KY Environmental Food Microbiology and WGS Incorporation and Expansion.

PAR-20-15 4/16/20

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