KY Environmental Food Microbiology and WGS Incorporation and Expansion.

肯塔基州环境食品微生物学和 WGS 合并和扩展。

• 批准号: 10174084
• 负责人: Beth D Johnson
• 金额: $ 11万
• 依托单位: KY ST CABINET/HEALTH/FAMILY SERVICES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10174084
• 关键词: KY; Environmental; Food; Microbiology; WGS

PAR-20-15 4/16/20 Project 045-Summary: KY Environmental Food Microbiology and WGS Incorporation and Expansion The Kentucky Division of Lab Services has had the capability for Whole Genome Sequencing (WGS) since November of 2017, with the purchase of our own Illumina MiSeq analyzer. Since that time, we have been able to implement WGS for environmental microbiological food samples to complement testing performed on clinical samples in outbreak situations. This has resulted in faster action taken with more accurate information for potential linkage of food pathogens implicated in outbreaks. We intend to add WGS to our ISO17025 scope of accreditation this fall. We have been able to purchase advanced equipment such as, the Qubit and the QiaCube. We have also been trained to use and allowed access to the Hamilton Library Preparation Robot which we (Env. Micro) have already validated for use with the microbiology food lab isolates. Division of Lab Services, is the only State Public Health lab in KY and we are heavily relied upon to provide the most up to date and reliable testing options in all areas of public health but especially in environmental testing. We continually reach out to other public health labs offering assistance on backlogged samples and have established relationships with some FDA/FERN labs, as well as USDA labs, for sequencing of not only food isolates but agricultural water and animal sample isolates. We have sequenced approximately 142 Listeria isolates for the FDA and 85 Salmonella isolates for the USDA. DLS has been contributing data to Genome Trakr since 2018 and is active in the Genome Trakr network meetings, calls, and trainings. Our lead analyst has gone through the Galaxy Trakr training. Currently, metadata is being submitted to Genome Trakr via email and sequencing projects are shared through BaseSpace. Strain name and NCBI accessions (BioSample and SRR) are used to confirm that the isolate sequences have been uploaded to the NCBI Pathogen Detection Browser. The goal is that DLS will develop the capability to submit metadata and sequences in real-time to NCBI directly, using the NCBI submission portal in coordination with FDA/CFSAN. We rely greatly on Federal funding to sustain the majority of Regulatory food/commodity testing as well as improving our lab space, adding new test methods and instrumentation and in some cases, qualified analyst retention. 1

PAR-20-15 4/16/20 项目 045-摘要：KY 环境食品微生物学和 WGS 合并和 扩张 肯塔基州实验室服务部已具备全基因组测序能力 (WGS) 自 2017 年 11 月起，购买了我们自己的 Illumina MiSeq 分析仪。 从那时起，我们就能够对环境微生物食品实施全基因组测序（WGS） 样本以补充疫情爆发时对临床样本进行的测试。这有 导致采取更快的行动，获得更准确的信息，以实现食品的潜在联系 与疫情有关的病原体。我们打算将 WGS 添加到我们的 ISO17025 范围中 今年秋天获得认证。我们已经能够购买先进的设备，例如 量子位和 QiaCube。我们还接受过使用和允许访问的培训 我们 (Env. Micro) 已验证其使用的 Hamilton 文库制备机器人 与微生物食品实验室分离。 实验室服务部是肯塔基州唯一的州立公共卫生实验室，我们受到高度依赖 致力于在公共卫生的所有领域提供最新、可靠的检测选项 但尤其是在环境测试方面。 我们不断与其他公共卫生实验室联系，为积压的问题提供帮助 样品并与一些 FDA/FERN 实验室以及 USDA 建立了关系 实验室，不仅可以对食品分离物进行测序，还可以对农业用水和动物样本进行测序 隔离。我们已为 FDA 对大约 142 个李斯特菌分离株进行了测序，并对 85 个李斯特菌分离株进行了测序。 美国农业部分离沙门氏菌。自此以来，DLS 一直在向 Genome Trakr 贡献数据 2018 年，积极参加 Genome Trakr 网络会议、电话会议和培训。我们的领先 分析师已接受 Galaxy Trakr 培训。目前，元数据正在提交给 Genome Trakr 通过电子邮件和测序项目通过 BaseSpace 共享。拉紧 名称和 NCBI 登记号（BioSample 和 SRR）用于确认分离株 序列已上传至 NCBI 病原体检测浏览器。目标是 DLS 将开发向 NCBI 实时提交元数据和序列的能力 与 FDA/CFSAN 协调，直接使用 NCBI 提交门户。 我们很大程度上依赖联邦资金来维持大部分监管食品/商品 测试并改善我们的实验室空间，添加新的测试方法和仪器， 在某些情况下，合格的分析师会被保留。 1