Prospective modeling and estimating the epidemiologically informative match rate within large foodborne pathogen genomic databases.

ABSTRACT:

Objectives

Much has been written about the utility of genomic databases to public health. Within food safety these databases contain data from two types of isolates-those from patients (i.e., clinical) and those from non-clinical sources (e.g., a food manufacturing environment). A genetic match between isolates from these sources represents a signal of interest. We investigate the match rate within three large genomic databases (Listeria monocytogenes, Escherichia coli, and Salmonella) and the smaller Cronobacter database; the databases are part of the Pathogen Detection project at NCBI (National Center for Biotechnology Information).

Results

Currently, the match rate of clinical isolates to non-clinical isolates is 33% for L. monocytogenes, 46% for Salmonella, and 7% for E.

SUBMITTER: Yin L 

PROVIDER: S-EPMC11232179 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature