Antimicrobial prophylaxis in companion animal surgery: A scoping review for European Network for Optimization of Antimicrobial Therapy (ENOVAT) guidelines.

Surgical antimicrobial prophylaxis (SAP) is widely used to reduce the risk of surgical site infections (SSI), but there is uncertainty as to what the proportion of SSI reduction is. Therefore, it is difficult for surgeons to properly weigh the costs, risks and benefits for individual patients when deciding on the use of SAP, making it challenging to promote antimicrobial stewardship in primary practice settings. The objective of this study was to map the veterinary evidence focused on assessing the effect of SAP on SSI development and in order to identify surgical procedures with some research evidence and possible knowledge gaps. In October 2021 and December 2022, Scopus, CAB Abstracts, Web of Science Core Collection, Embase and MEDLINE were systematically searched. Double blinded screening of records was performed to identify studies in companion animals that reported on the use of SAP and SSI rates. Comparative data were available from 34 out of 39123 records screened including: eight randomised controlled trials (RCT), 23 cohort studies (seven prospective and 16 retrospective) and three retrospective case series representing 12476 dogs and cats in total. Extracted data described peri- or post-operative SAP in nine, and 25 studies, respectively. In the eight RCTs evaluating SAP in companion animals, surgical procedure coverage was skewed towards orthopaedic stifle surgeries in referral settings and there was large variation in SAP protocols, SSI definitions and follow-up periods. More standardized data collection and agreement of SSI definitions is needed to build stronger evidence for optimized patient care.

Efficacy of antimicrobial and nutraceutical treatment for canine acute diarrhoea: A systematic review and meta-analysis for European Network for Optimization of Antimicrobial Therapy (ENOVAT) guidelines.

Systemic antimicrobial treatments are commonly prescribed to dogs with acute diarrhoea, while nutraceuticals (prebiotics, probiotics, and synbiotics) are frequently administered as an alternative treatment. The aim of this systematic review and meta-analysis was to assess the effectiveness of antimicrobials and nutraceutical preparations for treatment of canine acute diarrhoea (CAD). The results of this study will be used to create evidence-based treatment guidelines. PICOs (population, intervention, comparator, and outcome) were generated by a multidisciplinary expert panel taking into account opinions from stakeholders (general practitioners and dog owners). The Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to evaluate the certainty of the evidence. The systematic search yielded six randomised controlled trials (RCT) for antimicrobial treatment and six RCTs for nutraceutical treatment meeting the eligibility criteria. Categories of disease severity (mild, moderate, and severe) were created based on the presence of systemic signs and response to fluid therapy. Outcomes included duration of diarrhoea, duration of hospitalization, progression of disease, mortality, and adverse effects. High certainty evidence showed that antimicrobial treatment did not have a clinically relevant effect on any outcome in dogs with mild or moderate disease. Certainty of evidence was low for dogs with severe disease. Nutraceutical products did not show a clinically significant effect in shortening the duration of diarrhoea (based on very low to moderate certainty evidence). No adverse effects were reported in any of the studies.

Feline panleukopenia virus DNA shedding following modified live virus vaccination in a shelter setting.

This study assessed the frequency and timing of feline panleukopenia virus (FPV) shedding in feces following administration of a modified live FPV vaccine. Feces were collected from 37 shelter cats that did not meet clinical criteria for panleukopenia on the day of vaccination or on days 3, 7, 14, and 21 post-vaccination (NCL group). A commercial quantitative PCR (qPCR) fecal pathogen panel and a canine parvovirus point-of-care antigen test were performed. FPV DNA copy numbers from a concurrent study of 39 cats with panleukopenia (CL group) were compared with the NCL group. Of the 165 samples from the NCL group, one had a weak positive antigen test result on day 7, while nine samples (5.5%) from eight cats (21.6%) produced positive FPV qPCR test results, one on day 3 and eight on day 7. There were no day 21-positive qPCR results in the 11 cats that were revaccinated on day 14. There was no association between the number of additional fecal pathogens identified and a positive FPV qPCR result. Of the cats with positive results, FPV DNA copy numbers differed between NCL group and CL group (median 1.13 × 107 and 5.01 × 108 copies/g feces, respectively; P < 0.001). The FPV qPCR cannot differentiate subclinical infection from vaccine virus shedding. To avoid unnecessary isolation and euthanasia, shelters should therefore limit FPV PCR testing to cats with a high index of suspicion of panleukopenia. The timing of recent vaccination should also be considered when interpreting test results.

