Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak

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.

Usefulness of the European Epidemic Intelligence Information System in the management of an outbreak of listeriosis, Belgium, 2011

A cluster of time-linked cases and the identification of a clonal strain suggest the occurrence of an outbreak of listeriosis in Belgium in 2011, presumably due to the consumption of hard cheese made with pasteurised milk and produced by a Belgium manufacturer. The outbreak clone was identified as Listeria monocytogenes serovar 1/2a, sensitive to arsenic and cadmium and of multilocus sequence typing MLST-type 37. Food investigation of this outbreak was facilitated by the European Epidemic Intelligence Information System and data exchanged between French and Belgium listeriosis surveillance systems.

Usefulness of the European Epidemic Intelligence Information System in the management of an outbreak of listeriosis, Belgium, 2011

A cluster of time-linked cases and the identification of a clonal strain suggest the occurrence of an outbreak of listeriosis in Belgium in 2011, presumably due to the consumption of hard cheese made with pasteurised milk and produced by a Belgium manufacturer. The outbreak clone was identified as Listeria monocytogenes serovar 1/2a, sensitive to arsenic and cadmium and of multilocus sequence typing MLST-type 37. Food investigation of this outbreak was facilitated by the European Epidemic Intelligence Information System and data exchanged between French and Belgium listeriosis surveillance systems.

Lessons learned from the management of a national outbreak of Salmonella ohio linked to pork meat processing and distribution

During the summer of 2005, an increase in reports of human cases of Salmonella enterica serovar Ohio infection was observed in Belgium. During 11 weeks, between 1 July and 13 September, 60 cases of laboratory-confirmed Salmonella Ohio infection were reported to the National Reference Centre for Salmonella, with a peak onset of symptoms in the third week of July. All clinical isolates caused self-limiting gastroenteritis; both genders (32 males and 28 females) and all age groups (three children <5 years of age, three children 5 to 14 years of age, 32 adults 15 to 64 years of age, and 22 adults >65 years of age) were affected. The isolates were distributed throughout Belgium but a cluster of several cases was observed around Brussels. At the same time, an increase in the incidence of this serovar was observed in the Salmonella isolates originating from the official surveillance campaign conducted by the Federal Agency for the Safety of the Food Chain, which identified pork as a likely source of the outbreak strain. Pulsed-field gel electrophoresis typing confirmed the clonal relationship between the human isolates, the isolates from samples collected in the cutting plants, and the isolates from pork meat in distribution. Further epidemiological investigations indicated that one particular slaughterhouse was involved. In that slaughterhouse, the carcasses were contaminated during the evisceration process because of contaminated equipment and uncontrolled environmental conditions. This study highlights the importance of a centralized surveillance laboratory in the management of outbreaks and the need of strict implementation of hygienic rules to avoid this type of outbreak.

Influence of agar gel properties on the in vitro micropropagation of different clones of Thuja plicata

The influence of four agar-type polysaccharides, used as solidifying agents for culture media and differing in their sulfate content (0.14 to 10.95 % w/w), was tested on the budding and the elongation of five clones of Thuja plicata. Budding is reduced on the most sulfated polysaccharide and the differences observed between clones in elongation are as important as those observed between agar types.