Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples.

The laboratory diagnosis of infectious diseases, especially those caused by mixed infections, is challenging. Routinely, it requires submission of multiple samples to separate laboratories. Advances in next-generation sequencing (NGS) have provided the opportunity for development of a comprehensive method to identify infectious agents. This study describes the use of target-specific primers for PCR-mediated amplification with the NGS technology in which pathogen genomic regions of interest are enriched and selectively sequenced from clinical samples. In the study, 198 primers were designed to target 43 common bovine and small-ruminant bacterial, fungal, viral, and parasitic pathogens, and a bioinformatics tool was specifically constructed for the detection of targeted pathogens. The primers were confirmed to detect the intended pathogens by testing reference strains and isolates. The method was then validated using 60 clinical samples (including tissues, feces, and milk) that were also tested with other routine diagnostic techniques. The detection limits of the targeted NGS method were evaluated using 10 representative pathogens that were also tested by quantitative PCR (qPCR), and the NGS method was able to detect the organisms from samples with qPCR threshold cycle (CT ) values in the 30s. The method was successful for the detection of multiple pathogens in the clinical samples, including some additional pathogens missed by the routine techniques because the specific tests needed for the particular organisms were not performed. The results demonstrate the feasibility of the approach and indicate that it is possible to incorporate NGS as a diagnostic tool in a cost-effective manner into a veterinary diagnostic laboratory.

Granulomatous dermatitis caused by Exserohilum mcginnisii infection in a cow.

A 5-y-old, Piedmontese cow had a 4-mo history of ongoing development of skin masses. This was the only cow affected in a herd of 20 cows. Up to 12, hairless, red-to-black, raised nodules-to-plaques were distributed along the dorsum and tail head. Biopsies were taken for histopathology and ancillary testing. An ulcerated skin section contained dermal infiltrates of eosinophils, plasma cells, neutrophils, macrophages, lymphocytes, and multinucleate giant cells, and pyogranulomas. Fungal hyphae were seen within the dermis, multinucleate giant cells, and pyogranulomas. In pyogranulomas, fungi were surrounded by a Splendore-Hoeppli reaction. Dematiaceous (pigmented) hyphae were rarely observed with H&E-stained and unstained (cleared and mounted) sections, but stained well with a Fontana-Masson stain. Exserohilum mcginnisii was identified by fungal culture, followed by PCR assay and sequencing. Exserohilum is a dematiaceous fungus that causes disease in humans and rarely in animals. The use of unstained sections and Fontana-Masson stain are important to demonstrate pigment because dematiaceous fungi have little melanin and appear as hyaline hyphae histologically. PCR assay and sequencing aid in the differentiation and classification of fungal species. To our knowledge, E. mcginnisii dermal granulomas have not been reported previously in cattle.

Retrospective study of laboratory-based surveillance of rabies in wild and domestic animals in the southern United States, 2010-2021.

We performed a retrospective study of all case submissions for the rabies virus (RABV) direct fluorescent antibody test (DFAT) requested of the Tifton Veterinary Diagnostic and Investigational Laboratory (Tifton, GA, USA) between July 2010 and June 2021. Submitted were 792 samples from 23 animal species from 89 counties in Georgia, and 4 neighboring counties in Florida, 1 in South Carolina, and 1 in Alabama. In 13 (1.6%) cases, the DFAT result was inconclusive; 779 (98.4%) cases had a conclusive (positive or negative) test result. Of these 779 cases, 79 (10.1%) tested positive across 10 species. The remaining 700 (89.9%) cases were negative. The main reason for submission for RABV testing was human exposure to a potentially rabid animal in 414 (52.3%) cases. Among the 79 positive cases, 74 (93.7%) involved wildlife; raccoons (51 cases; 68.9%) were the primary host confirmed with RABV infection, followed by skunk and fox (8 cases each; 10.8%), bobcat (5 cases; 6.8%), and bats (2 cases; 2.7%). Only 5 domestic animals (6.3% of the positive cases) tested positive during our study period; one from each of the bovine, canine, caprine, equine, and feline species. Hence, the sylvatic cycle plays the predominant role in circulating RABV infection in our study area.

Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples.