A multidisciplinary approach to reduce and refine antimicrobial drugs use for diarrhoea in dairy calves.

This study evaluated the impact of a multidisciplinary intervention to reduce and refine antimicrobial drug use for treatment of diarrhoea in dairy calves. The intervention consisted of modification of management practices for disease prevention, health evaluation training of farm staff, implementation of an algorithm directed at antimicrobial therapy for diarrhoeic calves, and monthly farm visits. A combination of retrospective (before intervention period [BP], 1 year) and prospective (immediately after intervention period [AP], 1 year) cohorts were used. Health outcomes measured included incidence of diarrhoea and overall mortality. Antimicrobial treatment rates for diarrhoea and total mass of antimicrobial drugs used at the calf and farm level were also evaluated. Outcomes were assessed using the χ2 or Fisher's exact test, and odds ratios and 95% confidence intervals (95% CI) were calculated. Records of 2049 and 2251 calves from 10 farms were available in the BP and AP, respectively. Reduced antimicrobial treatment rates occurred on seven farms (P < 0.01), but not on three farms in the AP. A total of 85% (1303/1573) and 18% (310/1698) of diarrhoeic calves were treated with antimicrobial drugs in the BP and AP (P < 0.001), respectively. There were no differences in the incidence of diarrhoea or mortality between periods. In the AP, the use sulfamethazine and trimethoprim decreased on eight farms, one farm discontinued use of lincomycin and spectinomycin, while two farms discontinued use and one reduced use of cephalosporins. This multidisciplinary approach was effective in reducing antimicrobial drug use for calf diarrhoea on dairy farms without negative impacts on calf health.

Knowledge, attitudes and influencers of North American dog-owners surrounding antimicrobials and antimicrobial stewardship.

OBJECTIVES: To quantify the individual influences of antimicrobial cost, method of administration and drug importance in human medicine on dog-owner antimicrobial preference, and determine knowledge, attitudes and influencers of dog-owners surrounding antimicrobials and antimicrobial stewardship. MATERIALS AND METHODS: Data were collected through an online survey targeting three dog-owner participant groups. These consisted of individuals residing in: (1) Canada, (2) USA and (3) any country recruited through an educational social media site. USA and Canadian participants were financially compensated. Conjoint analysis was used to quantify the influence of antimicrobial cost, method of administration and drug importance in human medicine. Descriptive and analytical statistics were used for data evaluation. RESULTS: A total of 809 surveys were completed. Antimicrobial cost accounted for 47% of dog-owner preferences, followed by method of administration (31%) and drug importance in human medicine (22%). All groups preferred lower cost drugs that were administered once by injection. Participants were more likely to prefer drugs considered "very important" in human medicine, except for the social media participants, who preferred drugs that were "not at all important." Most respondents (86%) reported antimicrobial resistance as important in human medicine and 29% believed antimicrobial use in pets posed a risk for antimicrobial resistance in humans. Participants recruited through social media, and those in the highest education category, were significantly more likely to report antimicrobial use in pets as a risk to people. CLINICAL SIGNIFICANCE: Cost was the most important factor in dog-owner antimicrobial preferences. There is a need for dog-owner antimicrobial stewardship education.

The application of next-generation sequence-based DNA barcoding for bloodmeal detection in host-seeking wild-caught Ixodes scapularis nymphs.

OBJECTIVE: Our objective was to apply next-generation sequence-based DNA barcoding to identify the remnant larval bloodmeals in wild-caught host-seeking (unengorged) Ixodes scapularis nymphs (n = 216). To infer host species identification, vertebrate DNA was amplified using universal primers for cytochrome c oxidase subunit I (COI) and sequenced using next-generation sequencing (NGS) for comparison against known barcode references. RESULTS: Bloodmeal identification was unsuccessful in most samples (99% of 216 specimens) demonstrating a very low detection rate of this assay. Sequences that surpassed quality thresholds were obtained for 41.7% of nymphs (n = 90) and of those, confident species identification was obtained for 15.6% of nymphs (n = 14). Wild host identifications were only obtained from 2 specimens, where DNA from the eastern grey squirrel (Sciurus carolinensis) was identified. Human and bovine DNA was identified in remaining nymphs and considered to be contaminants. Further optimization of the technique is required to improve detection of remnant bloodmeals in host-seeking nymphs.

Effects of parity, blood progesterone, and non-steroidal anti-inflammatory treatment on the dynamics of the uterine microbiota of healthy postpartum dairy cows.

