Genomics‐based food‐borne pathogen testing and diagnostics: Possibilities for the U.S. department of agriculture's food safety and inspection service

Abstract

The use of genomic technologies at the U.S. Department of Agriculture could enhance inspection, monitoring, and risk assessment capabilities within its Food Safety and Inspection Service (FSIS). Molecular assays capable of detecting hundreds of microbial DNA sequences within a single food sample that identify food-borne pathogens of concern and characterize their traits most relevant to human health risk are of great interest for FSIS. For example, a high-density assay, or combination of assays, could screen FSIS inspected food for pathogens relevant to public health (e.g., Salmonella, Listeria, and toxic E. coli) as well as their associated virulence factors and antibiotic resistance genes. Because most genotype assays can be completed in one working day with a minimum of reagents, use of such assays could potentially save FSIS a significant amount of cost/time for analyses. Further, a genotype assay can detect specific microbial traits relevant to human health risk based on the DNA sequence of toxin producing genes, antibiotic resistance alleles, and more. By combining rapid analysis with specific data on human health risks, information from such high-density genotype assays could provide expanded support for test and hold situations, recalls, outbreak management, and microbial risk assessments (e.g., provide data needed for food-borne illness source attribution). Environ. Mol. Mutagen.

Isolation, serotype diversity and antibiogram of Salmonella enterica isolated from different species of poultry in India

“…[8,9] . Various serotype-specific PCR have also been developed for some common serovars to reduce time and cost in processing isolates by conventional serotyping which is very much labor intensive and time-consuming [10].…”

Trends in Population-Based Studies of Human Genetics in Infectious Diseases

“…For example, analysis of pathogen restriction-fragment length polymorphism has been used since the 1980s to identify epidemic strains and describe transmission patterns, and genetic changes in influenza viruses are being closely monitored for the emergence of strains with pandemic potential [27]. Researchers are currently investigating the use of additional genomic techniques to improve surveillance of food-borne pathogens [28], [29] and enhance food safety, e.g., by determining safe thresholds of contaminants for vulnerable population sub-groups [29]. Advancements in informatics have led to the development of crucial resources such as continuously updated online databases; one example is the National Center for Biotechnology Information's Entrez Genome database, which contains complete sequence data for more than 1,000 microbes (http://www.ncbi.nlm.nih.gov/sites/entrez).…”

Methods and Tools for Comparative Genomics of Foodborne Pathogens

“…Several regulatory and law enforcement agencies are actively considering the use of techniques such as high density genotype assays for pathogen identification and multilocus informative polymorphism analysis0 which may soon replace current serological and pulse field gel electrophoresis (PFGE) systems (Withee and Dearfield, 2007). Outbreak strains with identical serological and PFGE patterns have exhibited different biochemical properties; therefore, limitations of the current subtyping systems are evident (Shen et al, 2006).…”