Data standardization implementation and applications within and among diagnostic laboratories: integrating and monitoring enteric coronaviruses
de S. Magalhães, Edison
Every day, thousands of samples from diverse populations of animals are submitted to veterinary diagnostic laboratories (VDLs) for testing. Each VDL has its own laboratory information management system (LIMS), with processes and procedures to capture submission information, perform laboratory tests, define the boundaries of test results (i.e., positive or negative), and report results, in addition to internal business and accounting applications. Enormous quantities of data are accumulated and stored within VDL LIMSs. There is a need for platforms that allow VDLs to exchange and share portions of laboratory data using standardized, reliable, and sustainable information technology processes. Here we report concepts and applications for standardization and aggregation of data from swine submissions to multiple VDLs to detect and monitor porcine enteric coronaviruses by RT-PCR. Oral fluids, feces, and fecal swabs were the specimens submitted most frequently for enteric coronavirus testing. Statistical algorithms were used successfully to scan and monitor the overall and state-specific percentage of positive submissions. Major findings revealed a consistently recurrent seasonal pattern, with the highest percentage of positive submissions detected during December–February for porcine epidemic diarrhea virus, porcine deltacoronavirus, and transmissible gastroenteritis virus (TGEV). After 2014, very few submissions tested positive for TGEV. Monitoring VDL data proactively has the potential to signal and alert stakeholders early of significant changes from expected detection. We demonstrate the importance of, and applications for, data organized and aggregated by using LOINC and SNOMED CTs, as well as the use of customized messaging to allow inter-VDL exchange of information.
This is a manuscript of an article published as Trevisan, Giovani, Leticia CM Linhares, Kent J. Schwartz, Eric R. Burrough, Edison de S. Magalhães, Bret Crim, Poonam Dubey, Rodger G. Main, Phillip C. Gauger, Mary Thurn, Paulo T. F. Lages, Cesar A. Corzo, Jerry Torrison, Jamie Henningson, Eric Herrman, Rob McGaughey, Giselle Cino, Jon Greseth, Travis Clement, Jane Christopher-Hennings, and Daniel C. L. Linhares. "Data standardization implementation and applications within and among diagnostic laboratories: integrating and monitoring enteric coronaviruses." Journal of Veterinary Diagnostic Investigation (2021): 10406387211002163. DOI: 10.1177%2F10406387211002163. Reprinted by permission of SAGE Publications.