This readme file was generated on 2025-04-17 by Joy Tomlinson GENERAL INFORMATION Title of Dataset: Molecular Detection of Pathogens in an Equine Fever Diagnostic Panel: 2019-2023 Author/Principal Investigator Information Name: Joy E. Tomlinson ORCID: 0000-0001-7365-3967 Institution: University of Pennsylvania Address: 382 W Street Road, Kennett Square, PA 19348 Email: joytom@upenn.edu Author/Associate or Co-investigator Information Name: Toby Pinn-Woodcock ORCID:0000-0003-0946-1893 Institution: Cornell University Address: 618 Tower Road, Ithaca, NY 14853 Email: tlp52@cornell.edu Date of data collection: 2024-11-22 data pulled from server. Data collection range 2019-07-26 to 2023-04-24 Geographic location of data collection: Ithaca, NY USA Information about funding sources that supported the collection of the data: none SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: n/a Links to publications that cite or use the data: Pinn-Woodcock et al., Molecular Detection of Pathogens in an Equine Fever Diagnostic Panel: 2019-2023. Equine Veterinary Journal, 2025. DOI: 10.1111/evj.14527 Links to other publicly accessible locations of the data: n/a Links/relationships to ancillary data sets: n/a Was data derived from another source? If yes, list source(s): Data pulled from a diagnostic laboratory data management system. Recommended citation for this dataset: Pinn-Woodcock TL, Aprea MS, Lejeune M, Tomlinson JE. Data from: Molecular Detection of Pathogens in an Equine Fever Diagnostic Panel: 2019-2023. ScholarlyCommons. Deposited May 5, 2025. doi: https://doi.org/10.48659/b6f0-6e54. DATA & FILE OVERVIEW File List: Tomlinson_Pinn_EFDP_2025_Readme.txt - metadata Tomlinson Pinn EFDP 2025.csv - dataset, spreadsheet of all diagnostic laboratory data pulled for this study Relationship between files, if important: n/a Additional related data collected that was not included in the current data package: n/a Are there multiple versions of the dataset? No If yes, name of file(s) that was updated: Why was the file updated? When was the file updated? METHODOLOGICAL INFORMATION Description of methods used for collection/generation of data: Data from all EFDP run at the AHDC between July 2019 and April 2023 on equids over 1 year of age was acquired from the AHDC laboratory information management system software (VetView) using the panel test code ‘EFUOP’ as the keyword. Historical information, physical examination findings, and other descriptive case information was lacking in the majority of submissions and therefore could not be evaluated or used for inclusion or exclusion criteria. Panels were excluded if any of the tests were cancelled for any reason, e.g. due to incorrect sample handling or correct sample type not supplied. Samples with no patient age reported were included. The following data from each finalized panel were captured when available: signalment, date of submission, submitting veterinarian location, EFDP PCR results (‘detected’ or ‘not detected’) and the results of other ancillary testing submitted simultaneously using the same submission form. Methods for processing the data: Patient_age column reports age as recorded in the VetView system. Ages were converted to nearest integer year in column patient_age_num. Missing data were left blank. Instrument- or software-specific information needed to interpret the data: n/a Standards and calibration information, if appropriate: n/a Environmental/experimental conditions: n/a Describe any quality-assurance procedures performed on the data: For submissions with reported age > 30, the original paper submission form