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Background: Bovine respiratory disease (BRD) is an important cause of morbidity and mortality and is responsible for most of the injectable antimicrobial use in the feedlot industry. Traditional bacterial culture can be used to diagnose BRD by confirming the presence of causative pathogens and to support antimicrobial selection. However, given that bacterial culture takes up to a week and early intervention is critical for treatment success, culture has limited utility for informing rapid therapeutic decision-making. In contrast, metagenomic sequencing has the potential to quickly resolve all nucleic acid in a sample, including pathogen biomarkers and antimicrobial resistance genes. In particular, third-generation Oxford Nanopore Technology sequencing platforms provide long reads and access to raw sequencing data in real-time as it is produced, thereby reducing the time from sample collection to diagnostic answer. The purpose of this study was to compare the performance of nanopore metagenomic sequencing to traditional culture and sensitivity methods as applied to nasopharyngeal samples from segregated groups of chronically ill feedlot cattle, previously treated with antimicrobials for nonresponsive pneumonia or lameness. Results: BRD pathogens were isolated from most samples and a variety of different resistance profiles were observed across isolates. The sequencing data indicated the samples were dominated by Moraxella bovoculi, Mannheimia haemolytica, Mycoplasma dispar, and Pasteurella multocida, and included a wide range of antimicrobial resistance genes (ARGs), encoding resistance for up to seven classes of antimicrobials. Genes conferring resistance to beta-lactams were the most commonly detected, while the tetH gene was detected in the most samples overall. Metagenomic sequencing detected the BRD pathogens of interest more often than did culture, but there was limited concordance between phenotypic resistance to antimicrobials and the presence of relevant ARGs. Conclusions: Metagenomic sequencing can reduce the time from sampling to results, detect pathogens missed by bacterial culture, and identify genetically encoded determinants of resistance. Increasing sequencing coverage of target organisms will be an essential component of improving the reliability of this technology, such that it can be better used for the surveillance of pathogens of interest, genetic determinants of resistance, and to inform diagnostic decisions. [ABSTRACT FROM AUTHOR]

Background: Stoat (Mustela erminea) and weasel (Mustela nivalis) populations in south-west England are declining whilst polecats (Mustela putorius), absent for over a century, are increasing. Little is known about the health status of these species nationally. This study aimed at investigating respiratory disease in specimens found dead in south-west England. Results: Trauma caused by road traffic, predator attack or being trapped was the predominant cause of death in 42 stoats, 31 weasels and 20 polecats; most were in good physical condition. Skrjabingylus nasicola was present in all species (weasels 37 %, polecats 39 %, stoats 41 %) and infected animals showed no evidence of loss of body condition. Even in carcases stored frozen L1 larvae were frequently alive and highly motile. Angiostrongylus vasorum infection was diagnosed in two stoats and one weasel: in stoats infections were patent and the lung lesions were likely of clinical significance. These are believed to be the first records of A. vasorum in small mustelids. Pleuritis and pyothorax was seen in two polecats, in one case due to a migrating grass awn. Histological examination of lungs showed granulomata in stoats (38 %), weasels (52 %) and polecats (50 %). Spherules consistent with Emmonsia spp. adiaspores were present in the granulomata of stoats (60 %), weasels (36 %) and polecats (29 %). Adiaspore diameter in all three species was similar (means: stoats 39 μm, weasels 30 μm, polecats 36 μm); these are markedly smaller than that normally recorded for E. crescens. Although they lie within the accepted range for spores of Emmonsia parva this arid-zone species is not found in Britain, thus raising a question over the identity of the fungus. Cases showing numerous granulomata but few or no adiaspores were Ziehl-Neelsen-stain negative for acid-fast bacilli and IHC negative for Mycobacterium spp. However, in some cases PCR analyses revealed mycobacteria, including Mycobacterium kumamotonense and Mycobacterium avium Complex. One stoat had numerous unidentified small organisms present centrally within granulomata. Conclusions: Stoats, weasels and polecats in south-west England share several respiratory diseases, often of high prevalence, but the pathology would appear insufficient to impact on the health status of the populations and other ultimate causes of death should be investigated when examining these species. [ABSTRACT FROM AUTHOR]

