Infectious agents associated with diarrhoea in neonatal foals in central Kentucky: a comprehensive molecular study

Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health

Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.

Diagnosis of Potomac horse fever (syn. equine neorickettsiosis) in 2 foals in southwestern Ontario

Potomac horse fever (PHF) is characterized by fever, depression, anorexia, ileus, diarrhea, and occasionally, laminitis. The disease is caused by infection with Neorickettsia risticii and/or N. findlayensis. Equids of all ages may be affected; however, the condition has not been well-characterized in foals. This report describes clinical signs, laboratory findings, and treatment of 2 foals diagnosed with PHF in southwestern Ontario. Feces submitted for an equine PCR panel tested positive for Neorickettsia spp. and were subsequently confirmed to be N. risticii (Case 1) and N. findlayensis (Case 2). Both foals recovered following hospitalization and intensive care. Key clinical message: The purpose of this report is to make veterinarians aware that foals may develop PHF. During summer (July to September), when encountering foals in endemic areas with clinical signs compatible with PHF, veterinarians should consider PHF as a diagnostic rule-out. For confirmation of the diagnosis, blood and feces should be submitted for PCR testing for Neorickettsia spp.

Evaluation of the diagnostic performance of EpiTuub® Fecal Rotavirus Antigen Rapid Test Kit in Amhara National Regional State, Ethiopia: A multi-center cross-sectional study

Rotavirus is the leading cause of morbidity and mortality due to acute gastroenteritis among children under five years globally. Early diagnosis of rotavirus infection minimizes its spread and helps to determine the appropriate management of diarrhea. The aim of this study was to evaluate the performance of EpiTuub® Fecal Rotavirus Antigen Rapid Test Kit for the diagnosis of rotavirus infection among diarrheic children under five years in Ethiopian healthcare settings. A total of 537 children with diarrhea were enrolled from three referral hospitals in Amhara National Regional State, Ethiopia. The samples were tested using one-step RT-PCR and EpiTuub® Fecal Rotavirus Antigen Rapid Test Kit (KTR-917, Epitope Diagnostics, San Diego USA) in parallel. Diagnostic performance of the rapid test kit was evaluated using the one-step RT-PCR as a gold standard. The sensitivity, specificity, and predictive values of the rapid test kit were determined. Moreover, the agreement of the rapid test kit with one step RT-PCR was determined by kappa statistics and receiver operators' curve (ROC) analysis was done to assess the overall diagnostic accuracy of the rapid test kit. Fecal Rotavirus Antigen Rapid Test Kit has shown a sensitivity of 75.5% and specificity of 98.2%. The kit was also found to have 89.9% and 95.0% positive and negative predictive values, respectively. The Fecal Rotavirus Antigen Rapid Test Kit has shown a substantial agreement (78.7%, p = 0.0001) with one-step RT-PCR. The overall accuracy of the Fecal Rotavirus Antigen Rapid Test Kit was excellent with the area under the ROC curve of 86.9% (95% CI = 81.6, 92.1%) (p = .0001). Thus, Fecal Rotavirus Antigen Rapid Test is a sensitive, specific, user-friendly, rapid, and equipment-free option to be used at points of care in Ethiopian health care settings where resource is limited precluding the use of one step RT-PCR. Furthermore, the kit could be used in the evaluation and monitoring of rotavirus vaccine effectiveness in the aforementioned settings.

Diagnostic approaches, aetiological agents and their associations with short-term survival and laminitis in horses with acute diarrhoea admitted to referral institutions

BACKGROUND

An international description of the diagnostic approaches used in different institutions to diagnose acute equine diarrhoea and the pathogens detected is lacking.

OBJECTIVES

To describe the diagnostic approach, aetiological agents, outcome, and development of laminitis for diarrhoeic horses worldwide.

STUDY DESIGN

Multicentre retrospective case series.

METHODS

Information from horses with acute diarrhoea presenting to participating institutions between 2016 and 2020, including diagnostic approaches, pathogens detected and their associations with outcomes, were compared between institutions or geographic regions.

RESULTS

One thousand four hundred and thirty-eight horses from 26 participating institutions from 4 continents were included. Overall, aetiological testing was limited (44% for Salmonella spp., 42% for Neorickettsia risticii [only North America], 40% for Clostridiodes difficile, and 29% for ECoV); however, 13% (81/633) of horses tested positive for Salmonella, 13% (35/262) for N. risticii, 9% (37/422) for ECoV, and 5% (27/578) for C. difficile. C. difficile positive cases had greater odds of non-survival than horses negative for C. difficile (OR: 2.69, 95%CI: 1.23-5.91). In addition, horses that were positive for N. risticii had greater odds of developing laminitis than negative horses (OR: 2.76, 95%CI: 1.12-6.81; p = 0.029).

MAIN LIMITATIONS

Due to the study's retrospective nature, there are missing data.

CONCLUSIONS

This study highlighted limited diagnostic investigations in cases of acute equine diarrhoea. Detection rates of pathogens are similar to previous reports. Non-survival and development of laminitis are related to certain detected pathogens.

Quadruplex Real-Time TaqMan® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes

Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.

Equine Rotaviral Diarrhea

Equine rotavirus is one of the most common causes of infectious diarrhea in foals. Although the infection itself is self-limiting, the resulting diarrhea is due to multiple mechanisms and can be severe, requiring supportive care including fluid and electrolyte support. Prompt diagnosis is important for treatment and biosecurity decisions and can be achieved by several means. Prevention, while imperfect, currently relies on vaccination of pregnant mares before parturition, ingestion of adequate colostrum from vaccinated mares and biosecurity measures.

RT-PCR-based assessment of the SD Bioline Rota/Adeno Antigen-based test in infants with and without diarrhea

BACKGROUND

Rotavirus A (RVA) infections remain a major cause of severe acute diarrhea affecting children worldwide. To date, rapid diagnostic tests (RDT) are widely used to detect RVA. However, paediatricians question whether the RDT can still detect the virus accurately. Therefore, this study aimed to evaluate the performance of the rapid rotavirus test in comparison to the one-step RT-qPCR method.

METHODS

A cross-sectional study was conducted in Lambaréné, Gabon, from April 2018 to November 2019. Stool samples were collected from children under 5 years of age with diarrhoea or a history of diarrhoea within the last 24 h, and from asymptomatic children from the same communities. All stool samples were processed and analysed using the SD BIOLINE Rota/Adeno Ag RDT against a quantitative reverse transcription PCR (RT-qPCR), which is considered the gold standard.

RESULTS

For a total of 218 collected stool samples, the overall sensitivity of the RDT was 46.46% (confidence interval (CI) 36.38-56.77), with a specificity of 96.64% (CI 91.62-99.08) compared to one-step RT-qPCR. After confirming the presence or absence of RVA gastroenteritis, the RDT showed suitable results in detecting rotavirus A-associated disease, with a 91% concordance with the RT-qPCR. Furthermore, the performance of this test varied when correlated with seasonality, symptoms, and rotavirus genotype.

