Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study

Saltykova, Assia; Buytaers, Florence E.; Denayer, Sarah; Verhaegen, Bavo; Piérard, Denis; Roosens, Nancy H. C.; Marchal, Kathleen; De Keersmaecker, Sigrid C. J.

doi:10.3390/ijms21165688

Open AccessArticle

Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study

by

Assia Saltykova

^1,2,†,

Florence E. Buytaers

^1,2,†,

Sarah Denayer

³,

Bavo Verhaegen

³

,

Denis Piérard

⁴

,

Nancy H. C. Roosens

¹

,

Kathleen Marchal

^2,5,6

and

Sigrid C. J. De Keersmaecker

^1,*

¹

Transversal Activities in Applied Genomics (TAG), Sciensano, 1050 Brussels, Belgium

²

IDLab, Department of Information Technology, Ghent University, IMEC, 9052 Ghent, Belgium

³

National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC), Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium

⁴

National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC STEC), Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium

⁵

Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium

⁶

Department of Genetics, University of Pretoria, Pretoria 0083, South Africa

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this study.

Int. J. Mol. Sci. 2020, 21(16), 5688; https://doi.org/10.3390/ijms21165688

Submission received: 13 July 2020 / Revised: 4 August 2020 / Accepted: 6 August 2020 / Published: 8 August 2020

(This article belongs to the Special Issue In Silico Analyses: Translating and Making Sense of Omics Data)

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Abstract

Culture-independent diagnostics, such as metagenomic shotgun sequencing of food samples, could not only reduce the turnaround time of samples in an outbreak investigation, but also allow the detection of multi-species and multi-strain outbreaks. For successful foodborne outbreak investigation using a metagenomic approach, it is, however, necessary to bioinformatically separate the genomes of individual strains, including strains belonging to the same species, present in a microbial community, which has up until now not been demonstrated for this application. The current work shows the feasibility of strain-level metagenomics of enriched food matrix samples making use of data analysis tools that classify reads against a sequence database. It includes a brief comparison of two database-based read classification tools, Sigma and Sparse, using a mock community obtained by in vitro spiking minced meat with a Shiga toxin-producing Escherichia coli (STEC) isolate originating from a described outbreak. The more optimal tool Sigma was further evaluated using in silico simulated metagenomic data to explore the possibilities and limitations of this data analysis approach. The performed analysis allowed us to link the pathogenic strains from food samples to human isolates previously collected during the same outbreak, demonstrating that the metagenomic approach could be applied for the rapid source tracking of foodborne outbreaks. To our knowledge, this is the first study demonstrating a data analysis approach for detailed characterization and phylogenetic placement of multiple bacterial strains of one species from shotgun metagenomic WGS data of an enriched food sample.

Keywords: public health; foodborne outbreak investigation; strain-level metagenomics

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MDPI and ACS Style

Saltykova, A.; Buytaers, F.E.; Denayer, S.; Verhaegen, B.; Piérard, D.; Roosens, N.H.C.; Marchal, K.; De Keersmaecker, S.C.J. Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study. Int. J. Mol. Sci. 2020, 21, 5688. https://doi.org/10.3390/ijms21165688

AMA Style

Saltykova A, Buytaers FE, Denayer S, Verhaegen B, Piérard D, Roosens NHC, Marchal K, De Keersmaecker SCJ. Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study. International Journal of Molecular Sciences. 2020; 21(16):5688. https://doi.org/10.3390/ijms21165688

Chicago/Turabian Style

Saltykova, Assia, Florence E. Buytaers, Sarah Denayer, Bavo Verhaegen, Denis Piérard, Nancy H. C. Roosens, Kathleen Marchal, and Sigrid C. J. De Keersmaecker. 2020. "Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study" International Journal of Molecular Sciences 21, no. 16: 5688. https://doi.org/10.3390/ijms21165688

APA Style

Saltykova, A., Buytaers, F. E., Denayer, S., Verhaegen, B., Piérard, D., Roosens, N. H. C., Marchal, K., & De Keersmaecker, S. C. J. (2020). Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study. International Journal of Molecular Sciences, 21(16), 5688. https://doi.org/10.3390/ijms21165688

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Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study

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