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

项目摘要/摘要 作为FDA兽医实验室信息响应网络(VET-LIRN)倡议的一部分 动物健康实验室(AHL)被收购，以支持增强人类和动物食品安全 MiSeq Illumina，并受命建立一个加拿大兽医诊断实验室单位 (5个源实验室和1个WGS区域实验室)支持和推广Vet-LIRN的抗菌剂 抗性-全基因组测序(AMR-WGS)计划。这个单位成立于 2018年，该计划在2019年全年运行，细菌分离(604)，元数据和 部分菌株药敏结果收集及全基因组测序 分离株(270株)。Isolate收集在2020年第二季度放缓，原因是 新冠肺炎，还有一个实验室由于人员短缺而退出了该项目。作为一名 因此，我们这个多年项目的目标是： 1.招聘另一个来源实验室进行分离、元数据和抗菌药物敏感性研究 2021年的结果收集。 2.继续与其他来源实验室建立合作，向他们提供 提供用品，并支付隔离和数据收集的季度运费。 3.继续在AHL进行分离株收集。 4.增加AHL的喘振能力和能力，以帮助Vet-LIRN AMR 使用统一方法进行监测工作和临床疾病调查 依据： A.使用Illumina MiSeq按规程进行细菌分离的WGS 由Vet-LIRN提供。 B.参加GenomeTrakr提供的能力测试。 C.将序列信息提交给NCBI，使其公开可用。

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.