CONCLUSION

This RDT showed high sensitivity and was suitable for the detection of RVA in patients with RVA gastroenteritis, although some asymptomatic RVA shedding was missed by RT-qPCR. It could be a useful diagnostic tool, especially in low-income countries.

Risk factors associated with an outbreak of equine coronavirus at a large farm in North Carolina

Background

Equine coronavirus (ECoV) leads to outbreaks with variable morbidity and mortality. Few previous reports of risk factors for infection are available in the literature.

Objectives

To describe unique clinical findings and risk factors for infection and development of clinical disease.

Animals

135 horses on a farm affected by ECoV outbreak.

Methods

Retrospective cohort study. Data obtained included age, breed, gender, activity level, housing, and feed at the onset of the outbreak. Factors were evaluated for assessment of risk of infection using simple logistic regression or Fisher's exact test. Significance was set at p ≤ 0.05.

Results and findings

Forty-three of 54 (79.6%) horses tested on the farm were positive on fecal PCR for ECoV, and 17 horses (12.6%) developed clinical signs consistent with ECoV. Out of 17 horses in which the presence or absence of signs of colic was noted, 6 of 17 (35.3%) showed signs of colic. Three of these horses had small colon impactions, 2 of which required surgical intervention. Significant risk factors for having positive PCR results included being primarily stalled (OR 167.1, 95% CI 26.4-1719), housing next to a positive horse (OR 7.5, 95% CI 3.1-19.0), being in work (OR 26.9, 95% CI 4.6-281.9), being fed rationed hay vs. ad libitum (OR 1,558, 95% CI 130.8-15,593), and being fed alfalfa hay (OR 1,558, 95% CI 130.8-15,593).

Conclusions and clinical importance

This report describes risk factors for ECoV infection many of which were associated with intensive management of show horses. Clinicians should be aware that clinical signs vary and can include severe colic.

Serosurveillance of equine coronavirus infection among Thoroughbreds in Japan

BACKGROUND

Equine coronavirus (ECoV) causes fever, lethargy, anorexia and gastrointestinal signs in horses. There has been limited information about the prevalence and seasonality of ECoV among Thoroughbreds in Japan.

OBJECTIVES

To understand the epidemiology and to evaluate the potential risk of ECoV infection to the horse industry in Japan.

STUDY DESIGN

Longitudinal.

METHODS

The virus-neutralisation (VN) test was performed using sera collected three times a year at 4 months intervals from 161 yearlings and at 6-7 months intervals from 181 active racehorses in Japan in 2017-18, 2018-19 and 2019-20. VN titre ≥1:8 was defined as seropositive, and ≥ 4-fold increase in titres between paired sera was regarded as indicative of infection.

RESULTS

The VN test showed that 44.1% (71/161) of yearlings were seropositive in August, when they first entered the yearling farm. The infection rate was significantly higher between August and December (60.9%, 98/161) than between December and the following April (5.6%, 9/161; P = 0.002). Among the racehorses, it was significantly higher between November and the following May (15.5%, 28/181) than between the preceding April/May and November (0%; P = 0.02). The morbidity rates during the estimated periods of viral exposure were 39.2% in the yearlings and 4% in the racehorses. No horses showed any severe clinical signs.

MAIN LIMITATIONS

Clinical records did not cover the period during horses' absence from the training centre.

CONCLUSIONS

ECoV was substantially prevalent in Thoroughbred yearlings and racehorses in Japan, and there was a difference in epizootic pattern between these populations in terms of predominant periods of infection. ECoV infection was considered to be responsible for some of the pyretic cases in the yearlings. However, no diseased horses were severely affected in either population, suggesting that the potential risk of ECoV infection to the horse industry in Japan is low.

Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses

The origin and host range of SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), are important scientific questions as they might provide insight into understanding of the potential future spillover to infect humans. Here, we tested the binding between equine angiotensin converting enzyme 2 (eqACE2) and the receptor binding domains (RBDs) of SARS-CoV, SARS-CoV-2 prototype (PT) and variant of concerns (VOCs), as well as their close relatives bat-origin coronavirus (CoV) RaTG13 and pangolin-origin CoVs GX/P2V/2017 and GD/1/2019. We also determined the crystal structures of eqACE2/RaTG13-RBD, eqACE2/SARS-CoV-2 PT-RBD and eqACE2/Omicron BA.1-RBD. We identified S494 of SARS-COV-2 PT-RBD as an important residue in the eqACE2/SARS-COV-2 PT-RBD interaction and found that N501Y, the commonly recognized enhancing mutation, attenuated the binding affinity with eqACE2. Our work demonstrates that horses are potential targets for SARS-CoV-2 and highlights the importance of continuous surveillance on SARS-CoV-2 and related CoVs to prevent spillover events.

This study documents equine ACE2 (eqACE2) binding to the RBDs of SARS-CoV-2 and related CoVs, revealing a mechanism of eqACE2 binding with RaTG13-RBD, SARS-CoV-2 prototype-RBD and Omicron BA.1-RBD.

Assessing the potential for infections of Echinococcus multilocularis in dogs in a hotspot of human alveolar echinococcosis infections in North America

Echinococcus multilocularis is a zoonotic tapeworm, whose metacestode larval stage is the etiological agent for alveolar echinococcosis in humans and is a parasite of emerging concern according to the World Health Organization which is difficult to diagnose and has a case mortality rate of >90% when left untreated. Echinococcus multilocularis requires two mammalian hosts to complete its lifecycle: wild and domestic canids as definitive hosts, and small mammals (mostly rodents) as intermediate ones. Because of their close relations with humans, domestic dogs have been indicated as a mean of infection to people. Human alveolar echinococcosis has historically been rare in North America, however, since 2013, at least seventeen diagnoses have been confirmed in Alberta, Canada. Because of this unprecedented series of cases, assessing the frequency of infections in dogs in Alberta is key to estimate risk for dog owners and animal health professionals. This study was carried out in Edmonton to determine the frequency of E. multilocularis infection in domestic dogs and potential risk factors. Fecal samples and corresponding behavior risk surveys were collected from 775 dogs in seven urban off-leash parks within Edmonton city limits during the summer of 2020. A quantitative PCR fecal test was used to diagnose E. multilocularis infection. We found a single case of E. multilocularis infection (1/775) and determined that the overall true prevalence was 0.2% (95% CrI: 0.0-0.7%) corrected for detection sensitivity and specificity. Overall, these findings confirm the presence of E. multilocularis infection in domestic dogs in Edmonton although further work is required to fully understand the risk factors that may contribute to infection and potential transmission to humans.