This study evaluated the effects of treatment with meloxicam (a non-steroidal anti-inflammatory drug), parity, and blood progesterone concentration on the dynamics of the uterine microbiota of 16 clinically healthy postpartum dairy cows. Seven primiparous and 9 multiparous postpartum Holstein cows either received meloxicam (0.5 mg/kg SC, n = 7 cows) once daily for 4 days (10 to 13 days in milk (DIM)) or were untreated (n = 9 cows). Endometrial cytology samples were collected by cytobrush at 10, 21, and 35 DIM, from which the microbiota analysis was conducted using 16S rRNA gene sequence analysis. A radioimmunoassay was used to measure progesterone concentration in blood serum samples at 35 DIM and cows were classified as ˃ 1 ng/mL (n = 10) or ≤ 1 ng/mL (n = 6). Alpha diversity for bacterial genera (Chao1, Shannon-Weiner, and Camargo's evenness indices) were not affected by DIM, meloxicam treatment, parity, or progesterone category. For beta diversity (genera level), principal coordinate analysis (Bray-Curtis) showed differences in microbiota between parity groups. At the phylum level, the relative abundance of Actinobacteria was greater in primiparous than multiparous cows. At the genus level, there was lesser relative abundance of Bifidobacterium, Lactobacillus, Neisseriaceae, Paracoccus, Staphylococcus, and Streptococcus and greater relative abundance of Bacillus and Fusobacterium in primiparous than multiparous cows. Bray-Curtis dissimilarity did not differ by DIM at sampling, meloxicam treatment, or progesterone category at 35 DIM. In conclusion, uterine bacterial composition was not different at 10, 21, or 35 DIM, and meloxicam treatment or progesterone category did not affect the uterine microbiota in clinically healthy postpartum dairy cows. Primiparous cows presented a different composition of uterine bacteria than multiparous cows. The differences in microbiota associated with parity might be attributable to changes that occur consequent to the first calving, but this hypothesis should be investigated further.

Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis.

Our objectives were to describe and compare the uterine bacterial composition of postpartum Holstein cows diagnosed as healthy (n = 8), subclinical endometritis (SCE; n = 8), or clinical endometritis (CE; n = 5) in the fifth week postpartum. We did metagenomic analyses of 16S rRNA gene sequences from endometrial cytobrush samples at 10, 21, and 35 days in milk (DIM), and endometrial bacterial culture at 35 DIM. Uterine bacterial composition in healthy, SCE, and CE was stable at 10, 21, and 35 DIM. Alpha and beta diversities showed a different uterine microbiome from CE compared to healthy or SCE, but no differences were found between healthy and SCE cows. At the phylum level, the relative abundance of Bacteroidetes and Fusobacteria, and at genera level, of Trueperella was greater in CE than healthy or SCE cows. Trueperella pyogenes was the predominant bacteria cultured in cows with CE, and a wide variety of bacterial growth was found in healthy and SCE cows. Bacteria that grew in culture were represented within the most abundant bacterial genera based on metagenomic sequencing. The uterine microbiota was similar between SCE and healthy, but the microbiome in cows with CE had a loss of bacterial diversity.

A cross-sectional study of environmental, dog, and human-related risk factors for positive canine leptospirosis PCR test results in the United States, 2009 to 2016.

BACKGROUND: Canine leptospirosis is a reemerging zoonotic disease concern in North America, and a better understanding of its epidemiology is needed. Wide-scale use and subsequent analyses of polymerase chain reaction (PCR) testing may provide additional insight into leptospirosis. This study aimed to describe temporal trends, to descriptively map, and to identify environmental, dog, and human-level factors associated with positive canine leptospirosis PCR test results in the United States. RESULTS: Data obtained from IDEXX Laboratories, Inc. on 40,118 canine leptospirosis PCR tests run in the United States between 2009 and 2016 were evaluated. Climate and socioeconomic (e.g. urban influence, income) data were obtained from public databases. Choropleth maps were created to identify high test-positive proportion areas and a cross-sectional analysis was completed with generalized (univariable, followed by multivariable) mixed logistic regression models accounting for county within state to identify significant predictors for a positive test. Overall test-positive proportion was 5.4% across the United States, with the regional point estimate highest in the southwest (8.1%). In the final multivariable model, the odds of a positive test were greater for male dogs (Odds Ratio [OR] = 1.28) and dogs 0-4 years of age (ORs ranged from 0.35-0.71 for the other age groups). The odds of a positive test were greater for dogs living in areas with wet environmental conditions (OR = 1.24). Season and temperature, as well as the interaction between them, were significant predictors of a positive test. Dogs had a greater probability of testing positive during cool temperatures (< 4 °C) compared to the other temperature categories in the fall season. CONCLUSIONS: These findings based on PCR testing allow for an improved understanding of factors influencing a positive canine leptospirosis PCR test and will assist targeted education and prevention efforts.

