Genomic perspectives on foodborne illness

Whole-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. A "contamination episode" refers to one or more contamination events from a single source over a period of time. We examine clusters of sequenced clinical isolates of <i>Salmonella</i>, <i>Escherichia coli</i>, <i>Campylobacter</i>, and <i>Listeria</i> that differ by only a small number of mutations (SNPs) to identify features of the underlying contamination episodes. These analyses provide additional evidence that the youngest age groups have greater susceptibility to infection by <i>Salmonella</i>, <i>E. coli</i>, and <i>Campylobacter</i> than older age groups. This age bias is weaker for the common <i>Salmonella</i> serovar Enteritidis than <i>Salmonella</i> in general. A large fraction of the contamination episodes causing sickness appear to have a long duration. For example, 50% of the <i>Salmonella</i> cases are in clusters that persist for almost 3 y. 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. <i>Salmonella</i> infections in infants under 3 mo are predominantly acquired from the same contaminated food, pet food, or environmental sources as older individuals, rather than infant formula contaminated during production.