Effect of season and geographic location in the United States on detection of potential enteric pathogens or toxin genes in horses ≥6-mo-old

We investigated the effects of season and geographic location on detection of nucleic acids of potential enteric pathogens (PEPs) or their toxins (PEP-Ts) in feces of horses ≥6-mo-old in the United States. Results of 3,343 equine diarrhea PCR panels submitted to Idexx Laboratories for horses >6-mo-old were reviewed. Submission months were grouped into 4 seasons, and states were grouped into 4 geographic regions. Logistic regression was performed to assess effects of season and region on detection rates of PEPs and PEP-Ts. Agresti-Coull CIs were determined. Detection rate of Salmonella enterica was higher in the South in summer compared to all other regions, and was also higher in the South in fall compared to the Midwest and Northeast. The Neorickettsia risticii detection rate was lower during summer in the West and higher in fall in the Midwest. Detection of Cryptosporidium spp. was lower during spring, summer, and winter in the West. Differences were not identified for detection rates of Clostridioides difficile, Clostridium perfringens, Lawsonia intracellularis, Rhodococcus equi, equine rotavirus, and equine coronavirus. Overall, our data support seasonal and regional differences in detection rates of S. enterica, N. risticii, and Cryptosporidium spp. in horses ≥6-mo-old in the United States.

Bacterial and viral enterocolitis in horses: a review

Enteritis, colitis, and enterocolitis are considered some of the most common causes of disease and death in horses. Determining the etiology of these conditions is challenging, among other reasons because different causes produce similar clinical signs and lesions, and also because some agents of colitis can be present in the intestine of normal animals. We review here the main bacterial and viral causes of enterocolitis of horses, including Salmonella spp., Clostridium perfringens type A NetF-positive, C. perfringens type C, Clostridioides difficile, Clostridium piliforme, Paeniclostridium sordellii, other clostridia, Rhodococcus equi, Neorickettsia risticii, Lawsonia intracellularis, equine rotavirus, and equine coronavirus. Diarrhea and colic are the hallmark clinical signs of colitis and enterocolitis, and the majority of these conditions are characterized by necrotizing changes in the mucosa of the small intestine, colon, cecum, or in a combination of these organs. The presumptive diagnosis is based on clinical, gross, and microscopic findings, and confirmed by detection of some of the agents and/or their toxins in the intestinal content or feces.

Gut Microbiota Manipulation in Foals-Naturopathic Diarrhea Management, or Unsubstantiated Folly?

Diarrhea in foals is a problem of significant clinical and economic consequence, and there are good reasons to believe microbiota manipulation can play an important role in its management. However, given the dynamic development of the foal microbiota and its importance in health and disease, any prophylactic or therapeutic efforts to alter its composition should be evidence based. The few clinical trials of probiotic preparations conducted in foals to date show underwhelming evidence of efficacy and a demonstrated potential to aggravate rather than mitigate diarrhea. Furthermore, recent studies have affirmed that variable but universally inadequate quality control of probiotics enables inadvertent administration of toxin-producing or otherwise pathogenic bacterial strains, as well as strains bearing transferrable antimicrobial resistance genes. Consequently, it seems advisable to approach probiotic therapy in particular with caution for the time being. While prebiotics show initial promise, an even greater scarcity of clinical trials makes it impossible to weigh the pros and cons of their use. Advancing technology will surely continue to enable more detailed and accurate mapping of the equine adult and juvenile microbiota and potentially elucidate the complexities of causation in dysbiosis and disease. In the meantime, fecal microbiota transplantation may be an attractive therapeutic shortcut, allowing practitioners to reconstruct a healthy microbiota even without fully understanding its constitution.

Detection of pathogens in blood or feces of adult horses with enteric disease and association with outcome of colitis

Background

Rates of detecting ≥1 potential enteric pathogens (PEP) or toxins (PEP‐T) in feces, blood, or both of horses ≥6 months of age with enteric disease and impact of multiple detections on outcome of horses with colitis has not been reported.

Objective

To determine detection rates of PEP/PEP‐T in feces, blood, or both of horses with enteric disease and effect of detecting multiple agents on outcome of horses with colitis.

Animals

Thirty‐seven hundred fifty‐three fecal samples submitted to IDEXX Laboratories and 239 fecal and blood samples submitted to Michigan State University's Veterinary Diagnostic Laboratory (MSUVDL).

Methods

Retrospective evaluation of PEP/PEP‐T testing results was performed to determine rates of detection of 1 or more PEP/PEP‐T. Impact of detecting multiple agents on outcome was assessed in 239 horses hospitalized for colitis.

Results

One or more PEP/PEP‐T was detected in 1175/3753 (31.3%) and 145/239 (60.7%) of samples submitted to IDEXX Laboratories and MSUVDL, respectively. In a hospitalized cohort, survival to discharge was lower (76%) in horses with 1 agent, compared to horses with either no (88%) or multiple (89%) agents. There was no difference (P = .78) in days of hospitalization between horses with 0 (1–17), 1 (1–33), and > 1 positive (1–20) result. There was no difference in cost of hospitalization (P = .25) between horses with 0 ($2357, $1110‐15 553), 1 ($2742, $788‐11 005), and >1 positive ($2560, $1091‐10 895) result.

Conclusions and Clinical Importance

Detection rates of PEP/PEP‐T in horses with colitis vary with cohorts and tests performed. Detection of more than 1 PEP or PEP‐T did not affect outcome.

RT-qPCR assay for detection of mink astrovirus in outbreaks of diarrhea on Danish mink farms

Diarrhea in mink kits is a major cause of disease and mortality in the mink production. The etiology remains unknown in most outbreaks due to a lack of diagnostic assays. In the current study we present an RT-qPCR method to detect mink astrovirus in fecal samples from mink kits with diarrhea. All sampled animals were classified based on age and patoanatomical evaluation as having pre-weaning diarrhea, diarrhea in the growth period or as having no macroscopic signs of diarrhea. Fecal samples were analyzed for MiAstV with RT-qPCR, next generation sequencing and electron microscopy in parallel. Mink astrovirus was detected with RT-qPCR in 92 out of 203 samples. This detection was confirmed by next generation sequencing in a high proportion of samples (22/27), and by visualization of astrovirus particles with EM in some of the samples. Mink astrovirus was highly prevalent (68%) among kits in the outbreaks of pre-weaning diarrhea, in particular outbreaks from May, while less prevalent in outbreaks in June. Mink astrovirus was detected in outbreaks of diarrhea in the growth period, though in a much lesser extent than in the pre-weaning period. The role of mink astrovirus in the diarrhea disease complex of mink remain to be investigated, and for that purpose this sensitive and robust RT-qPCR can be a valuable tool in the future.

Clinical and molecular aspects of veterinary coronaviruses

Coronaviruses are a large group of RNA viruses that infect a wide range of animal species. The replication strategy of coronaviruses involves recombination and mutation events that lead to the possibility of cross-species transmission. The high plasticity of the viral receptor due to a continuous modification of the host species habitat may be the cause of cross-species transmission that can turn into a threat to other species including the human population. The successive emergence of highly pathogenic coronaviruses such as the Severe Acute Respiratory Syndrome (SARS) in 2003, the Middle East Respiratory Syndrome Coronavirus in 2012, and the recent SARS-CoV-2 has incentivized a number of studies on the molecular basis of the coronavirus and its pathogenesis. The high degree of interrelatedness between humans and wild and domestic animals and the modification of animal habitats by human urbanization, has favored new viral spreads. Hence, knowledge on the main clinical signs of coronavirus infection in the different hosts and the distinctive molecular characteristics of each coronavirus is essential to prevent the emergence of new coronavirus diseases. The coronavirus infections routinely studied in veterinary medicine must be properly recognized and diagnosed not only to prevent animal disease but also to promote public health.

