Skip to main content
. 2020 Dec 11;33(2):227–234. doi: 10.1177/1040638720978381

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).