Background: Little is known on the effects of common calf diseases on mortality and carcass traits in the white veal industry (special-fed veal), a highly integrated production system, currently criticized for the intensive pro- and metaphylactic use of antimicrobials. The objective of the present study was to determine the impact of bovine respiratory disease (BRD), diarrhea, arthritis and otitis on the economically important parameters of mortality, hot carcass weight (HCW), carcass quality, fat cover and meat color. For this purpose, a prospective study on 3519 white veal calves, housed in 10 commercial herds, was conducted. Case definitions were based on clinical observation by the producers and written treatment records were used. Results: Calves received oral antimicrobial group treatments in the milk during 25.2% of the production time on average. With an increasing percentage of the production cycle spent on oral antimicrobials, HCW reduced, whereas the odds for insufficient fat cover or an undesirable red meat color both decreased. Of the calves, 14.8%, 5.3%, 1.5% and 1.6% were individually diagnosed and treated for BRD, diarrhea, arthritis and otitis, respectively. Overall, 5.7% of the calves died and the mortality risk was higher in the first weeks after arrival. Calves that experienced one BRD episode showed a 8.2 kg reduction in HCW, a lower fat cover and an increased mortality risk (hazard ratio (HR) = 5.5), compared to calves which were not individually diagnosed and treated for BRD. With an increasing number of BRD episodes, these losses increased dramatically. Additionally, calves, which experienced multiple BRD episodes, were more likely to have poor carcass quality and an undesirable red meat color at slaughter. Arthritis increased the mortality risk (HR = 3.9), and reduced HCW only when associated with BRD. Otitis did only increase the mortality risk (HR = 7.0). Diarrhea severely increased the mortality risk (HR = 11.0), reduced HCW by 9.2 kg on average and decreased carcass quality. Conclusions: Despite the massive use of group and individual treatments to alleviate the most prevalent health issues at the fattening period, the effects of BRD, diarrhea, otitis and arthritis on survival and performance are still considerable, especially in cases of chronic pneumonia with or without arthritis. Controlling calf health by effective preventive and therapeutic strategies and in particular the prevention of chronic BRD is key for the profitability of veal operations. [ABSTRACT FROM AUTHOR]

Background: Spontaneous gastrointestinal neoplasms in non-human primates are commonly seen in aged individuals. Due to genetic similarities between human and non-human primates, scientists have shown increasing interest in terms of comparative oncology studies. Case presentation: The present study is related to a case of an intestinal leiomyoma in a black crested macaque (Macaca nigra), kept on captivity by Matecaña Zoo, Pereira City, Colombia. The animal had abdominal distension, anorexia, vomiting, diarrhea and behavioral changes. Clinical examination showed an increased volume in the upper right abdominal quadrant caused by a neoplastic mass. The patient died during the surgical procedure. Necropsy revealed several small nodules in the peritoneum with adhesion to different portions of the small and large intestines, liver, stomach and diaphragm. Tissue samples were collected, routinely processed and stained by H&E. Microscopic examination revealed a mesenchymal tumor limited to tunica muscularis, resembling normal smooth muscle cells. Neoplastic cells were positive for alpha-smooth muscle actin and vimentin, and negative for cytokeratin AE1/AE3 by immunohistochemistry. Those morphological and immunohistochemical findings allowed to diagnose the intestinal leiomyoma referred above. Conclusion: Neoplastic diseases in primates have multifaceted causes. Their manifestations are understudied, leading to a greater difficulty in detection and measurement of the real impact provides by this disease. [ABSTRACT FROM AUTHOR]

In recent years, outbreaks caused by multi-host pathogens (MHP) have posed a serious challenge to public and animal health authorities. The frequent implication of wildlife in such disease systems and a lack of guidelines for mitigating these diseases within wild animal populations partially explain why the outbreaks are particularly challenging. To face these challenges, the French Ministry of Agriculture launched a multi-disciplinary group of experts that set out to discuss the main wildlife specific concepts in the management of MHP disease outbreaks and how to integrate wildlife in the disease management process. This position paper structures the primary specific concepts of wildlife disease management, as identified by the working group. It is designed to lay out these concepts for a wide audience of public and/or animal health officers who are not necessarily familiar with wildlife diseases. The group's discussions generated a possible roadmap for the management of MHP diseases. This roadmap is presented as a cycle for which the main successive step are: step 1-descriptive studies and monitoring; step 2-risk assessment; step 3-management goals; step 4-management actions and step 5-assessment of the management plan. In order to help choose the most adapted management actions for all involved epidemiological units, we integrated a decision-making framework (presented as a spreadsheet). This tool and the corresponding guidelines for disease management are designed to be used by public and health authorities when facing MHP disease outbreaks. These proposals are meant as an initial step towards a harmonized transboundary outbreak response framework that integrates current scientific understanding adapted to practical intervention. [ABSTRACT FROM AUTHOR]