Coronaviruses in farm animals: Epidemiology and public health implications

Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross-species transmission easy. In fact, increasing contact between different animal species fosters cross-species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human-animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.

Co-occurrence of mcr-1, mcr-3, mcr-7 and clinically relevant antimicrobial resistance genes in environmental and fecal samples

Multidrug-resistant bacteria harboring different antimicrobial resistance genes (ARGs) have been detected worldwide. The association of plasmid-mediated colistin resistance genes (mcr-like) and other ARGs in bacteria isolated from animals is a huge concern worldwide. Therefore, this study aimed to investigate the presence of mcr-like genes and clinically relevant ARGs as well as plasmids in samples from a zoo. Fecal and environmental (soil and water) samples were collected from a zoo and the DNA of cultivable aerobic bacteria was extracted. ARGs were screened by PCR and the plasmids were detected using the PCR-based replicon typing method. A total of 74 amplicons from 27 ARGs [mcr-1, mcr-3, mcr-7.1, bla_CTX-M-Gp1, bla_CTX-M-Gp2, bla_CTX-M-Gp9, bla_VEB, bla_PER, bla_CMY, tetA, tetB, tetC, aadA, aac(6')-Ib, aph(3')-Ia, ant(2'')-Ia, qnrA, qnrB, qnrS, oqxA, oqxB, sul1, sul2, sul3, cmlA, mefAE, ermB] and 21 amplicons from eight plasmid families (IncY, ColE-like, IncF_repB, IncFIA, IncFIB, IncHI1, IncFIC, IncP) were detected. These findings reinforce that the zoo acts as a reservoir of clinically relevant ARGs, including mcr-like, and call attention to the monitoring studies in the zoo. Therefore, to the best of our knowledge, this is the first report of the world of mcr-1, mcr-3 and mcr-7.1 in environmental samples from the zoo.

Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes

Antimicrobial resistance has become a global threat to public health since multidrug-resistant (MDR) bacteria have been reported worldwide carrying different antimicrobial resistance genes (ARGs), and animals have been described as a reservoir of ARGs. The presence of antimicrobial-resistant bacteria and ARGs in the food matrix is a risk to public health. This study aimed to research the presence of clinically relevant ARGs for important antimicrobials and genetic elements in fecal samples from dairy cows and calves on a Brazilian farm. In this study, a total of 21 fecal samples were collected, and then, the DNA of cultivable aerobic bacteria was extracted. Fifty-seven ARGs and twenty-three genetic elements were researched by PCR and confirmed by sequencing. Several ARGs that confer resistance to β-lactams, tetracyclines, fluoroquinolones, sulphonamides, phenicols, aminoglycoside, glycopeptides, and macrolides were detected. A total of 200 amplicons from 23 ARGs (bla_CTX-M-Gp2, bla_CMY, bla_SHV, tetA, tetB, tetC, qepA, qnrB, qnrS, oqxA, oqxB, vanC1, vanC2/3, aadA, sul1, sul2, sul3, ermB, mefAE, floR, cmlA, aadA, aph(3')-Ia, aac(3')-Ia), and 145 amplicons from 12 genetic elements (IncF, IncFIA, IncFIB, IncI1, IncY, IncU, IncK, IncP, IncR, IncHI1, ColE-like, intI1) were detected. The results presented in this study call attention to the monitoring of antimicrobial resistance in dairy farms worldwide. MDR bacteria and ARGs can spread to different sources, including milk products, which are one of the most consumed products worldwide, representing a potential risk to human health.

NetF-producing Clostridium perfringens and its associated diseases in dogs and foals

The role of type A Clostridium perfringens in canine acute hemorrhagic diarrhea syndrome and foal necrotizing enteritis is poorly characterized. However, a highly significant association between the presence of novel toxigenic C. perfringens and these specific enteric diseases has been described. These novel toxigenic strains produce 3 novel putative toxins, which have been designated NetE, NetF, and NetG. Although not conclusively demonstrated, current evidence suggests that NetF is likely the major virulence factor in strains responsible for canine acute hemorrhagic diarrhea syndrome and foal necrotizing enteritis. NetF is a beta-pore-forming toxin that belongs to the same toxin superfamily as CPB and NetB toxins produced by C. perfringens. The netF gene is encoded on a conjugative plasmid that, in the case of netF, also carries another putative toxin gene, netE. In addition, these strains consistently also carry a cpe tcp-conjugative plasmid, and a proportion also carry a separate netG tcp-conjugative plasmid. The netF and netG genes form part of a locus with all the features of the pathogenicity loci of tcp-conjugative plasmids. The netF-positive isolates are clonal in origin and fall into 2 clades. Disease in dogs or foals can be associated with either clade. Thus, these are strains with unique virulence-associated characteristics associated with serious and sometimes fatal cases of important enteric diseases in 2 animal species.

The First Detection of Equine Coronavirus in Adult Horses and Foals in Ireland

The objective of this study was to investigate the presence of equine coronavirus (ECoV) in clinical samples submitted to a diagnostic laboratory in Ireland. A total of 424 clinical samples were examined from equids with enteric disease in 24 Irish counties between 2011 and 2015. A real-time reverse transcription polymerase chain reaction was used to detect ECoV RNA. Nucleocapsid, spike and the region from the p4.7 to p12.7 genes of positive samples were sequenced, and sequence and phylogenetic analyses were conducted. Five samples (1.2%) collected in 2011 and 2013 tested positive for ECoV. Positive samples were collected from adult horses, Thoroughbred foals and a donkey foal. Sequence and/or phylogenetic analysis showed that nucleocapsid, spike and p12.7 genes were highly conserved and were closely related to ECoVs identified in other countries. In contrast, the region from p4.7 and the non-coding region following the p4.7 gene had deletions or insertions. The differences in the p4.7 region between the Irish ECoVs and other ECoVs indicated that the Irish viruses were distinguishable from those circulating in other countries. This is the first report of ECoV detected in both foals and adult horses in Ireland.

Clinical presentation, diagnostic findings, and outcome of adult horses with equine coronavirus infection at a veterinary teaching hospital: 33 cases (2012-2018)

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Equine coronavirus (ECoV) is a differential diagnosis for adult horses with fever, mild colic signs, and anorexia.

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Leukopenia tends to be more severe in ECoV-infected horses than uninfected horses with similar signs.

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Horses shedding ECoV should be evaluated for co-infections.

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ECoV-infected horses may require intensive care to treat systemic inflammation, dehydration, and electrolyte derangements.

Equine coronavirus (ECoV) is a recently described enteric virus with worldwide outbreaks; however, there are little data available on clinical presentation, diagnosis, and outcome. The study objective was to document case management of ECoV in adult horses presented to a referral hospital and compare to a cohort of horses that tested negative for ECoV. A retrospective case series was performed based on positive real-time quantitative PCR results for ECoV on faeces from horses treated at the UC Davis Veterinary Medical Teaching Hospital from 1 March 2012 to 31 March 2018. Horses negative for ECoV were matched to the ECoV-positive group as controls. Data collected included signalment, history, exam findings, diagnostics, treatment, and follow-up.

