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) 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.