Equine infectious disease outbreaks may have profound economic impact, resulting in losses of millions of dollars of revenue as a result of horse loss, quarantine, and cancelled events. Early and accurate diagnosis is essential to limit the spread of infectious diseases. However, laboratory detection of infectious agents, especially the simultaneous detection of multiple agents, can be challenging to the clinician and diagnostic laboratory. Next-generation sequencing (NGS), which allows millions of DNA templates to be sequenced simultaneously in a single reaction, is an ideal technology for comprehensive testing. We conducted a proof-of-concept study of targeted NGS to detect 62 common equine bacterial, viral, and parasitic pathogens in clinical samples. We designed 264 primers and constructed a bioinformatics tool for the detection of targeted pathogens. The designed primers were able to specifically detect the intended pathogens. Results of testing 27 clinical samples with our targeted NGS assay compared with results of routine tests (assessed as a group) yielded positive percent agreement of 81% and negative percent agreement of 83%, overall agreement of 81%, and kappa of 0.56 (moderate agreement). This moderate agreement was likely the result of low sensitivity of some primers. However, our NGS assay successfully detected multiple pathogens in the clinical samples, including some pathogens missed by routine techniques.

An outbreak of Neospora caninum abortion in a dairy herd from the State of Georgia, United States.

An outbreak of 92 abortions out of 1,700 pregnant cows (5.41%) in a period of 3 weeks (19 May to 05 June 2019) occurred in a Georgia Dairy, USA, in cattle that were between 3 and 7 months of gestation. Two sets of samples (aborted fetuses' organs, placental tissues, aborted cows blood) were submitted for laboratory investigations at the Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia (TVDIL, Tifton, GA, USA). An abortion panel testing for the major abortion-causing agents [e.g. Bovine Viral Diarrhoea Virus (BVDV), Infectious Bovine Rhinotracheitis Virus/ Bovine Herpes Virus-I (IBR/ BHV-I), Brucella spp., Leptospira spp.] was conducted on several of the samples. On the first set of samples, microbial cultures, serology and PCR tests for the common abortifacient agents revealed the presence of Neospora caninum (N. caninum) DNA, which was positive by PCR on the placenta and fetal tissues. The second set of diagnostic investigations also identified two out of three submitted freshly aborted fetuses to be positive for N. caninum by PCR and immunohistochemistry. Moreover, all three dams were also sero-positive for N. caninum. The entire herd was being fed on grass silage harvested from a pasture where feral pigs were hunted previously and carcasses were left behind. As a consequence of this action a large population of wild coyotes were attracted to these carcasses, and likely contaminated the pasture with potential N. caninum-infected feces. After the abortion outbreak was resolved, it was recommended that the farmers should avoid disposal of cadavers of hunted animals in the wild, as it could attract carnivorous and omnivorous animals that may potentially spread the disease to the cattle and other wildlife.

Meningoencephalitis caused by Mycoplasma edwardii in a dog.

A 6-week-old, female, mixed-breed dog with a clinical history of sudden onset of neurologic signs was presented for necropsy. The dog was diagnosed with suppurative and histiocytic meningoencephalitis based on necropsy findings and histopathology. Mycoplasma sp. was isolated in pure culture from the brain and meninges and was identified as Mycoplasma edwardii using DNA sequencing.

Ligneous conjunctivitis secondary to a congenital plasminogen deficiency in a dog.

CASE DESCRIPTION: A 7-month-old 16.6-kg (36.5-lb) sexually intact female Golden Retriever was evaluated because of progressive severe bilateral membranous conjunctivitis, oral lesions, nasal discharge, and cough. CLINICAL FINDINGS: Histologic examination of conjunctival biopsy specimens revealed findings consistent with ligneous conjunctivitis. Circulating plasminogen activity was repeatedly low, and congenital plasminogen deficiency was identified as the underlying cause of the ocular, oral, and respiratory lesions. TREATMENT AND OUTCOME: Topical and subconjunctival administrations of fresh frozen plasma (FFP), topical administration of cyclosporine, and oral administration of azathioprine had no effect on the conjunctival membranes. Excision of the membranes followed by intensive treatment with topical applications of heparin, tissue plasminogen activator, corticosteroid, and FFP and IV administration of FFP prevented membrane regrowth. Intravenous administration of FFP increased plasma plasminogen activity to within reference limits, improved respiratory and oral lesions, and resulted in weight gain; discontinuation of this treatment resulted in weight loss, signs of depression, and worsening of lesions. After euthanasia because of disease progression, necropsy findings included mild hydrocephalus; multifocal intestinal hemorrhages; and fibrinous plaques in the oral cavity, nasopharynx, trachea, esophagus, and pericardium. Microscopically, the plaques were composed of fibrin and poorly organized granulation tissue. Fibrin thrombi were present within vessels in the lungs, oral cavity, and trachea. CLINICAL RELEVANCE: In dogs, congenital plasminogen deficiency can occur and may be the underlying cause of ligneous conjunctivitis. A combination of surgical and medical treatments may improve conjunctival membranes, and administration of FFP IV appears to be effective in treating nonocular signs of plasminogen deficiency.

