Genomic perspectives on foodborne illness

Abstract

AbstractWhole-genome sequencing of bacterial pathogens is used by public health agencies to link cases of food poisoning caused by the same source of contamination. The vast majority of these appear to be sporadic cases associated with small contamination episodes and do not trigger investigations. We analyzed clusters of sequenced clinical isolates ofSalmonella,Escherichia coli,Campylobacter, andListeriathat differ by only a small number of mutations to provide a new understanding of the underlying contamination episodes. These analyses provide new evidence that the youngest age groups have greater susceptibility to infection fromSalmonella,Escherichia coli, andCampylobacterthan older age groups. This age bias is weaker for the commonSalmonellaserovar Enteritidis than Salmonella in general. Analysis of these clusters reveals significant regional variations in relative frequencies ofSalmonellaserovars across the United States. A large fraction of the contamination episodes causing sickness appear to have long duration. For example, 50% of theSalmonellacases are in clusters that persist for almost three years. For all four pathogen species, the majority of the cases were part of genetic clusters with illnesses in multiple states and likely to be caused by contaminated commercially distributed foods. The vast majority ofSalmonellacases among infants < 6 months of age appear to be caused by cross-contamination from foods consumed by older age groups or by environmental bacteria rather than infant formula contaminated at production sites.