was reviewed for clerical errors. None were found. People involved with sample collection, processing, analysis and/or submission: Joy Tomlinson, Toby Pinn-Woodcock, Melissa Aprea. DATA-SPECIFIC INFORMATION FOR: Tomlinson Pinn EFDP 2025.csv Number of variables: 21 Number of cases/rows: 961 Variable List: Day of Accession Received Date - Date sample was received by lab, M/D/YY Client State - State of origin of the submitting client Client Zip - Zip code of origin of the submitting client Breed - Horse breed as reported by submitter Gender - sex of the horse; castrate = gelding, male = stallion, female = mare patient_age - age of the horse at time of sampling as reported on submission form, units and format varied patient_age_num - age of the horse at time of sampling converted to nearest integer year Ancillary Tests? - whether the submission included request for other tests in addition to the EFUOP test code; Yes/No Positive Panel? - whether any of the EFUOP tests were PCR positive; 0 = no, 1 = yes # Positives? - how many of the EFUOP tests were PCR positive; integer number BCOR - Beta-coronavirus PCR result; Not Detected, POSITIVE EAD1 - Equine adenovirus-1 PCR result; Not Detected, POSITIVE EAD2 - Equine adenovirus-2 PCR result; Not Detected, POSITIVE EAR - Equine arteritis virus PCR result; Not Detected, POSITIVE EHRE - Anaplasma phagocytophilum (Ehrlichia Etui) PCR result; Not Detected, POSITIVE EHRR - Potomac Horse Fever (Ehrlichia equi, Neorickettsia equi) PCR result; Not Detected, POSITIVE EHV1PCR - Equine herpesvirus-1 PCR result; Not Detected, POSITIVE EHV4PCR - Equine herpesvirus-4 PCR result; Not Detected, POSITIVE ERHA - Equine rhinitis A virus PCR result; Not Detected, POSITIVE ERHB - Equine rhinitis B virus PCR result; Not Detected, POSITIVE IVMPCR - Influenza A virus matrix PCR result; Not Detected, POSITIVE SEQUPCR - Streptococcus equi sbsp equi (Strangles) PCR result; Not Detected, POSITIVE Ancillary? - how many ancillary tests were performed; integer number VI - virus isolation; text results of viral species ABCISO identified organism - aerobic blood culture results; text description of bacterial organism ACTHEQ ACTH baseline - equine ACTH hormone concentration; pg/mL AER CULTURE Result - aerobic culture result; text description of findings ANAER CULTURE RESULT - anaerobic culture result; text description of findings BACISO IDENTIFIED ORGANISM - aerobic culture result; text description of bacterial organism BL SMEAR BAND_NEUT% - band neutrophils observed on blood smear; % of white blood cells BL SMEAR BASO% - basophils observed on blood smear; % of white blood cells BL SMEAR EOSIN% - eosinophils observed on blood smear; % of white blood cells BL SMEAR HEMATOLOGY COMMENTS - descriptive comments on blood smear cytologic review; text BL SMEAR LYMPH% - lymphocytes observed on blood smear; % of white blood cells BL SMEAR MONO% - monocytes observed on blood smear; % of white blood cells BL SMEAR NRBC - nucleated red blood cells; #/100 white blood cells BL SMEAR OTHER_WBC% - other white blood cells observed on blood smear; % of white blood cells BL SMEAR PARASITE(S) - description of red or white blood cell parasites observed on blood smear; text BL SMEAR PLT_SMEAR - subjective evaluation of platelet numbers; adequate, low BL SMEAR RBC_MORPH - subjective description of red blood cell morphology; text BL SMEAR SEG_NEUT% - segmented neutrophils observed on blood smear; % of white blood cells BL SMEAR WBC_EX - morphologic description of WBC; text BLDAER CULTURE RESULT - aerobic blood culture result; text BMCIT RESULTS - Babesia microti PCR