Table 1.
List and source of isolates and reference strains of the pathogens that can be detected by the targeted NGS assay.
| Pathogen | Source* |
|---|---|
| Eastern equine encephalitis virus | B |
| Equine rhinitis A virus | A |
| Equine rhinitis B virus | A |
| Equine arteritis virus | A |
| Equine herpesvirus1 | A |
| Equine herpesvirus 2 | A |
| Equine herpesvirus 3 | A |
| Equine herpesvirus 4 | A |
| Equine herpesvirus 5 | B |
| Equine influenza A virus, Miami (H3N8) | A |
| Equine influenza A virus, Prague (H7N7) | A |
| Rotavirus A, Nebraska strain | A |
| Saint Louis encephalitis virus | B |
| Western equine encephalitis virus | B |
| West Nile virus | B |
| Vesicular stomatitis virus, Indiana strain | B |
| Vesicular stomatitis virus, New Jersey strain | B |
| Clostridioides difficile strains that possess A, B, and binary toxin genes | B |
| Clostridium perfringens strains that possess alpha (α), beta (β), beta-2 (β-2) enterotoxin (CPE), epsilon (ε), iota (ι) toxin genes | B |
| E. coli strains that possess Shiga toxin 1 (stx1), intimin (eae), alpha hemolysin (hlyA), cytotoxic necrotizing factor (cnf1 and cnf2), enterotoxin (STa), fimbrial (k99), and F41 virulence factor genes | C |
| Actinobacillus sp. (A. pleuropneumoniae tested) | B |
| Anaplasma phagocytophilum | D |
| Aspergillus spp. (A. fumigatus tested) | B |
| Bordetella bronchiseptica | B |
| Borrelia burgdorferi | B |
| Chlamydia sp. (C. felis tested) | B |
| Cryptococcus spp. (C. neoformans tested) | C |
| Dermatophilus congolensis | B |
| Giardia intestinalis | C |
| Histoplasma capsulatum | B |
| Klebsiella sp. (K. pneumoniae tested) | B |
| Lawsonia intracellularis | B |
| Leptospira spp. (serovar Pomona tested) | B |
| Listeria monocytogenes | B |
| Mycoplasma sp. (M. bovis tested) | B |
| Neorickettsia risticii | E |
| Neospora caninum | F |
| Nocardia sp. (N. nova tested) | B |
| Pneumocystis carinii | B |
| Prototheca spp. (P. zopfii tested) | H |
| Pseudomonas sp. (P. aeruginosa tested) | B |
| Pythium spp. (P. insidiosum tested) | B |
| Rhodococcus equi | B |
| Salmonella spp. | B |
| Sarcocystis neurona | G |
| Sporothrix spp. (S. schenckii tested) | B |
| Staphylococcus aureus | B |
| Streptococcus equi subsp. equi (S. equi) | B |
| Streptococcus sp. (S. dysgalactiae tested) | B |
| Toxoplasma gondii | F |
A = USDA National Veterinary Services Laboratories; B = detected in a diagnostic sample and identified and isolated in the TVDIL according to a validated protocol as follows: bacterial isolates were identified via biochemical testing and a commercial microtiter system; viral isolates were identified via fluorescent antibody test or RT-qPCR; C = E. coli Reference Center, Pennsylvania State College of Agriculture Sciences, University Park, PA; D = detected in a diagnostic sample and identified via specific qPCR by the Clinical Immunology and Virology laboratory, College of Veterinary Medicine, University of Tennessee (Knoxville, TN); E = detected in a diagnostic sample by specific qPCR by the Indiana Animal Disease Diagnostic laboratory, Purdue College of Veterinary Medicine, University of Purdue (West Lafayette, IN); F = validated reference kindly provided by Drs. Chunlei Su and Rick Gerhold, University of Tennessee; G = validated reference kindly provided by Dr. Daniel K. Howe, University of Kentucky (Lexington, KY); H = validated reference kindly provided by Dr. Amy Swinford, Texas A&M Veterinary Medical Diagnostic Laboratory (College Station, TX).