Abstract:
Food-borne
outbreak investigation currently relies on the time-consuming
and challenging bacterial isolation from food, to be
able to link food-derived
strains to more easily obtained isolates from infected people. When no food isolate can be obtained,
the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food
samples could circumvent this need for isolation from the suspected source, but require downstream strain-level
data analysis
to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings
to analyse real food-borne
outbreak samples. In September 2019, a Salmonella outbreak occurred in a hotel school in Bruges,
Belgium, affecting over 200 students and teachers. Following standard procedures, the Belgian National Reference Center
for human salmonellosis and the National Reference Laboratory for Salmonella in food and feed used conventional analysis
based on isolation, serotyping and MLVA (multilocus variable number tandem repeat analysis) comparison, followed by whole-genome
sequencing, to confirm the source of the contamination over 2 weeks after receipt of the sample, which was freshly
prepared tartar sauce in a meal cooked at the school. Our team used this outbreak as a case study to deliver a proof of concept
for a short-read
strain-level
shotgun metagenomics approach for source tracking. We received two suspect food samples: the
full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After analysis, we could
prove, without isolation, that Salmonella was present in both samples, and we obtained an inferred genome of a Salmonella
enterica subsp. enterica serovar Enteritidis that could be linked back to the human isolates of the outbreak in a phylogenetic
tree. These metagenomics-derived
outbreak strains were separated from sporadic cases as well as from another outbreak
circulating in Europe at the same time period. This is, to our knowledge, the first Salmonella food-borne
outbreak investigation
uniquely linking the food source using a metagenomics approach and this in a fast time frame.