result; Not detected, POSITIVE CAMPYJ CULTURE RESULT - Campylobacter jejuni culture result; text CBCA BASO_A - basophils by automated complete blood count; thou/ul CBCA CH - CBCA CHCM - CBCA EOSIN_A - eosinophils by automated complete blood count; thou/ul CBCA HB - hemoglobin; g/dL CBCA HCT - hematocrit; % CBCA HEMATOLOGY COMMENTS - descriptive comments from slide review; text CBCA LUC_A - CBCA LYMPH_A - lymphocytes by automated complete blood count; thou/ul CBCA MCH - mean corpuscular hemoglobin; pg CBCA MCHC - mean corpuscular hemoglobin concentration; g/dL CBCA MCV - mean corpuscular volume; fL CBCA MONO_A - monocytes by automated complete blood count; thou/ul CBCA MPV - mean platelet volume; fL CBCA MPXI CBCA PCT CBCA PDW CBCA PLATA - platelets by automated complete blood count; thou/ul CBCA RBC - red blood cell count by automated complete blood count; thou/ul CBCA RDW - red cell distribution width by automated complete blood count; % CBCA SEG_NEUT_A - segmented neutrophil count by automated complete blood count; thou/ul CBCA WBC - white blood cell count by automated complete blood count; thou/ul CBCA WBCP - CLDT BACTERIOLOGY COMMENTS - Clostridium difficile toxin (A/B) ELISA comments; text CLDT RESULTS - Clostridium difficile toxin (A/B) ELISA; negative, positive CLPT RESULTS - Clostridium perfringens enterotoxin ELISA; negative, positive CREAT CREAT - creatinine; mg/dl CYSMR E SLIDE EVALUATION - cytology smear slide evaluation; descriptive text EHV2PCR RESULTS - Equine herpesvirus-2 PCR result; Not Detected, POSITIVE, LOW POSITIVE EHV5PCR RESULTS - Equine herpesvirus-5 PCR result; Not Detected, POSITIVE, MODERATE POSITIVE EHVN EHV1 GENOTPYE - Equine herpesvirus-1 neuropathic genotype PCR; ORF30-A2254 ELP ALPHA 1 - serum electrophoresis alpha 1 globulin; g/dL ELP ALPHA 2 - serum electrophoresis alpha 2 globulin; g/dL ELP ELP A/G - serum electrophoresis albumin/globulin ratio ELP ELP ALB - serum electrophoresis albumin; g/dL ELP GAMMA - serum electrophoresis gamma globulin; g/dL ELP T ALPHA - serum electrophoresis total alpha globulin; g/dL ELP T BETA - serum electrophoresis total beta globulin; g/dL EPGVPCRT RESULTS - Equine pegivirus PCR results; Not detected, POSITIVE EQLM OSPA - Equine Lyme multiplex outer surface protein A; MFI and interpretation (negative, equivocal, positive) EQLM OSPC - Equine Lyme multiplex outer surface protein C; MFI and interpretation (negative, equivocal, positive) EQLM OSPF - Equine Lyme multiplex outer surface protein F; MFI and interpretation (negative, equivocal, positive) EQPVPCR RESULT - Equine parvovirus-hepatitis PCR result; Not detected, Detected EQUINE IGG EQUINE IGG - Equine immunoglobulin G; mg/dL EQUINE LIVER AST - Aspartate aminotransferase; U/L EQUINE LIVER BA-R - Bile acids-resting; mg/dL EQUINE LIVER CK - Creatine kinase; U/L EQUINE LIVER DBili - Direct bilirubin; mg/dL EQUINE LIVER GGT - Gamma glutamyltransferase; U/L EQUINE LIVER GLDH - Glutamate dehydrogenase; U/L EQUINE LIVER HI - Hemolysis index; approximate measure of hemoglobin concentration in mg/dL. <20 correlates to a visual estimate of no hemolysis. EQUINE LIVER IBILI - Indirect bilirubin; mg/dL EQUINE LIVER II - Icteric index; approximate measure of the total bilirubin concentration in mg/dL and will be increased by non-bilirubin chromogens (e.g. carotenoids) EQUINE LIVER LI - Lipemia index; approximate measure of large lipid-containing particles in the sample and is weakly associated with triglycerides concentrations, attributed predominantly to chylomicrons. <30 correlates to a visual estimate of no lipemia. EQUINE LIVER SDH - Sorbitol