Wastewater-based microbial genomics to enhance surveillance for foodborne pathogens - overall project summary/abstract whole genome sequencing (WGS) is an established method for identifying and…

The Food and Drug Administration awarded The Pennsylvania State University a $330,000 cooperative agreement on September 20, 2025, under the Food and Drug Administration Research program (CFDA 93.103) to conduct wastewater-based microbial genomics surveillance for foodborne pathogens.

Penn State will continue generating whole genome sequences of foodborne pathogens under Analytical Track A5 of the FDA's GenomeTrakr program and develop bioinformatic pipelines to assess the relatedness of Salmonella enterica sequences detected in wastewater metagenomes against genomes deposited in NCBI through Analytical Track A8. The work builds on an existing nine-year collaboration between Penn State and the Pennsylvania Department of Health addressing public health problems through genomic sequencing. The team brings complementary expertise in microbial genomics, epidemiology, and metagenomic analysis.

Work is performed in Pennsylvania and runs through June 30, 2030. The award obligates $330,000.

Wastewater-based microbial genomics to enhance surveillance for foodborne pathogens - overall project summary/abstract whole genome sequencing (WGS) is an established method for identifying and tracking foodborne pathogens in the united states and in other countries. Maintaining its impact requires active sequencing of circulating pathogens, and development of bioinformatic tools that are accessible and leverage the rapid growth of WGS databases. Penn state and the pennsylvania department of health have an active nine-year collaboration using WGS to address public health problems primarily through the US food and drug administration's genometrakr program. We have met all yearly goals and continuously supported a postdoctoral fellow or graduate student to collect and sequence the isolates. Over the next five years of our partnership, we propose to continue generating sequences of foodborne pathogens within analytical track A5. Simultaneously, we aim to enhance our existing wastewater-based surveillance programs by developing pipelines capable of assessing the relatedness of salmonella enterica sequences within wastewater metagenomes to genomes deposited on ncbi through analytical track A8. The team includes established investigators with complementary expertise in microbial genomics, epidemiology, and metagenomic analysis pipelines, leveraging the excellent facilities and collaborative environment of our two organizations.