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Using next gen sequencing to detect pathogenic strains in food products

By Aaron Walsh, PhD student, APC Microbiome Institute, Teagasc Food Research


Foodborne pathogens are responsible for millions of illnesses annually.  The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole metagenome assembly, which is a computationally demanding process.

New research from our group demonstrates that three short read alignment-based methods, MetaMLST, PanPhlAn and StrainPhlAn, can accurately and rapidly identify pathogenic strains in foods which were intentionally spiked with Shiga toxin-producing Escherichia coli. Subsequently, we employed these methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product which is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples are frequently contaminated with bacteria associated with the bovine gut, and worryingly we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples.

The methods we have used are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly, and thus they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole metagenome sequencing can be used as a practical food safety tool to prevent diseases or link outbreaks to specific food products. Other potential applications of these tools involve the identification of pathogenic strains in clinical stool samples to determine the causes of foodborne outbreaks or other illnesses.

“To our knowledge, we are the first to use these tools to identify pathogens at a strain level” said Paul Cotter, leader of the project. “This has important implications in terms of the future use of this technology for food testing.”

Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks. Walsh AM, Crispie F, Daari K, O’Sullivan O, Martin JC, Arthur CT, Claesson MJ, Scott KP, Cotter PD.

Appl Environ Microbiol. 2017 Jun 16. pii: AEM.01144-17. doi: 10.1128/AEM.01144-17. [Epub ahead of print]

PMID: 28625983

Photo: Dr Fiona Crispie, Aaron Walsh, Dr Paul Cotter, APC Microbiome Institute & Teagasc Food Research Centre, Moorepark.