Septicemia and meningoencephalitis caused by Listeria monocytogenes in two neonatal llamas.

Listeriosis is a disease of humans and domestic mammals (mainly ruminants) with variable manifestations, primarily encephalitis, septicemia, and abortion. Although Listeria monocytogenes readily causes illness in ruminants, the prevalence among domestic South American camelids (llamas and alpacas) is low and has not been documented in their wild counterparts, the vicuna and guanaco. We describe herein the clinical signs, autopsy findings, and histopathology of septicemia and suppurative meningoencephalitis caused by L. monocytogenes in 2 neonatal llamas ( Llama glama) from the same herd. L. monocytogenes was isolated in pure culture and identified by real-time PCR on fresh and paraffin-embedded tissue samples of the brain from both crias. This presentation of septicemic listeriosis with meningoencephalitis in 2 animals from the same group is unusual, especially among llamas.

Clinical, pathological and immunohistochemical study of feline mammary fibroepithelial hyperplasia following a single injection of depot medroxyprogesterone acetate.

Feline mammary fibroepithelial hyperplasia (FMFH) following a single injection of depot medroxyprogesterone acetate (MPA) was observed in eight intact young queens. The repository compound is marketed as a veterinary product by a local pharmaceutical company with an indication for contraception in cats. The drug was administered according to the recommended doses and injection frequencies. Serum hormone assays performed immediately before neutering and 3 weeks after neutering detected persistently high levels of progesterone suggesting that depot MPA was still exerting its influence. No corpora lutea were found in those cases ruling out ovaries as the main site of progesterone. Immunohistochemistry performed on the hyperplastic mammary glands detected progesterone receptors in the nuclei of ductal cells, and growth hormone (GH) and insulin-like growth factor-I (IGF-I) in the cytoplasm of ductal epithelium. Overdosing should be considered here as the animals received at least 10 mg/kg of depot MPA in a single injection. Progestin-induced local synthesis of GH and IGF-I in mammary epithelial cells is suggested as one of the pathogenic mechanisms involved in the development of FMFH.

Detection of asymptomatic renal Leptospira infection in abattoir slaughtered cattle in southeastern Georgia, United States.

OBJECTIVES: Leptospirosis is one of the most widespread zoonotic infectious diseases affecting humans and animals. Several animal species, including cattle, can act as potential asymptomatic carriers facilitating zoonotic transmission of Leptospira. This study was conducted to assess the occurrence of asymptomatic renal Leptospira carriers among cattle slaughtered in southeastern Georgia, United States. METHODS: A battery of diagnostic tests, including dark field microscopy, direct fluorescent antibody staining, polymerase chain reaction, and culture, were performed on a set of bovine kidneys (n = 37) collected from an abattoir in southeastern Georgia, United States. Virulence of a field isolate obtained from this study was tested in a hamster experimental model. RESULTS: Motile spirochete-like structures were observed by dark field microscopy in 23 (59%) out of 37 kidney samples tested. In all, 29 samples (78%) were positive by direct fluorescent antibody staining. Only 11 (29.7%) samples by polymerase chain reaction and 3 (8.1%) by culture were positive for Leptospira sp. The isolates obtained by culture were confirmed as Leptospira borgpetersenii. Hamsters experimentally infected with one of the Leptospira field isolates obtained from this study did not show clinical signs but developed renal infection with interstitial nephritis and tubular necrosis. CONCLUSIONS: This study confirms that asymptomatic Leptospira renal infection is present among cattle in the region. Our findings underscore the need for future studies to assess the potential environmental contamination and transmission to humans in contact with infected cattle.

Evaluation of novel oral vaccine candidates and validation of a caprine model of Johne's disease.

Johne's disease (JD) caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a major threat to the dairy industry and possibly some cases of Crohn's disease in humans. A MAP vaccine that reduced of clinical disease and/or reduced fecal shedding would aid in the control of JD. The objectives of this study were (1) to evaluate the efficacy of 5 attenuated strains of MAP as vaccine candidates compared to a commercial control vaccine using the protocol proposed by the Johne's Disease Integrated Program (JDIP) Animal Model Standardization Committee (AMSC), and (2) to validate the AMSC Johne's disease goat challenge model. Eighty goat kids were vaccinated orally twice at 8 and 10 weeks of age with an experimental vaccine or once subcutaneously at 8 weeks with Silirum® (Zoetis), or a sham control oral vaccine at 8 and 10 weeks. Kids were challenged orally with a total of approximately 1.44 × 10(9) CFU divided in two consecutive daily doses using MAP ATCC-700535 (K10-like bovine isolate). All kids were necropsied at 13 months post-challenge. Results indicated that the AMSC goat challenge model is a highly efficient and valid model for JD challenge studies. None of the experimental or control vaccines evaluated prevented MAP infection or eliminated fecal shedding, although the 329 vaccine lowered the incidence of infection, fecal shedding, tissue colonization and reduced lesion scores, but less than the control vaccine. Based on our results the relative performance ranking of the experimental live-attenuated vaccines evaluated, the 329 vaccine was the best performer, followed by the 318 vaccine, then 316 vaccine, 315 vaccine and finally the 319 vaccine was the worst performer. The subcutaneously injected control vaccine outperformed the orally-delivered mutant vaccine candidates. Two vaccines (329 and 318) do reduce presence of JD gross and microscopic lesions, slow progression of disease, and one vaccine (329) reduced fecal shedding and tissue colonization.

