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.

Pathology in Practice.

In collaboration with the American College of Veterinary Pathologists.

Characterization of a Novel Reassortant Epizootic Hemorrhagic Disease Virus Serotype 6 Strain Isolated from Diseased White-Tailed Deer (Odocoileus virginianus) on a Florida Farm.

We report an outbreak of a novel reassortant epizootic hemorrhagic disease virus serotype 6 (EHDV-6) in white-tailed deer (WTD) on a Florida farm in 2019. At necropsy, most animals exhibited hemorrhagic lesions in the lung and heart, and congestion in the lung, liver, and spleen. Histopathology revealed multi-organ hemorrhage and congestion, and renal tubular necrosis. Tissues were screened by RT-qPCR and all animals tested positive for EHDV. Tissues were processed for virus isolation and next-generation sequencing was performed on cDNA libraries generated from the RNA extracts of cultures displaying cytopathic effects. Six isolates yielded nearly identical complete genome sequences of a novel U.S. EHDV-6 strain. Genetic and phylogenetic analyses revealed the novel strain to be most closely related to a reassortant EHDV-6 strain isolated from cattle in Trinidad and both strains received segment 4 from an Australian EHDV-2 strain. The novel U.S. EHDV-6 strain is unique in that it acquired segment 8 from an Australian EHDV-8 strain. An RNAscope® in situ hybridization assay was developed against the novel U.S. EHDV-6 strain and labeling was detected within lesions of the heart, kidney, liver, and lung. These data support the novel U.S. reassortant EHDV-6 strain as the cause of disease in the farmed WTD.

Comparison of oseltamivir and α-galactosylceramide for reducing disease and transmission in pigs infected with 2009 H1N1 pandemic influenza virus.

Influenza virus infections are a major cause of respiratory disease in humans. Neuraminidase inhibitors (NAIs) are the primary antiviral medication used to treat ongoing influenza infections. However, NAIs are not always effective for controlling virus shedding and lung inflammation. Other concerns are the emergence of NAI-resistant virus strains and the risk of side effects, which are occasionally severe. Consequently, additional anti-influenza therapies to replace or combine with NAIs are desirable. Here, we compared the efficacy of the NAI oseltamivir with the invariant natural killer T (iNKT) cell superagonist, α-galactosylceramide (α-GalCer), which induces innate immune responses that inhibit influenza virus replication in mouse models. We show that oseltamivir reduced lung lesions and lowered virus titers in the upper respiratory tract of pigs infected with A/California/04/2009 (CA04) pandemic H1N1pdm09. It also reduced virus transmission to influenza-naïve contact pigs. In contrast, α-GalCer had no impact on virus replication, lung disease, or virus transmission, even when used in combination with oseltamivir. This is significant as iNKT-cell therapy has been studied as an approach for treating humans with influenza.

Central nervous system diseases of cattle in Georgia, 2001-2017.

In a review of 159 archived bovine autopsy cases submitted to the Georgia Veterinary Diagnostic Laboratory System from 2001 to 2017, we evaluated histologic lesions and other laboratory test results in cases diagnosed with central nervous system (CNS) disease to determine the most common disorders and the rate of definitive morphologic and etiologic diagnosis within the population. The most common breed was Aberdeen Angus or Angus (31%), and female animals comprised 60% of the overall submissions. Gross anatomic changes were described in 33% of cases that had histologic lesions. Suppurative meningoencephalitis was the most common diagnosis (28% of cases overall) and was frequently associated with bacterial sepsis. Lymphocytic meningoencephalitis without an identified etiology was diagnosed in 17% of cases. Polioencephalomalacia was the most commonly identified noninfectious diagnosis (17%). Hydrocephalus was the most common CNS comorbidity and potential congenital defect. Identification of specific agents was sporadic, and infectious disease testing was largely dependent on fluorescent antibody testing, almost all of which were negative. Our findings indicate the common differential diagnoses for cattle with neurologic signs in the southeastern United States, as well the need for a well-defined, methodical diagnostic approach, including autopsy, histology, and appropriate additional laboratory testing.

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.

Outbreak of equine piroplasmosis in Florida.

CASE DESCRIPTION: A 7-year-old Quarter Horse gelding was hospitalized in Ocala, Fla, because of lethargy, fever, anorexia, and swelling of distal aspects of the limbs. A tentative diagnosis of equine piroplasmosis (EP) was made on the basis of examination of a blood smear. The case was reported to the Florida State Veterinarian, and infection with Babesia equi was confirmed. The subsequent investigation included quarantine and testing of potentially exposed horses for B equi and Babesia caballi infections, tick surveillance, and owner-agent interviews. CLINICAL FINDINGS: 210 horses on 25 premises were tested for infection with EP pathogens. Twenty B equi-infected horses on 7 premises were identified; no horses tested positive for B caballi. Seven horses, including the index case, had clinical findings consistent with EP Dermacentor variabilis was considered the only potential tick vector for B equi collected, and all D variabilis specimens tested negative for Babesia organisms via PCR assay. Results of the epidemiological investigation suggested that B equi was spread by use of shared needles and possibly blood transfusions. All horses that tested positive were involved in nonsanctioned Quarter Horse racing, and management practices were thought to pose substantial risk of transmission of blood-borne pathogens. TREATMENT AND OUTCOME: Final outcome of B equi-infected horses was euthanasia, death from undetermined causes, or shipment to a US federal research facility. CLINICAL RELEVANCE: This investigation highlights the importance of collaboration between private veterinary practitioners, state veterinary diagnostic laboratories, and regulatory officials in the recognition, containment, and eradication of foreign animal disease.