KY Environmental Food Microbiology and WGS Incorporation and Expansion.

PAR-20-15 4/16/20 项目045-总结：KY环境食品微生物学和WGS公司和 膨胀 肯塔基州实验室服务部已经具备了全基因组测序的能力 (WGS)自2017年11月以来，我们购买了自己的Illumina MiSeq分析仪。 从那时起，我们已经能够为环境微生物食品实施WGS 在爆发疫情时，对临床样本进行补充检测。这 导致采取更快的行动，并提供更准确的信息，以了解食品的潜在联系， 与疫情有关的病原体。我们打算将WGS添加到我们的ISO 17025范围内， 今年秋天的认证。我们已经能够购买先进的设备，如， Qubit和QiaCube我们还接受了使用并允许进入 汉密尔顿图书馆准备机器人，我们（环境。Micro）已经过使用验证 微生物食品实验室分离物 实验室服务部是肯塔基州唯一的国家公共卫生实验室，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测试选项 尤其是在环境测试中。 我们不断地联系其他公共卫生实验室，为积压的工作提供帮助。 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，不仅用于食品分离物的测序，还用于农业用水和动物样本的测序 分离株我们已经为FDA和85个国家的大约142个李斯特菌分离株进行了测序。 美国农业部的沙门氏菌分离株自2008年以来，DLS一直在为Genome Trakr提供数据。 2018年，并积极参加Genome Trakr网络会议，电话和培训。我们的首席 分析师已经接受了Galaxy Trakr培训。目前，元数据正在提交给 基因组Trakr通过电子邮件和测序项目通过BaseSpace共享。应变 使用名称和NCBI登记（BioSample和SRR）来确认分离物 序列已上传到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 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监管食品/商品 测试以及改善我们的实验室空间，增加新的测试方法和仪器， 在某些情况下，保留合格的分析师。 1

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