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A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking
Florence E Buytaers1,2, Assia Saltykova1,2, Sarah Denayer3
1Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.
Microorganisms
|August 9, 2020
Summary
Shotgun metagenomics can identify foodborne pathogens directly from food, bypassing lengthy isolation steps. This rapid method aids in quickly linking food contamination to human cases for effective outbreak investigation.
Area of Science:
- Food microbiology
- Genomics
- Public health
Background:
- Effective foodborne outbreak management relies on swift identification of the contaminated food source.
- Traditional methods involve pathogen isolation and real-time polymerase chain reaction (qPCR), which can be time-consuming and not always successful.
- Whole genome sequencing (WGS) offers high-resolution strain characterization and contamination source tracing but requires prior bacterial isolation.
Purpose of the Study:
- To develop and validate a method for characterizing foodborne pathogens directly from food matrices without prior isolation.
- To enable rapid linkage of foodborne pathogens to human cases for improved outbreak investigation and source tracking.
- To establish a practical workflow for reference laboratories using shotgun metagenomics.
Main Methods:
- A shotgun metagenomics approach was developed and tested using Shiga toxin-producing Escherichia coli (STEC) spiked into various food matrices.
- Optimization of DNA extraction kits and enrichment procedures was performed to establish a practical workflow.
- The method's ability to infer pathogen genomes and characterize strains was compared to standard methods (ISO/TS 13136:2012) and WGS of isolates.
Main Results:
- Shotgun metagenomics successfully generated comparable genomic information to conventional methods and WGS, but in a significantly shorter timeframe.
- The method was effective for characterizing different E. coli strains, including mixed STEC strains, directly within food samples.
- For the first time, individual foodborne pathogen strains were successfully linked to isolates from human cases using shotgun metagenomics.
Conclusions:
- Shotgun metagenomics provides a feasible and rapid alternative for characterizing foodborne pathogens directly from food vehicles.
- This approach significantly accelerates outbreak investigations and enhances the accuracy of source tracking by linking food and human isolates.
- The developed method offers a powerful tool for public health laboratories to improve the management of foodborne disease outbreaks.
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