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

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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 wholegenome 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.
Keywords
food surveillance, metagenomics, outbreak, Salmonella, SNP analysis, strain-level

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MLA
Buytaers, Florence, et al. “Application of a Strain- Level Shotgun Metagenomics Approach on Food Samples : Resolution of the Source of a Salmonella Food-Borne Outbreak.” MICROBIAL GENOMICS, vol. 7, no. 4, 2021, doi:10.1099/mgen.0.000547.
APA
Buytaers, F., Saltykova, A., Mattheus, W., Laisnez, V., Verhaegen, B., Roosens, N. H. C., … De Keersmaecker, S. C. J. (2021). Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak. MICROBIAL GENOMICS, 7(4). https://doi.org/10.1099/mgen.0.000547
Chicago author-date
Buytaers, Florence, Assia Saltykova, Wesley Mattheus, Valeska Laisnez, Bavo Verhaegen, Nancy H. C. Roosens, Kevin Vanneste, et al. 2021. “Application of a Strain- Level Shotgun Metagenomics Approach on Food Samples : Resolution of the Source of a Salmonella Food-Borne Outbreak.” MICROBIAL GENOMICS 7 (4). https://doi.org/10.1099/mgen.0.000547.
Chicago author-date (all authors)
Buytaers, Florence, Assia Saltykova, Wesley Mattheus, Valeska Laisnez, Bavo Verhaegen, Nancy H. C. Roosens, Kevin Vanneste, Naiima Hammami, Brigitte Pochet, Vera Cantaert, Kathleen Marchal, Sarah Denayer, and Sigrid C. J. De Keersmaecker. 2021. “Application of a Strain- Level Shotgun Metagenomics Approach on Food Samples : Resolution of the Source of a Salmonella Food-Borne Outbreak.” MICROBIAL GENOMICS 7 (4). doi:10.1099/mgen.0.000547.
Vancouver
1.
Buytaers F, Saltykova A, Mattheus W, Laisnez V, Verhaegen B, Roosens NHC, et al. Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak. MICROBIAL GENOMICS. 2021;7(4).
IEEE
[1]
F. Buytaers et al., “Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak,” MICROBIAL GENOMICS, vol. 7, no. 4, 2021.
@article{8708272,
  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 wholegenome 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.}},
  articleno    = {{000547}},
  author       = {{Buytaers, Florence and Saltykova, Assia and Mattheus, Wesley and Laisnez, Valeska and Verhaegen, Bavo and Roosens, Nancy H. C. and Vanneste, Kevin and Hammami, Naiima and Pochet, Brigitte and Cantaert, Vera and Marchal, Kathleen and Denayer, Sarah and De Keersmaecker, Sigrid C. J.}},
  issn         = {{2057-5858}},
  journal      = {{MICROBIAL GENOMICS}},
  keywords     = {{food surveillance,metagenomics,outbreak,Salmonella,SNP analysis,strain-level}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{11}},
  title        = {{Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak}},
  url          = {{http://dx.doi.org/10.1099/mgen.0.000547}},
  volume       = {{7}},
  year         = {{2021}},
}

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