dehydrogenase; U/L EQUINE LIVER TBILI - Total bilirubin; mg/dL EQUINE LIVER TRIG - Triglycerides; mg/dL FE P FE - Serum iron; ug/dL FE P FE %SATUR - Iron percent saturation; % FE P HI - Hemolysis index; approximate measure of hemoglobin concentration in mg/dL. <20 correlates to a visual estimate of no hemolysis. FE P II - Icteric index; approximate measure of the total bilirubin concentration in mg/dL and will be increased by non-bilirubin chromogens (e.g. carotenoids) FE P LI - Lipemia index; approximate measure of large lipid-containing particles in the sample and is weakly associated with triglycerides concentrations, attributed predominantly to chylomicrons. <30 correlates to a visual estimate of no lipemia. FE P TIBC - Total iron binding capacity; ug/dL FE P UIBC - Unsaturated iron binding capacity; ug/dL FIB-SCH FIB-SCH - Schalm's measure of fibrinogen; mg/dL FLOAT FLOAT METHOD - method of fecal flotation; text FLOAT P.COUNT - parasite egg count; integer FLOAT PARASITE ID - parasite identification; text FLOAT PARASITOLOGY COMMENTS - comments; text HISTO PATHOLOGIST - pathologist name who read histology sample; text HISTO PATHOLOGIST FINAL REPORT - histology report; text IND HI - Hemolysis index; approximate measure of hemoglobin concentration in mg/dL. <20 correlates to a visual estimate of no hemolysis. IND II - Icteric index; approximate measure of the total bilirubin concentration in mg/dL and will be increased by non-bilirubin chromogens (e.g. carotenoids) IND LI - Lipemia index; approximate measure of large lipid-containing particles in the sample and is weakly associated with triglycerides concentrations, attributed predominantly to chylomicrons. <30 correlates to a visual estimate of no lipemia. INSEQ INSULIN - Equine insulin; uIU/ml LA CBC BAND-NEUT - Band neutrophil count; thou/ul LA CBC BASO - Basophils count; thou/ul LA CBC CH - LA CBC CHCM - LA CBC CP COMMENT - clinical pathologist comment; text LA CBC EOSIN - eosinophil count; thou/ul LA CBC HB - hemoglobin; g/dL LA CBC HCT - hematocrit; % LA CBC HDW - LA CBC HEMATOLOGY COMMENTS - descriptive comments from slide review; text LA CBC LYMPH - lymphocyte count; thou/ul LA CBC MCH - mean corpuscular hemoglobin; pg LA CBC MCHC - mean corpuscular hemoglobin concentration; g/dL LA CBC MCV - mean corpuscular volume; fL LA CBC MONO - monocyte count; thou/ul LA CBC MPV - mean platelet volume; fL LA CBC MPXI - LA CBC NRBC - Nucleated red blood cell count; per 100 WBC LA CBC OTHER_WBC - Other white blood cells; thou/ul LA CBC PARASITE(S) - Description of red or white blood cell parasites observed; text LA CBC PCT - Plateletcrit; percentage of blood volume occupied by platelets LA CBC PDW - Platelet distribution width LA CBC PL_AP - Description of plasma appearance; text LA CBC PLATA - Platelets by automated complete blood count; thou/ul LA CBC RBC - Red blood cell count by automated complete blood count; thou/ul LA CBC RBC_MORPH - Description of red blood cell morphology; text LA CBC RDW - red cell distribution width by automated complete blood count; % LA CBC SEG_NEUT - segmented neutrophil count; thou/ul LA CBC TP REF - total protein; g/dL LA CBC WBC - white blood cell count; thou/ul LA CBC WBCP - LA P A/G - Albumin/globulin ratio LA P ALB - albumin; g/dL LA P AN GAP - anion gap; mEq/L LA P AST - aspartate aminotransferase; U/L LA P BUN - blood urea nitrogen; mg/dL LA P CA - calcium; mg/dL LA P CK - creatine kinase; U/L LA P CL - chloride; mEq/L LA P CREAT - creatinine; mg/dL LA P DBILI - direct bilirubin; mg/dL LA P FE - iron; ug/dL LA P FE % SATUR - iron percent saturation; % LA P GGT - gamma glutamyl