Thirty-three horses (median age, 11 years; range, 2–37 years) tested ECoV-positive, including three horses with co-infections. Presenting complaints for ECoV-infected horses included historic fevers (n = 25/30; 83%), anorexia (n = 14/30; 47%), and colic (n = 13/30; 43%). ECoV-positive horses had significantly lower white blood cell (median, 3.0 × 10⁹/L; range, 0.68–16.2 × 10⁹/L), neutrophil (median, 1.26 × 10⁹/L; range, 0.15–14.4 × 10⁹/L), and lymphocyte (median, 0.86 × 10⁹/L; range, 0.42–3.47 × 10⁹/L) counts than ECoV-negative horses. Electrolyte and metabolic derangements and scant faeces were common. Twenty-seven horses were hospitalised for a median of 5 days (range, 0.5–14 days), with 26/27 (96%) horses surviving to discharge. ECoV infection should be a differential diagnosis for adult horses with fever, colic, anorexia, and leukopenia. The disease has a low mortality rate, but horses may require intensive care to resolve severe leukopenia, systemic inflammation, and metabolic disturbances.

Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning

A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.

Development and evaluation of a one-step multiplex real-time TaqMan® RT-qPCR assay for the detection and genotyping of equine G3 and G14 rotaviruses in fecal samples

Background

Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and has a negative impact on equine breeding enterprises worldwide. Among ERVA strains infecting foals, the genotypes G3P[12] and G14P[12] are the most prevalent, while infections by strains with other genomic arrangements are infrequent. The identification of circulating strains of ERVA is critical for diagnostic and surveillance purposes, as well as to understand their molecular epidemiology. Current genotyping methods available for ERVA and rotaviruses affecting other animal species rely on Sanger sequencing and are significantly time-consuming, costly and labor intensive. Here, we developed the first one-step multiplex TaqMan^® real-time reverse transcription polymerase chain reaction (RT-qPCR) assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes for the rapid detection and G-typing directly from fecal specimens.

Methods

A one-step multiplex TaqMan^® RT-qPCR assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes was designed. The analytical sensitivity was assessed using serial dilutions of in vitro transcribed RNA containing the target sequences while the analytical specificity was determined using RNA and DNA derived from a panel of group A rotaviruses along with other equine viruses and bacteria. The clinical performance of this multiplex assay was evaluated using a panel of 177 fecal samples and compared to a VP7-specific standard RT-PCR assay and Sanger sequencing. Limits of detection (LOD), sensitivity, specificity, and agreement were determined.

Results

The multiplex G3 and G14 VP7 assays demonstrated high specificity and efficiency, with perfect linearity. A 100-fold difference in their analytical sensitivity was observed when compared to the singleplex assays; however, this difference did not have an impact on the clinical performance. Clinical performance of the multiplex RT-qPCR assay demonstrated that this assay had a high sensitivity/specificity for every target (100% for NSP3, > 90% for G3 VP7 and > 99% for G14 VP7, respectively) and high overall agreement (> 98%) compared to conventional RT-PCR and sequencing.

Conclusions

This new multiplex RT-qPCR assay constitutes a useful, very reliable tool that could significantly aid in the rapid detection and G-typing of ERVA strains circulating in the field.

Clostridium difficile isolates derived from Czech horses are resistant to enrofloxacin; cluster to clades 1 and 5 and ribotype 033 predominates

Clostridium difficile has been recovered from the faeces of several animal species as well as horses. Between April 2015 and October 2016, 213 samples of faeces from non-hospitalized (n = 138) and hospitalized horses (n = 75) were investigated and eighteen C. difficile isolates were cultured using an enrichment method. Sixteen C. difficile positive samples were identified from hospitalised horses (p < 0.01). Molecular typing revealed seven ribotypes and sequence types (RT033/ST11 n = 8, 44.4%; RT081/ST9 n = 4, 22.2%; RT009/ST3 n = 2, 11.1%; RT003/ST12 n = 1, 5.6%; RT010/ST15 n = 1, 5.6%; RT012/ST54 n = 1, 5.6%; RT039/ST26 n = 1, 5.6%). Seven identified STs clustered to two clades (1 and 5). All C. difficile isolates were susceptible to amoxicillin, metronidazole, moxifloxacin, and vancomycin. One isolate (RT039) exhibited a high level of resistance to erythromycin and clindamycin (256 mg/L) and carried the ermB, adenine methylase gene. Five isolates were resistant to clindamycin at lower minimal inhibitory concentrations (MICs = 8-16 mg/L) and were susceptible to erythromycin and also ermB negative. All isolates were resistant to enrofloxacin (MICs ranged between 4 and 32 mg/L). Eight isolates were resistant to tetracycline (MICs 12-32 mg/L). Of them, four isolates carried the tetM gene and four isolates the tetW gene. In addition, the tetracycline resistance determinants identified were: tetA (P) (n = 4); tetB (P); and tetL (n = 1 each). The presence of tetW or tetM, together with other tet-class mechanisms, lead to an increase in the MICs to tetracycline. C. difficile isolates derived from Czech horses are identical to the ribotypes identified in humans and carry acquired antimicrobial resistance genes whose dissemination from veterinary healthcare sector to humans should be monitored by the "One health" approach.

Effect of oral supplementation of probiotic strains of Lactobacillus rhamnosus and Enterococcus faecium on the composition of the faecal microbiota of foals

Effects of probiotics on the intestinal microbiota of foals are yet insufficiently studied. The aim of this study was to investigate whether supplementation of Lactobacillus rhamnosus (DSM 7133) and Enterococcus faecium (DSM 7134) influences the bacterial composition of the faecal microbiota of foals. A total of 34 newborn foals were randomly assigned to the placebo group (PG, n = 16) and the treatment group (TG, n = 18). From day 1 to day 14 of life, foals orally received 3 ml of either a probiotic preparation (1.05 × 10⁹ CFU E. faecium and 4.50 × 10⁸ CFU L. rhamnosus) or placebo (carrier) once a day. Faeces were collected directly from the rectum immediately after birth (meconium) and at day 14 and day 56 of life. Samples of 12 foals per group were selected for microbiological analysis. DNA was extracted and used for polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR. No DNA or amplicons were obtained from meconium. There were no differences in richness of bands and Shannon index of diversity regarding the Clostridium cluster XIVa between groups. Cluster analysis and principal coordinate analysis of DGGE data showed a clear effect of age. Band-based similarity of bacterial clusters (Dice coefficient) decreased from day 14 to day 56 of life (p < 0.001) in PG foals only resulting in lower similarity in PG versus TG foals when 2 month old (p < 0.01). Five of thirty re-amplified bands were identified on species level. Others were assigned either to family (mainly Lachnospiraceae) or genus level (Akkermansia). The bands related to Akkermansia muciniphila or Akkermansia spp. appeared almost in all DGGE profiles. Two-week supplementation of the probiotic preparation to foals had no significant impact on the composition of the faecal microbiota but it appears to have prevented the reduction of bacterial similarity between 2 and 8 weeks of age observed in not treated foals.

