Vet-LIRN antimicrobial resistance surveillance through collection of AMR data and whole genome sequencing of isolates from Canadian provinces

Project Summary/Abstract As a part of the FDA Veterinary Laboratory Information Response Network (Vet-LIRN) cooperative agreement, Animal Health Laboratory (AHL) will continue supporting Vet- LIRN’s Antimicrobial Resistance-Whole Genome Sequencing (AMR-WGS) program. Through already established process we will continue with routine collection of clinical bacterial isolates in source labs, provide AMR data for all isolates collected and ship isolates quarterly to the core lab for WGS. Every month the source labs will collect 4 isolates of Escherichia coli and 4 isolates of Staphylococcus pseudintermedius from dogs as well as four Salmonella enterica isolates from any animal species. In addition, eight isolates from the other (OTH) category (Klebsiella spp., Enterobacter spp., Enterococcus spp., Pseudomonas spp., etc.) will be collected following the sampling plan provided by Vet-LIRN. Antimicrobial susceptibility data will be provided for all of these isolates. Furthermore, four Campylobacter spp. and four aquatic bacterial pathogens will be collected monthly if available. Metadata for all collected isolates as well as the susceptibility data will be provided to Vet-LIRN on a quarterly basis. To ensure harmonization of methodology and support surge capacity testing for Vet-LIRN during large-scale emergency events, AHL will continue using MiSeq to do WGS of bacterial isolate following protocols provided by Vet-LIRN. Based on Vet-LIRN quarterly selection, a subgroup of the bacterial isolates will be sequenced, and their metadata and sequence information will be submitted to the National Center for Biotechnology Information (NCBI) database for scientific community use. AHL will also continue participating in proficiency testing provided by Vet-LIRN and GenomeTrakr.