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公司的成立和 扩展 肯塔基州实验室服务部已经有能力进行全基因组测序 (WGS)自2017年11月起，购买了我们自己的Illumina MiSeq分析仪。 从那时起，我们已经能够对环境微生物食品实施WGS 用于补充在暴发情况下对临床样本进行检测的样本。这有 导致采取更快的行动，提供更准确的食品潜在联系信息 与疫情有关的病原体。我们打算将WGS添加到我们的ISO17025范围内 今年秋天的认证。我们已经能够购买先进的设备，如 量子比特和巧立方。我们还接受了使用培训，并允许访问 汉密尔顿图书馆准备机器人WE(环境Micro)已经过使用验证 微生物食品实验室的分离物。 实验室服务部，是肯塔基州唯一的州立公共卫生实验室，我们非常依赖 在公共卫生的所有领域提供最新和最可靠的检测选择 尤其是在环境测试方面。 我们不断联系其他公共卫生实验室，为积压的 样品，并与一些FDA/FERN实验室以及美国农业部建立了关系 实验室，不仅用于食品分离，而且用于农业水和动物样本的测序 分离株。我们已经为FDA测定了大约142株李斯特菌和85株李斯特菌的序列。 美国农业部的沙门氏菌分离株。自那以后，DLS一直在向Genome Trakr提供数据 2018年，并积极参与Genome Trakr网络会议、电话会议和培训。我们的领先优势 分析师已完成Galaxy Trakr培训。目前，元数据正在提交到 通过电子邮件和测序项目的基因组Trakr通过BaseSpace共享。菌种 NAME和NCBI访问(BiosSample和SRR)用于确认该分离物 序列已经上传到NCBI病原体检测浏览器。我们的目标是 DLS将开发向NCBI实时提交元数据和序列的能力 直接使用NCBI提交门户，与FDA/CFSAN协调。 我们在很大程度上依赖联邦资金来维持大多数受监管的食品/商品 测试以及改善我们的实验室空间，添加新的测试方法和仪器以及 在某些情况下，合格分析师的留任。 1