Cholesterol granuloma associated with otitis media in a cat.

An 8-year-old, male neutered Siamese cat was presented with Horner syndrome and right head tilt. A soft tissue mass was observed in the right tympanic cavity, and bulla osteotomy was performed. Tissue samples retrieved from the tympanic cavity were sent for histology, and a middle ear fluid swab was sent for bacterial culture and sensitivity. Histologic diagnosis was of otitis media associated with cholesterol granuloma (CG). Bacterial culture yielded Pasteurella multocida and Leifsonia (Corynebacterium) aquaticum. Middle ear CG is frequently seen in human beings and is associated with a variety of middle ear diseases including otitis media. Cholesterol granuloma of the middle ear has been experimentally induced in cats. The clinical and pathological findings of a spontaneous case of CG in the tympanic cavity of a cat with otitis media are described herein.

Extra-adrenal retroperitoneal paraganglioma in a dog.

An extra-adrenal retroperitoneal paraganglioma was observed in a 10.5-year-old male Boxer dog. Additionally, the dog had an aortic base tumor, multiple thyroid adenomas, multiple testicular interstitial cell tumors, bilateral nodular adrenal cortical hyperplasia, and parathyroid gland hyperplasia. The hypothesis that the retroperitoneal mass represents a primary extra-adrenal paraganglioma rather than metastatic mass from the aortic body tumor is considered. Either primary or metastatic extra-adrenal retroperitoneal paragangliomas are rarely reported in dogs.

The occurrence of Bovine viral diarrhea virus in hunter-harvested white-tailed deer (Odocoileus virginianus) in the state of Georgia, southeastern United States.

The prevalence of Bovine viral diarrhea virus (BVDV) in free-ranging white-tailed deer (WTD, Odocoileus virginianus) in the state of Georgia was evaluated using ear notches collected from hunter-harvested deer during the hunting season of 2010-2011. From September to December 2010, 367 ear samples from WTD were collected from 37 counties in Georgia. The samples were from 178 (48.5%) female deer, 187 (51%) male deer, and 2 (0.5%) of unknown sex. The age of the animals varied from 6 months to 6.5 years. The age was not recorded in 34 animals (9.3%). Of the animals with known ages, 42% were under 2 years. Screening of 367 samples for BVDV using an antigen-capture enzyme-linked immunosorbent assay (AgELISA) resulted in 364 negative samples and 3 suspect samples. The 3 suspect samples were negative for BVDV reverse transcription polymerase chain reaction (RT-PCR), virus isolation, and immunohistochemistry. A subpopulation of samples (n = 89) selected from various geographical regions also tested negative for BVDV RT-PCR. In conclusion, although a few of the samples were suspect for the presence of BVDV by AgELISA, the presence of the virus within the deer population studied could not be confirmed further.

Canine parvovirus-2b-associated erythema multiforme in a litter of English Setter dogs.

Erythema multiforme (EM) was diagnosed in a litter of English Setter puppies. The puppies developed erythematous cutaneous lesions at the age of 2 weeks. Microscopically, there was individual keratinocyte apoptosis associated with lymphocyte exocytosis in all layers of the epidermis. Intranuclear viral inclusions were seen in multiple tissues and organs. Tissues from the tongue, lymph node, spleen, skin, and small intestine were positive for Canine parvovirus-2 (CPV-2) and negative for Canine distemper virus (CDV) and Canid herpesvirus 1 by fluorescent antibody test. Negative-staining electron microscopy detected parvovirus particles in the intestinal contents. The skin and small intestine were positive for CPV-2b and negative for CDV by polymerase chain reaction. The mucocutaneous junctions and small intestines stained positive for CPV by immunohistochemistry. The present report documents CPV-2b-associated EM in a litter of English Setters and substantiates the single previous report associating EM with CPV-2. The finding suggests that CPV should be considered as a possible cause of EM in dogs.