Capacity for accredited pathogen WGS in veterinary diagnostics

Cornell University, Ithaca NY

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Abstract

Project Summary/Abstract There is a growing need for accredited bacterial whole genome sequencing capacity in veterinary diagnostic labs to support the mission of FDA. The capacity to perform advanced molecular characterization of bacterial isolates in a reliable manner is critical to our ability to respond quickly to suspected microbiological contamination and monitor antimicrobial resistance in animals and feed. We are one of the five Vet-LIRN whole genome sequencing reference labs and the first to achieve ISO:17025 accreditation for bacterial sequencing. Since this application optimally uses RNAses in the workflow, we have to sequester it in a dedicated area so as not to impact other clinical testing for RNA-based viral agents. In order to increase our sequencing capacity and support other network labs, we propose the following aims: 1) Expand network capacity for accredited bacterial WGS by evaluating an automated nucleic acid extraction platform. To accomplish this, we request the purchase of automation equipment to improve our capacity to provide these services under ISO:17025 scope. 2) Evaluate harmonized bioinformatics workflows with Ohio ADDL and share those with other network labs through the cloud-based GalaxyTrakr system. We will also support their efforts to obtain ISO:17025 accreditation for bacterial WGS. This work will be performed at the Vet-LIRN and NAHLN affiliated Cornell Animal Health Diagnostic Center, one of the most comprehensive veterinary diagnostic laboratories in the country. Our bacterial WGS services and previous methods development work for Vet-LIRN have supported a number of case investigations and resulted in prominent publications. We are currently supporting one other Vet-LIRN sequencing lab in obtaining ISO:17025 accreditation and will continue to sequence isolates from five additional network labs. The proposed studies will have important impacts for both human and veterinary health and will improve the capabilities of the Vet-LIRN to perform effective surveillance for food-borne pathogens.