Prevalence of Clostridium difficile and Clostridium perfringens in Swiss horses with and without gastrointestinal disease and microbiota composition in relation to Clostridium difficile shedding.

Overgrowth of enteric clostridia in dysbiosis in horses with colic is presumed but scarcely investigated. The objective was to provide prevalence data of Clostridium difficile and Clostridium perfringens in horses with and without gastrointestinal disease in Switzerland, and investigate microbiota differences between C. difficile shedders and non-shedders. Fecal samples were taken from healthy horses (n = 103), horses with colic (n = 98) and horses with diarrhea (n = 151). Colic horses were sampled on three days. Selective enrichment culture and molecular typing for C. difficile and C. perfringens was performed. Microbiota differences between horses with colic shedding (n = 7) and not shedding (n = 7) C. difficile were assessed using metagenomic sequencing. The cumulative prevalence (19% C. difficile; 16% C. perfringens) was higher compared to single day samples (1-10% C. difficile; 3-8% C. perfringens, all p < 0.003). Horses with colic shed significantly more C. difficile (p < 0.001) but not C. perfringens (p = 0.09) compared to healthy horses. Prevalence in horses with diarrhea was 8% for both Clostridium species. There were no significant microbiota differences between C. difficile shedders and non-shedders with regards to relative abundance on any phylogenetic level, and alpha diversity. Limited differences were seen on LEfSE analysis and in beta diversity indices. Multiple fecal samples should be taken when investigating shedding of enteric clostridia. As horses with colic shed more enteric clostridia compared to healthy horses special biosecurity protocols for horses with colic should be considered in hospitals. Differences in microbiota composition between C. difficile shedders and non-shedders were limited. Further studies on the role of dysbiosis in C. difficile are needed.

Evaluation of a multispecies probiotic as a supportive treatment for diarrhea in dairy calves: A randomized clinical trial.

The objectives of this randomized clinical trial were to determine whether the utilization of a multispecies probiotic bolus (MSP) in dairy calves with diarrhea led to a rapid resolution of diarrhea and improved average daily gain (ADG). Calves, from a convenience sample of dairy farms with diarrhea challenges, having fecal scores of ≥2 were randomly assigned to receive MSP or a placebo (PLB). The MSP bolus contained Pediococcus acidilactici, Enterococcus faecium, Lactobacillus acidophilus, Lactobacillus casei, Bifidobacterium bifidum, peptide extract, an enzyme blend, killed yeast extract, dried whey, and natural flavors (Revive, Partnar Animal Health, Ilderton, ON, Canada). The enrolled calves were fecal scored daily for 7 consecutive days and resolution of diarrhea was defined as having 2 consecutive days with a fecal score ≤1. Calves were also weighed at enrollment, 7, and 14 d following enrollment and ADG was calculated. A Cox proportional hazards model was built to investigate time to resolution of an abnormal fecal score. Two mixed linear regression models were created to evaluate the effect of treatment group on ADG in the first and second weeks following enrollment. A total of 148 calves were enrolled in the experiment and no differences were observed between the groups with respect to the age or weight at enrollment. The mean time to resolution of abnormal fecal score was 5.1 and 5.9 d in the MSP and PLB groups, respectively. In the Cox proportional hazards model, the calves in the MSP group had faster resolution of diarrhea when compared with the PLB group; however, an interaction between time from enrollment of the first calf and treatment group was present. No differences were found between the 2 groups with respect to ADG. This study demonstrates a multispecies probiotic and yeast bolus administered to calves at the onset of diarrhea reduced the duration of diarrhea; however, the clinical and economic relevance of this reduction requires further exploration.

Comparison of freeze-thaw cycles for nucleic acid extraction and molecular detection of Cryptosporidium parvum and Toxoplasma gondii oocysts in environmental matrices.

Freeze-thaw DNA extraction methods and PCR primers were compared to optimize detection of Cryptosporidium parvum and Toxoplasma gondii oocysts in different matrices. Increasing FT cycles did not increase parasite DNA detection, and primers targeting the 18S ssrRNA gene yielded the most sensitive detection of C. parvum oocysts.