Frequency of molecular detection of equine coronavirus in faeces and nasal secretions in 277 horses with acute onset of fever

CONTEXT

Due to the inconsistent development of enteric signs associated with ECoV infection in adult horses, many practitioners collect nasal secretions rather than feces for the molecular diagnostic work-up of such horses.

MAIN CONCLUSION

ECoV infection should be considered in horses presenting with acute onset of fever, especially when nasal discharge is absent as one of the cardinal clinical sign.

APPROACH

A total of 277 adult horses with acute onset of fever were enrolled in this study. Feces were tested for ECoV and nasal secretions for common respiratory pathogens (equine herpesvirus (EHV)-1, EHV-4, equine influenza virus (EIV), equine rhinitis viruses (ERVs) and Streptococcus equi ss. equi) and ECoV by qPCR. Each submission was accompanied by a questionnaire requesting information pertaining to signalment, use, recent transportation, number of affected horses on the premise and presence of clinical signs at the time of sample collection.

RESULTS

The total number of horses testing qPCR-positive for ECoV in feces was 20 (7.2%), 4 of which also tested qPCR-positive for ECoV in nasal secretions. In the same population 9.0% of horses tested qPCR-positive for EHV-4, 6.1% for EIV, 4.3% for Streptococcus equi ss. equi, 3.2% for ERVs and 0.7% for EHV-1. Draft horses, pleasure use, multiple horses affected on a premise and lack of nasal discharge were significantly associated with ECoV qPCR-positive horses.

INTERPRETATION

The present study results showed that 7.2% of horses with acute onset of fever tested qPCR-positive for ECoV in feces, highlighting the importance of testing such horses for ECoV in feces. The various prevalence factors associated with ECoV qPCR-positive status likely relate to the high infectious nature of ECoV and breed-specific differences in management and husbandry practices.

SIGNIFICANCE OF FINDINGS

ECoV infection should be suspected and tested for in horses presenting with acute onset of fever, lethargy and anorexia with no respiratory signs. A two-step approach should be consider in which respiratory secretions and feces should be collected from such horses and submitted to a diagnostic laboratory. If the respiratory secretions test negative by qPCR for a panel of respiratory pathogens, feces already submitted to the laboratory should be tested for ECoV.

Evaluation of equine coronavirus fecal shedding among hospitalized horses

BACKGROUND

Currently, diagnosis of equine coronavirus (ECoV) relies on the exclusion of other infectious causes of enteric disease along with molecular detection of ECoV in feces or tissue. Although this approach is complete, it is costly and may not always be achievable.

OBJECTIVE

We hypothesized that the overall fecal shedding of ECoV in hospitalized horses is low. Our objective was to determine whether systemically healthy horses and horses with gastrointestinal disorders shed ECoV in their feces at the time of admission to a referral hospital and after 48 hours of stress associated with hospitalization.

ANIMALS

One-hundred thirty adult horses admitted to the Washington State University Veterinary Teaching Hospital for gastrointestinal disease (n = 65) or for imaging under anesthesia (n = 65) that were hospitalized for 48 hours. Owner consent was obtained before sampling.

METHODS

Fecal samples were collected at admission and 48 hours later. Polymerase chain reaction (PCR) for ECoV and electron microscopy (EM) were performed on all samples.

RESULTS

Only 1 of 258 fecal samples was PCR-positive for ECoV. Electron microscopy identified ECoV-like particles in 9 of 258 samples, parvovirus-like particles in 4 of 258 samples, and rotavirus-like particles in 1 of 258 samples.

CONCLUSIONS AND CLINICAL IMPORTANCE

The presence of ECoV in feces of hospitalized adult horses was low. Thus, fecal samples that are PCR-positive for ECoV in adult horses that have clinical signs consistent with this viral infection are likely to be of diagnostic relevance. The clinical relevance of the viruses observed using EM remains to be investigated.

Detection, molecular characterization and phylogenetic analysis of G3P[12] and G14P[12] equine rotavirus strains co-circulating in central Kentucky

Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and a major health problem to the equine breeding industry worldwide. The G3P[12] and G14P[12] ERVA genotypes are the most prevalent in foals with diarrhea. Control and prevention strategies include vaccination of pregnant mares with an inactivated vaccine containing a prototype ERVA G3P[12] strain with limited and controversial field efficacy. Here, we performed the molecular characterization of ERVA strains circulating in central Kentucky using fecal samples collected during the 2017 foaling season. The data indicated for the first time that the G14P[12] genotype is predominant in this region in contrast to a previous serotyping study where only G3 genotype strains were reported. Overall, analysis of antigenic sites in the VP7 protein demonstrated the presence of several amino acid substitutions in the epitopes exposed on the surface including a non-conserved N-linked glycosylation site (D123N) in G14P[12] strains, while changes in antigenic sites of VP8* were minor. Also, we report the successful isolation of three ERVA G14P[12] strains which presented a high identity with other G14 strains from around the world. These may constitute ideal reference strains to comparatively study the molecular biology of G3 and G14 strains and perform vaccine efficacy studies following heterologous challenge in the future.

Novel findings from a beta coronavirus outbreak on an American Miniature Horse breeding farm in upstate New York

This case report describes an outbreak and novel findings associated with a beta coronavirus (BCoV) infection that occurred on an American Miniature Horse (AMH) breeding farm in upstate New York, in January and February of 2013. Twenty-nine AMH and one donkey were present on the farm when the outbreak occurred. One 10-year-old Quarter Horse mare, stabled at a separate location and owned by an employee of the farm, also tested positive. A polymerase chain reaction (PCR) assay for the detection of BCoV was performed at the Animal Health Diagnostic Center (AHDC) at Cornell on all faecal samples. The PCR assay used detects multiple beta coronaviruses, including, but not limited to, equine enteric coronavirus (ECoV). Novel findings regarding this BCoV infection in horses were recognised in this outbreak study. To the authors' knowledge, this is the largest outbreak of BCoV described thus far in a closed herd on a single premise. The case fatality rate was 0% unlike that described in a previous outbreak of ECoV involving miniature horses and a miniature donkey (Fielding et al. 2015). The morbidity rate was lower in this outbreak than in previously described studies (Oue et al. 2013; Pusterla et al. 2013). This outbreak also demonstrated the potential for BCoV transmission via farm personnel. The duration of shedding of virus in the faeces among some asymptomatic horses in this outbreak was longer than previously described clinical cases of ECoV (Pusterla et al. 2013; Nemoto et al. 2014). This study suggests that asymptomatic animals may play a role in the maintenance of BCoV during an outbreak; therefore, the need for diagnostic testing of both clinically affected and apparently clinically normal horses on a premises followed by appropriate biosecurity and control measures.

Foal Diarrhea: Established and Postulated Causes, Prevention, Diagnostics, and Treatments

Diarrhea is one of the most important diseases in young foals and may occur in more than half of foals until weaning age. Several infectious and noninfectious underlying causes have been implicated but scientific evidence of pathogenesis is evolving. It is important to investigate all known potential causes and identify infectious agents to avoid outbreaks, evaluate the level of systemic compromise, and establish adequate therapy. It is crucial to differentiate foals that can be managed in field conditions from those that should be sent to a referral center. This article reviews these aspects and recent developments in the diagnostic and therapeutic approaches.

