are not. DISCUSSION: Under the conditions of this experiment, super-shedding appears to be the result of cattle ingesting a high dose of any strain of E. coli O157:H7. Therefore strategies that minimize exposure to large numbers of E. coli O157:H7 should be beneficial against the super-shedding of E. coli O157:H7 in feedlots.