Examining the epidemiology and microbiology of Clostridium difficile carriage in elderly patients and residents of a healthcare facility in southern Ontario, Canada.

BACKGROUND: Whereas Clostridium difficile has been extensively studied in acute care facilities (ACFs), there is limited information about long-term care facilities (LTCFs), despite the high occurrence of putative risk factors (e.g. age, antimicrobial use, healthcare system contact). AIM: To evaluate C. difficile colonization in elderly patients and residents from one ACF and its associated LTCF. METHODS: Stool swabs were collected from 884 LTCF and elderly (>65 years) hospital patients. Selective culture, polymerase chain reaction ribotyping and toxin gene characterization were performed. FINDINGS: C. difficile was isolated from 92/410 (22.4%) ACF and 89/474 (18.8%) LTCF samples. Ribotypes 027 (35%) and 020 (10.4%) predominated in the LTCF whereas ribotypes AI-82/1 (20.7%) and ribotype O (14.1%) predominated at the ACF (P = 0.031). In the LTCF, C. difficile colonization was associated with a history of proton pump inhibitor (PPI) use, and the interaction terms of male residents with prior medical leave of absence, and a prior history of C. difficile infection (CDI) combined with fluoroquinolone use. In the ACF, C. difficile colonization was associated with length of stay, feeding through a tube, antibiotic use, immunosuppressive therapy and VRE colonization, as well as the interaction terms for cephalosporin and fluoroquinolone use, prior CDI and cephalosporin use, and prior CDI and fluoroquinolone use. CONCLUSION: C. difficile colonization by ACF and LTCF residents was common, despite a low apparent incidence of CDI. The association with PPI provides further evidence of the potential importance of this widely used drug class in C. difficile colonization. Wide genetic diversity was present, highlighting the likelihood of multiple unidentified routes of C. difficile acquisition.

Fecal microbiota transplantation in puppies with canine parvovirus infection.

BACKGROUND: Diarrhea associated with parvovirus infection is common in dogs. Supportive care is the mainstay of treatment, but recovery may be prolonged and mortality rate can be high. Modification of the intestinal bacterial microbiota has been promising in human and veterinary medicine as an adjunctive treatment of various enteric diseases. OBJECTIVES: To investigate the safety and efficacy of fecal microbiota transplantation (FMT) on the clinical recovery of puppies with acute hemorrhagic diarrhea syndrome. ANIMALS: Sixty-six puppies with parvovirus infection were evaluated at 2 veterinary hospitals. METHODS: Randomized clinical trial. Puppies were randomly distributed into 2 groups: standard treatment (STD) and standard treatment + FMT (STD + FMT). The STD puppies (n = 33) received only treatment with IV fluids and antimicrobials and the STD + FMT puppies (n = 33) received FMT in addition to standard treatment. For FMT, 10 g of feces from a healthy dog diluted in 10 mL of saline were administered rectally 6-12 hours post-admission. RESULTS: Among survivors, treatment with FMT was associated with faster resolution of diarrhea (P < .001) and shorter hospitalization time (P = .001; median, 3 days in STD + FMT; median, 6 days in STD) compared to standard treatment. Mortality in STD was 36.4% (12/33) as compared to 21.2% (7/33) in puppies treated with FMT, but there was no statistical difference between groups (P = .174). Polymerase chain reaction indicated that all animals carried canine parvovirus, strain CPV-2b. CONCLUSIONS: Fecal microbiota transplantation in parvovirus-infected puppies was associated with faster resolution of diarrhea.

Equine faecal microbiota transplant: Current knowledge, proposed guidelines and future directions.

While certainly not a novel concept, faecal microbiota transplant (FMT) has recently garnered renewed interest in veterinary medicine due to its remarkable success in treating recurrent Clostridium difficile infection (CDI) in man. There is a dearth of information on indications and efficacy of FMT for the treatment of gastrointestinal disorders in the horse; however, based on evidence in man and other veterinary species, and anecdotal reports in horses, FMT may be a useful treatment for selected cases of acute and chronic diarrhoea and inflammatory bowel disease (IBD) in the horse. In the absence of evidence, expert opinion is offered on case selection and FMT procedure. More research is needed to explore the efficacy, indications and optimal preparation, storage and delivery of FMT to horses.

Dog ecology and its implications for rabies control in Gwagwalada, Federal Capital Territory, Abuja, Nigeria.