Nutritional management of the foal with diarrhoea

Diarrhoea is a common problem in the neonatal and suckling foal. In certain circumstances supplemental nutrition is necessary depending on the age of foal, severity of diarrhoea and presence of other systemic manifestations. Nutritional supplementation can be provided either enterally or parenterally. Enteral nutrition is superior to parenteral nutrition because it is the most natural and physiologically sound means to provide nutritional support. Parenteral nutrition may be warranted if the foal is unable to receive or tolerate enteral nutrition. Dextrose alone or with amino acids and lipids can provide appropriate nutrition when enteral feeding is not tolerated. As soon as the foal stabilises enteral feeding can be reintroduced.

Enteric coronavirus infection in adult horses

A new enteric virus of adult horses, equine coronavirus (ECoV), has recently been recognized. It is associated with fever, lethargy, anorexia, and less frequently, colic and diarrhea. This enteric virus is transmitted via the feco-oral route and horses become infected by ingesting fecally contaminated feed and water. Various outbreaks have been reported since 2010 from Japan, Europe and the USA. While the clinical signs are fairly non-specific, lymphopenia and neutropenia are often seen. Specific diagnosis is made by the detection of ECoV in feces by either quantitative real-time PCR, electron microscopy or antigen-capture ELISA. Supportive treatment is usually required, as most infections are self-limiting. However, rare complications, such as endotoxemia, septicemia and hyperammonemia-associated encephalopathy, have been reported, and have been related to the loss of barrier function at the intestinal mucosa. This review article will focus on the latest information pertaining to the virus, epidemiology, clinical signs, diagnosis, pathology, treatment and prevention of ECoV infection in adult horses.

Viral enteritis in calves

A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods. These viruses include torovirus, norovirus, nebovirus, astrovirus, kobuvirus, and enterovirus. Most studies have involved epidemiologic investigations seeking to show association with diarrhea for each virus alone or in combination with potential pathogens. However, determining the contribution of these viruses to calf diarrhea has been challenging and much uncertainty remains concerning their roles as primary pathogens, co-infection agents, or commensals.

Review on Usage of Vancomycin in Livestock and Humans: Maintaining Its Efficacy, Prevention of Resistance and Alternative Therapy

Vancomycin is one of the “last-line” classes of antibiotics used in the treatment of life-threatening infections caused by Gram-positive bacteria. Even though vancomycin was discovered in the 1950s, it was widely used after the 1980s for the treatment of infections caused by methicillin-resistant Staphylococci, as the prevalence of these strains were increased. However, it is currently evident that vancomycin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci have developed for various reasons, including the use of avaparcin—an analog of vancomycin—as a feed additive in livestock. Therefore, prophylactic and empiric use of antibiotics and their analogues need to be minimized. Herein we discuss the rational use of vancomycin in treating humans, horses, farm animals, and pet animals such as dogs, cats, and rabbits. In present day context, more attention should be paid to the prevention of the emergence of resistance to antibiotics in order to maintain their efficacy. In order to prevent emergence of resistance, proper guidance for the responsible use of antimicrobials is indispensable. Therefore, almost all stakeholders who use antibiotics should have an in-depth understanding of the antibiotic that they use. As such, it is imperative to be aware of the important aspects of vancomycin. In the present review, efforts have been made to discuss the pharmacokinetics and pharmacodynamics, indications, emergence of resistance, control of resistance, adverse effects, and alternative therapy for vancomycin.

Seroprevalence and risk factors for infection with equine coronavirus in healthy horses in the USA

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Equine coronavirus has only recently been associated with emerging infections in adult horses.

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Seroprevalence data is needed to better understand the epidemiology of equine coronavirus in adult horses.

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The seroprevalence to equine coronavirus was 9.6% in 5247 healthy, adult horses from 18 states in the USA.

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Seropositivity was significantly associated with horses from the Mid-West, draft horses and ranch/farm and breeding use.

Equine coronavirus (ECoV) is considered an enteric pathogen of foals and has only recently been associated with infections in adult horses. Seroprevalence data is needed to better understand the epidemiology of ECoV in adult horses, evaluate diagnostic modalities and develop preventive measures. The objective of this study was to investigate the seroprevalence and selective risk factors for ECoV in 5247 healthy adult horses in the USA, using a recently established and validated IgG enzyme-linked immunosorbent assay. Prevalence factors analysed in this study included geographic region, age, breed, sex and use.

A total of 504/5247 horses (9.6%) horses tested seropositive. Geographic region (Mid-West; P = 0.008), breed (Draft horses; P = 0.003) and specific uses of horses (ranch/farm, P = 0.034; breeding use, P = 0.016) were all statistically significant risk factors for seropositivity.

Enteric Pathogens and Coinfections in Foals with and without Diarrhea

Diarrhea is a major clinical problem affecting foals up to 3 months of age. The aim of this study was to identify enteric microorganisms involved in monoinfections and coinfections and the associated virulence factors in healthy and diarrheic foals. Diarrheic (D) (n = 56) and nondiarrheic (ND) foals (n = 60) up to three months of age were studied. Fecal samples were analyzed for identification of infectious agents (microbiological culturing, molecular techniques, and microscopic analyses). Escherichia coli fimH (30% versus 25%), Salmonella spp. (25% versus 7%), Strongyloides westeri (25% versus 25%), Clostridium perfringens type A (21% versus 10%), E. coli ag43 (20% versus 35%), Strongylus (11% versus 18%), and vapA-positive Rhodococcus equi (5% versus 2%) were the most frequent enteric pathogens detected in D and ND foals, respectively. The frequency of toxin A-positive C. perfringens was significantly increased in the D (p = 0.033) compared with the ND animals. R. equi strains harboring virulent plasmids were also identified (VapA 85-kb type I and VapA 87-kb type I) in D and ND foals. Coinfections were observed in 46% of the D and 33% of the ND foals. Our results demonstrate the great diversity of enteric pathogens, virulence factors, and coinfections involved in enteric infections of foals.

Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species

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Agreement between molecular tests for Rotavirus group A (RVA) detection was 80–92%.

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The agreement between all assays was 81–100% in samples containing high viral loads.

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The sensitivity of RVA RT-iiPCR was 3–4 copies of in vitro transcribed dsRNA.

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The field-deployable RT-iiPCR system holds promise for on-site detection of RVA.

