Food
With the rise of whole genome sequencing over the past five years, higher resolution and more accurate data have been obtained for examining foodborne pathogens and the evolution of a set of isolates, which help health officials in identifying the source of a disease outbreak. In 2012, the GenomeTrakr project was established by the FDA, comprised of state and federal public health labs across the country, for the purposes of uploading the data obtained from sequencing microbial foodborne pathogens in real time. Over the years, the accumulation of data has included information on factors such as the geographic region, source and dates from food, environmental and clinical isolates. The data from GenomeTrakr can also be used to monitor antibiotic resistance genes.
As of August, Salmonella enterica, Listeria monocytogenes, Escherichia coli/Shigella, Campylobacter jejuni, and Vibrio parahaemolyticus are the five foodborne pathogens under surveillance on GenomeTrakr. The Salmonella database is the largest at more than 80,000 sequences; the Vibrio parahaemolyticus collection is the latest collection and contains approximately 1,000 sequences. The FDA uses this data to examine whether a sequence from an isolate that was obtained during a routine FDA inspection and uploaded to GenomeTrakr matches a set of clinical isolate sequences. If so, the Agency begins an inquiry, involving further collections of the original sample to determine whether there is a relationship between illness and processing facilities. If a link is found, the FDA implements regulatory action.
Source: R&D Magazine