The objectives of this study were to determine the characteristics of a dog population, including their accessibility to vaccination and health care, in urban and semiurban areas of Gwagwalada, Abuja, Nigeria. Direct street counts and a house-to-house survey of city streets were performed. A total of 451 households were surveyed comprising 43.7% urban and 53.3% semiurban areas. A total of 848 owned dogs were identified, along with 3,115 corresponding humans. With a dog-to-human ratio of 1:3.7, the dog population in the study area was estimated as 103,758. A total of 396 dogs were counted on the streets with the greater proportion (74%) in semiurban areas. Most dogs in semiurban areas (77.3%) had no certificate confirming vaccination against rabies, compared to 47.2% in urban areas (p = .004). The majority of dogs in the urban (60.9%) and semiurban (82.0%) were free roaming. In the multivariable model, age, presence of a collar, region, sex, use and having ever visited a veterinarian were significantly associated with rabies vaccination. The majority (125/197, 63.5%) of respondents with higher education were willing to pay more for the healthcare needs of their dogs as opposed to those with a lower level of education (93/251, 37.1%, p = .001). The study revealed a high dog population density, vaccination coverage below WHO recommendation of 70% and generally reduced healthcare-seeking behaviour among dog owners in Gwagwalada, Abuja, Nigeria.

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.

The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the "One Health" concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.

Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves.

BACKGROUND: BCoV is identified in both healthy and diarrheic calves, complicating its assessment as a primary pathogen. OBJECTIVES: To investigate the detection rates of bovine coronavirus (BCoV) in feces of healthy and diarrheic calves and to describe the usefulness of a pancoronavirus reverse transcriptase (RT) PCR (PanCoV-RT-PCR) assay to identify BCoV in samples of diarrheic calves. ANIMALS: Two hundred and eighty-six calves <21 days. Calves with liquid or semiliquid feces, temperature >39.5°C, and inappetence were considered as cases, and those that had pasty or firm feces and normal physical examination were designated as controls. METHODS: Prospective case-control study. A specific BCoV-RT-PCR assay was used to detect BCoV in fecal samples. Association between BCoV and health status was evaluated by exact and random effect logistic regression. Fecal (n = 28) and nasal (n = 8) samples from diarrheic calves were tested for the presence of BCoV by both the PanCoV-RT-PCR and a specific BCoV-RT-PCR assays. A Kappa coefficient test was used to assess the level of agreement of both assays. RESULTS: BCoV was detected in 55% (157/286) of calves; 46% (66/143), and 64% (91/143) of healthy and diarrheic calves, respectively. Diarrheic calves had higher odds of BCoV presence than healthy calves (OR: 2.16, 95% CI: 1.26 to 3.83, P = 0.004). A good agreement between PanCoV-RT-PCR and BCoV-RT-PCR to detect BCoV was identified (κ = 0.68, 95% CI: 0.392 to 0.967; P < 0.001). CONCLUSIONS AND CLINICAL IMPORTANCE: BCoV was more likely to be detected in diarrheic than healthy calves. The PanCoV-RT-PCR assay can be a useful tool to detect CoV samples from diarrheic calves.

Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life.

BACKGROUND: Diarrhea in foals affects up to 60% of foals during the first six months of life. The effect of diarrhea on the fecal bacterial microbiota in foals has not been investigated. Little is known on the fecal bacterial microbial richness and diversity of foals at a young age. The objective was to compare the fecal bacterial microbiota of healthy foals to foals with diarrhea at two and four weeks of life. METHODS: Fecal samples were collected from foals (n = 20) at 1-14 (T1) and 15-28 (T2) days of age and analyzed using high throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity and beta diversity indices were assessed between age-matched foals with diarrhea (n = 9) and healthy foals (n = 11), and between time points. RESULTS: Differences in microbial community composition based on time point and health status were observed on all taxonomic levels. Of 117 enriched species in healthy foals at T2, 50 (48%) were Lachnospiraceae or Ruminococcaceae. The Chao richness index was increased in healthy foals at T2 compared to T1 (p = 0.02). Foals with diarrhea had a significantly lower richness index than non-diarrheic foals at T2 (p = 0.04). Diarrhea had an inconsistent effect, while time point had a consistent effect on microbial community structure. CONCLUSIONS: Preventative and therapeutic measures for diarrhea should focus on maintaining bacterial microbiota richness. Lachnospiraceae and Ruminococcaceae were underrepresented in foals with diarrhea. These should be evaluated further as potential therapeutic options.