transferase; U/L LA P GLDH - glutamate dehydrogenase; U/L LA P GLOBULIN - globulin; g/dL LA P GLU - glucose; mg/dL LA P HCO3 - bicarbonate; mEq/L LA P HI - Hemolysis index; approximate measure of hemoglobin concentration in mg/dL. <20 correlates to a visual estimate of no hemolysis. LA P IBILI - indirect bilirubin; mg/dL LA P II - Icteric index; approximate measure of the total bilirubin concentration in mg/dL and will be increased by non-bilirubin chromogens (e.g. carotenoids) LA P K - Potassium; mEq/L LA P LI - Lipemia index; approximate measure of large lipid-containing particles in the sample and is weakly associated with triglycerides concentrations, attributed predominantly to chylomicrons. <30 correlates to a visual estimate of no lipemia. LA P MG - magnesium; mEq/L LA P NA - sodium; mEq/L LA P NA/K - sodium/potassium ratio LA P P - phosphate; mg/dL LA P SDH - sorbitol dehydrogenase; U/L LA P TBILI - total bilirubin; mg/dL LA P TIBC - total iron binding capacity; ug/dL LA P TP - total protein; g/dL LA P UIBC - unsaturated iron binding capacity; ug/dL LAWPCR CT VALUE - Lawsonia intracellularis PCR Ct value; cycle threshold LAWPCR RESULTS - Lawsonia intracellularis PCR results; text, Not detected, Detected LEPTO BACTERIOLOGY COMMENTS - Comments on leptospirosis serology; text LEPTO L. CANICOLA - Leptospira canicola serology; titer LEPTO L. GRIPPO - Leptospira grippotyphosa serology; titer LEPTO L. HARDJO - Leptospira hardjo serology; titer LEPTO L. ICTERO - Leptospira icterohemmorhagica serology; titer LEPTO L. POMONA - Leptospira pomona serology; titer LEPTOPNL BACTERIOLOGY COMMENTS - Comments on leptospirosis serology; text LEPTOPNL L. AUTUMNALIS - Leptospira autumnalis serology; titer LEPTOPNL L. BRATISLAVA - Leptospira bratislava serology; titer LEPTOPNL L. CANICOLA - Leptospira canicola serology; titer LEPTOPNL L. GRIPPO - Leptospira grippotyphosa serology; titer LEPTOPNL L. HARDJO - Leptospira hardjo serology; titer LEPTOPNL L. ICTERO - Leptospira icterohemmorhagica serology; titer LEPTOPNL L. POMONA - Leptospira pomona serology; titer LEPTPCR CT VALUE - Leptospira spp. PCR Ct value; Cycle threshold value LEPTPCR RESULTS - Leptospira spp. PCR results; text, Not detected; Detected MIN UR P CA UR - Mineral urine panel urine calcium; mEq/L MIN UR P CREAT UR - Mineral urine panel urine creatinine; mg/dL MIN UR P MG UR - Mineral urine panel urine magnesium; mg/dL MIN UR P P UR - Mineral urine panel urine phosphate; mg/dL MINLY P AN GAP - Mineral electrolytes panel anion gap; mEq/L MINLY P CA - Mineral electrolytes panel calcium; mg/dL MINLY P CL - Mineral electrolytes panel chloride; mEq/L MINLY P HCO3 - Mineral electrolytes panel bicarbonate; mEq/L MINLY P HI - Hemolysis index; approximate measure of hemoglobin concentration in mg/dL. <20 correlates to a visual estimate of no hemolysis. MINLY P II - Icteric index; approximate measure of the total bilirubin concentration in mg/dL and will be increased by non-bilirubin chromogens (e.g. carotenoids) MINLY P K - Mineral electrolytes panel potassium; mEq/L MINLY P LI - Lipemia index; approximate measure of large lipid-containing particles in the sample and is weakly associated with triglycerides concentrations, attributed predominantly to chylomicrons. <30 correlates to a visual estimate of no lipemia. MINLY P MG - Mineral electrolytes panel magnesium; mEq/L MINLY P NA - Mineral electrolytes panel sodium; mEq/L MINLY P P - Mineral electrolytes panel phosphate; mg/dL MINLY UR P CA UR - Mineral electrolytes urine panel urine calcium; mg/dL MINLY UR P CL UR - Mineral electrolytes urine panel urine