There is no gold standard for detection of Rotavirus Group A (RVA), one of the main causes of diarrhea in neonatal animals. Sensitive and specific real-time RT-PCR (rtRT-PCR) assays are available for RVA but require submission of the clinical samples to diagnostic laboratories. Patient-side immunoassays for RVA protein detection have shown variable results, particularly with samples from unintended species. A sensitive and specific test for detection of RVA on the farm would facilitate rapid management decisions. The insulated isothermal RT-PCR (RT-iiPCR) assay works in a portable machine to allow sensitive and specific on-site testing. The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. This assay was compared to an in-house rtRT-PCR assay and a commercially available rtRT-PCR kit, as well as an ELISA and EM for RVA detection. All three PCR assays targeted the well-conserved NSP5 gene. Clinical fecal samples from 108 diarrheic animals (mainly cattle and horses) were tested. The percentage of positive samples by ELISA, EM, in-house rtRT-PCR, commercial rtRT-PCR, and RT-iiPCR was 29.4%, 31%, 36.7%, 51.4%, 56.9%, respectively. The agreement between different assays was high (81.3–100%) in samples containing high viral loads. The sensitivity of the RT-iiPCR assay appeared to be higher than the commercially available rtRT-PCR assay, with a limit of detection (95% confidence index) of 3–4 copies of in vitro transcribed dsRNA. In conclusion, the user-friendly, field-deployable RT-iiPCR system holds substantial promise for on-site detection of RVA.

Identification of risk factors influencing Clostridium difficile prevalence in middle-size dairy farms

Farm animals have been suggested to play an important role in the epidemiology of Clostridium difficile infection (CDI) in the community. The purpose of this study was to evaluate risk factors associated with C. difficile dissemination in family dairy farms, which are the most common farming model in the European Union. Environmental samples and fecal samples from cows and calves were collected repeatedly over a 1 year period on 20 mid-size family dairy farms. Clostridium difficile was detected in cattle feces on all farms using qPCR. The average prevalence between farms was 10% (0–44.4%) and 35.7% (3.7–66.7%) in cows and calves, respectively. Bacterial culture yielded 103 C. difficile isolates from cattle and 61 from the environment. Most C. difficile isolates were PCR-ribotype 033. A univariate mixed effect model analysis of risk factors associated dietary changes with increasing C. difficile prevalence in cows (P = 0.0004); and dietary changes (P = 0.004), breeding Simmental cattle (P = 0.001), mastitis (P = 0.003) and antibiotic treatment (P = 0.003) in calves. Multivariate analysis of risk factors found that dietary changes in cows (P = 0.0001) and calves (P = 0.002) increase C. difficile prevalence; mastitis was identified as a risk factor in calves (P = 0.001). This study shows that C. difficile is common on dairy farms and that shedding is more influenced by farm management than environmental factors. Based on molecular typing of C. difficile isolates, it could also be concluded that family dairy farms are currently not contributing to increased CDI incidence.

Equine coronavirus: An emerging enteric virus of adult horses

Equine coronavirus (ECoV) is an emerging virus associated clinically and epidemiologically with fever, depression, anorexia and less frequently colic and diarrhoea in adult horses. Sporadic cases and outbreaks have been reported with increased frequency since 2010 from Japan, the USA and more recently from Europe. A faeco‐oral transmission route is suspected and clinical or asymptomatic infected horses appear to be responsible for direct and indirect transmission of ECoV. A presumptive clinical diagnosis of ECoV infection may be suggested by clinical presentation, haematological abnormalities such as leucopenia due to lymphopenia and/or neutropenia. Confirmation of ECoV infection is provided by specific ECoV nucleic acid detection in faeces by quantitative PCR (qPCR) or demonstration of coronavirus antigen by immunohistochemistry or electron microscopy in intestinal biopsy material obtained ante or post mortem. The disease is generally self‐limiting and horses typically recover with symptomatic supportive care. Complications associated with disruption of the gastrointestinal barrier have been reported in some infected horses and include endotoxaemia, septicaemia and hyperammonaemia‐associated encephalopathy. Although specific immunoprophylactic measures have been shown to be effective in disease prevention for closely‐related coronaviruses such as bovine coronavirus (BCoV), such strategies have yet not been investigated for horses and disease prevention is limited to basic biosecurity protocols. This article reviews current knowledge concerning the aetiology, epidemiology, clinical signs, diagnosis, pathology, treatment and prevention of ECoV infection in adult horses.

Low prevalence of equine coronavirus in foals in the largest thoroughbred horse breeding region of Japan, 2012-2014

Background

Equine coronavirus (ECoV) is considered to be a diarrheic pathogen in foals. In central Kentucky in the United States, it has been shown that approximately 30 % of thoroughbred foals are infected with ECoV and thus it is considered widely prevalent. In contrast, the epidemiology of ECoV and its relationship to diarrhea in foals are poorly understood in Japan. We investigated ECoV in rectal swabs collected from thoroughbred foals in Japan.

Results

We collected 337 rectal swabs from 307 diarrheic foals in the Hidaka district of Hokkaido, the largest thoroughbred horse breeding region in Japan, between 2012 and 2014. In addition, 120 rectal swabs were collected from 120 healthy foals in 2012. These samples were tested by reverse transcription loop-mediated isothermal amplification and a real-time reverse transcription-polymerase chain reaction. All samples collected from diarrheic foals were negative, and only three samples (2.5 %) collected from healthy foals were positive for ECoV. Compared with central Kentucky, ECoV is not prevalent among thoroughbred foals in the Hidaka district of Hokkaido.

Conclusion

ECoV is not prevalent and was not related to diarrhea in thoroughbred foals in the Hidaka district of Hokkaido between 2012 and 2014.

Comparison of two commercial kits and an in-house ELISA for the detection of equine rotavirus in foal feces

Group A rotaviruses (RVA) are important infectious agents associated with diarrhea in the young of several animal species including foals. Currently, a variety of diagnosis methods are commercially available, like ELISA, latex agglutination and immunochromatographic assays. These commercial tests are mainly designed for the detection of human RVA; its applicability in veterinary diagnosis has been poorly studied. The aim of this study was to compare the sensitivity and specificity of two commercial diagnostic kits, Pathfinder™ Rotavirus and FASTest Rota® strip, with an in-house KERI ELISA, for the detection of equine RVA. A total of 172 stool samples from Thoroughbred foals with diarrhea were analyzed. The presence of equine RVA in samples in which only one of the three methods showed positive results was confirmed by RT-PCR. A sample was considered "true positive" when RVA was detected by at least two of the methods, and "true negative" when it tested negative by the three assays. Following these criteria, 50 samples were found positive and 122 were found negative, and were handled as reference population for the assay validation. Pathfinder™ Rotavirus assay showed 32% sensitivity and 97% specificity, FASTest Rota® strip, 92% sensitivity and 97% specificity, and KERI ELISA, 76% sensitivity and 93% specificity. Pathfinder™ Rotavirus showed 77%, FASTest Rota® strip 95%, and KERI ELISA 88% accuracy to correctly classify the samples as equine RVA positive or negative. Pathfinder failed specifically to detect equine RVA G3P12I6 genotype; such performance might be related to the specificity of the monoclonal antibody included in this kit. According to our results, differences among VP6 genotypes could influence the sensitivity to detect equine RVA in foal feces, and thus assay validation of diagnostic kits for each species is necessary. In conclusion, FASTest Rota® strip is more suitable than ELISA Pathfinder™ Rotavirus for the screening of rotavirus infection in foals. The KERI ELISA showed an acceptable performance, and could be considered a proper economic alternative for equine RVA diagnosis.