Background: Although mustelids occur worldwide and include a wide range of species, little is known about the diseases affecting them. Mustelids have regularly been submitted for post mortem investigation in the framework of the program for general wildlife health surveillance in Switzerland, which has been in place for nearly 60 years. We performed a retrospective analysis of the necropsy reports on mustelids submitted to the diagnostic service of the University of Bern. The aims of this study were to present an overview of the causes of mortality and morbidity observed in these carnivores, to assess differences among species, to assess changes in disease detection over the study period, and to describe the pathology of selected diseases. Results: Five hundred and sixty-six reports from 1958 to 2015 were analyzed. Most animals were stone martens (Martes foina, 46%) and badgers (Meles meles, 44%); the remaining species were polecats (Mustela putorius, 4.7%), pine martens (Martes martes, 2%), stoats (Mustela erminea, 1.4%), weasels (Mustela nivalis, 0.8%) and otters (Lutra lutra, 0.3%). Infectious diseases (n = 262) were frequent and were mostly bacterial or viral; non-infectious conditions (n = 169) were less common and were mostly traumatic or due to metabolic disorders. The most frequent diagnoses included distemper (75% were badgers), amyloidosis (96% were martens), bacterial respiratory infections (all mustelids), biting lice (badgers only) and pulmonary and gastro-intestinal helminths (all species). Less frequent diseases included histoplasmosis (badgers only), aspergillosis, toxoplasmosis, hepatozoonosis, and sarcoptic mange. Lesions due to infection with distemper virus were primarily appreciated in the respiratory tract and central nervous system; they presented species-specific characteristics such as necrosis in the ependyma in badgers and absence of syncytia in stone martens. Amyloidosis in martens was multisystemic in most cases and included both AA and AL amyloidosis; the main macroscopic change was severe splenomegaly. Conclusion: Infectious diseases were the most frequent causes of morbidity and mortality of mustelids, with marked species-specific differences. Lung and skin were the most commonly affected organs. Contagious diseases such as canine distemper, sarcoptic mange and rabies in mustelids showed a similar temporal pattern as in red foxes (Vulpes vulpes), suggesting pathogen spillovers from foxes to mustelids. [ABSTRACT FROM AUTHOR]

Background: High throughput sequencing allows identification of small non-coding RNAs. Transfer RNA Fragments are a class of small non-coding RNAs, and have been identified as being involved in inhibition of gene expression. Given their role, it is possible they may be involved in mediating the infection-induced defense response in the host. Therefore, the objective of this study was to identify 5′ transfer RNA fragments (tRF5s) associated with a serum antibody response to M. bovis in beef cattle. Results: The tRF5s encoding alanine, glutamic acid, glycine, lysine, proline, selenocysteine, threonine, and valine were associated (P < 0.05) with antibody response against M. bovis. tRF5s encoding alanine, glutamine, glutamic acid, glycine, histidine, lysine, proline, selenocysteine, threonine, and valine were associated (P < 0.05) with season, which could be attributed to calf growth. There were interactions (P < 0.05) between antibody response to M. bovis and season for tRF5 encoding selenocysteine (anticodon UGA), proline (anticodon CGG), and glutamine (anticodon TTG). Selenocysteine is a rarely used amino acid that is incorporated into proteins by the opal stop codon (UGA), and its function is not well understood. Conclusions: Differential expression of tRF5s was identified between ELISA-positive and negative animals. Production of tRF5s may be associated with a host defense mechanism triggered by bacterial infection, or it may provide some advantage to a pathogen during infection of a host. Further studies are needed to establish if tRF5s could be used as a diagnostic marker of chronic exposure. [ABSTRACT FROM AUTHOR]