chloride; mEq/L MINLY UR P CREAT UR - Mineral electrolytes urine panel urine creatinine; mg/dL MINLY UR P K UR - Mineral electrolytes urine panel urine potassium; mEq/L MINLY UR P MG UR - Mineral electrolytes urine panel urine magnesium; mg/dL MINLY UR P NA UR - Mineral electrolytes urine panel urine sodium; mEq/L MINLY UR P P UR - Mineral electrolytes urine panel urine phosphate; mg/dL NDIK VIT E CONCENTRATION - Vitamin E alcohol in serum; ug/dL NPHVPCR CT VALUE - Nonprimate hepacivirus, aka equine hepacivirus PCR Ct value; cycle threshold value NPHVPCR RESULTS - Nonprimate hepacivirus, aka equine hepacivirus PCR; Not detected, Detected PHF RESULTS - Potomac horse fever serology; interpretation text and titer PHF VIROLOGY COMMENTS - Interpretive comments for PHF serology; text PTFE CLINICAL PATHOLOGIST - peritoneal fluid evaluation name of attending clinical pathologist; text PTFE COLOR_CY - peritoneal fluid color; text PTFE NUCL CELLS Z - peritoneal fluid nucleated cell count; thou/ul PTFE RBC FL Z - peritoneal fluid red blood cell count; thou/ul PTFE SLIDE EVALUATION - peritoneal fluid slide evaluation comments; text PTFE TURBIDITY_CY - peritoneal fluid turbidity; text PTFE VOL_CY - peritoneal fluid volume; ml REPMSR TEST RESULT - referral test for EPM CSF:serum ratio; ratio RGEN TEST RESULT - general referral test code; text RLA RESULTS - Rotavirus antigen detection, group A; text, negative, positive RSALMNC SALMONELLA CULTURE - Salmonella culture speciation; text RSEQT TEST RESULT - referral test; text RSTREQ REF CASE NO - case number for referral test RSTREQ REF DESTINATION - lab referral test sent to; text SAA SAA - serum amyloid A; ug/mL SAA VET HI - Hemolysis index; approximate measure of hemoglobin concentration in mg/dL. <20 correlates to a visual estimate of no hemolysis. SAA VET II - Icteric index; approximate measure of the total bilirubin concentration in mg/dL and will be increased by non-bilirubin chromogens (e.g. carotenoids) SAA VET LI - Lipemia index; approximate measure of large lipid-containing particles in the sample and is weakly associated with triglycerides concentrations, attributed predominantly to chylomicrons. <30 correlates to a visual estimate of no lipemia. SAA VET SAA-VET - serum amyloid A; ug/mL SALM CULTURE RESULT - salmonella culture result; text SALMISO QUANTITY - semi-quantification of salmonella culture; text SEISO IDENTIFIED ORGANISM - Streptococcus equi culture results; text SEISO QUANTITY - semi-quantification of streptococcus equi culture; text SEL SELENIUM CONCENTRATION - whole blood selenium; ug/dL SEQUCUL CULTURE RESULT - streptococcus equi culture results; text SPCR RESULTS - Salmonella PCR results; text, Not detected, POSITIVE STISO ORGANISM OBSERVED - Culture result; text STISO QUANTITY - semi-quantification of culture; text THMP ARSENIC - toxic heavy metal panel arsenic quantitation; ppm THMP CADMIUM - toxic heavy metal panel cadmium quantitation; ppm THMP LEAD - toxic heavy metal panel lead quantitation; ppm THMP SELENIUM - toxic heavy metal panel selenium quantitation; ppm THMP THALLIUM - toxic heavy metal panel thallium quantitation; ppm THMP TOXICOLOGY COMMENTS - toxicology interpretive comments; text TP TP - total protein; g/dL TRIG TRIG - triglycerides; mg/dL TWE SLIDE EVALUATION - tracheal wash slide evaluation; text URCUL CULTURE RESULT - urine culture results; text WNVIGG TEST RESULT - West Nile virus IgG serology; text INVIGME TEST RESULT - West Nile virus IgM serology; text Missing data codes: empty cell = test not run on that patient samples Specialized formats or other abbreviations used: n/a