As a part of the FDA Veterinary Laboratory Information Response Network (Vet-LIRN) initiative ?to support enhanced human and animal food safety? Animal Health Laboratory (AHL) acquired MiSeq Illumina and was tasked to established a Canadian veterinary diagnostics laboratory unit (5 source labs and 1 WGS regional lab) to support and expand Vet-LIRN's Antimicrobial Resistance-Whole Genome Sequencing (AMR-WGS) program. This unit was established in 2018 and the program ran throughout 2019 with bacterial isolates (604), metadata and antimicrobial susceptibility results collection and whole genome sequencing (WGS) of selected isolates (270). The isolate collection slowed down in the second quarter of 2020 because of COVID-19, and also one laboratory dropped out of the program due to a staffing shortage. As a result, our objectives for this multiyear project are: 1. To recruit another source laboratory for isolate, metadata and antimicrobial susceptibility results collection for 2021. 2. To continue established collaboration with other source laboratories by providing them with supplies and covering quarterly shipping expenses for isolates and data collection. 3. To continue with isolates collection at AHL. 4. To increase surge capacity and capability of AHL in order to aid Vet-LIRN AMR surveillance efforts and clinical disease investigations using harmonized methodology by: a. Using Illumina MiSeq to do WGS of bacterial isolates following protocols provided by Vet-LIRN. b. Participating in proficiency testing provided by GenomeTrakr. c. Submitting sequence information to NCBI to make them publicly available.
This work will increase capacity and capability of veterinary diagnostic laboratories through use of harmonized analytical methods to combat antimicrobial resistance and to swiftly respond to animal foodborne illness outbreaks. It started and will continue by laying the important groundwork in establishing antimicrobial susceptibility trends in bacterial isolates recovered from companion animals across the USA and Canada and by submitting whole genome sequences (WGS) of selected isolates to National Center for Biotechnology Information (NCBI). By gathering all information and performing WGS veterinary laboratories are building their capacity for timely responses to outbreaks while at the same time providing significant amount of data available to general scientific community through NCBI for future work (i.e., monitoring antimicrobial resistance trends, exploring virulence factors, tracing outbreak sources, etc.).
