Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks

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dc.contributor.author Walsh, Aaron M.
dc.contributor.author Crispie, Fiona
dc.contributor.author Daari, Kareem
dc.contributor.author O'Sullivan, Orla
dc.contributor.author Martin, Jennifer C.
dc.contributor.author Arthur, Cornelius T.
dc.contributor.author Claesson, Marcus J.
dc.contributor.author Scott, Karen P.
dc.contributor.author Cotter, Paul D.
dc.date.accessioned 2017-06-23T13:46:39Z
dc.date.available 2017-06-23T13:46:39Z
dc.date.issued 2017-06-16
dc.identifier.citation Walsh, A. M., Crispie, F., Daari, K., O'Sullivan, O., Martin, J. C., Arthur, C. T., Claesson, M. J., Scott, K. P. and Cotter, P. D. (2017) 'Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks', Applied and Environmental Microbiology. In Press, doi: 10.1128/aem.01144-17 en
dc.identifier.issn 0099-2240
dc.identifier.uri http://hdl.handle.net/10468/4188
dc.identifier.doi 10.1128/aem.01144-17
dc.description.abstract 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. Here, we demonstrate that three short read alignment-based methods, MetaMLST, PanPhlAn, and StrainPhlAn, can accurately, and rapidly, identify pathogenic strains in spinach metagenomes which were intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employ the 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 show that nunu samples are frequently contaminated with bacteria associated with the bovine gut, and worryingly, we detect putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short read alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilisation. Importance: Foodborne pathogens are responsible for millions of illnesses, annually. Here, we demonstrate that short read alignment-based bioinformatics tools can accurately, and rapidly, detect pathogenic strains in food products from shotgun metagenomics data. The methods used here 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. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher American Society for Microbiology en
dc.rights © 2017 American Society for Microbiology en
dc.subject Foodborne pathogens en
dc.subject Bioinformatics en
dc.subject Pathogenic strains en
dc.subject Food safety en
dc.subject Nunu en
dc.subject Escherichia coli en
dc.title Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Marcus Claesson, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: m.claesson@ucc.ie en
dc.internal.availability Full text available en
dc.check.info Access to this article is restricted until 6 months after publication at the request of the publisher. en
dc.check.date 2017-12-16
dc.date.updated 2017-06-23T13:39:40Z
dc.description.version Accepted Version en
dc.internal.rssid 400214344
dc.description.status Peer reviewed en
dc.identifier.journaltitle Applied and Environmental Microbiology en
dc.internal.copyrightchecked No !!CORA!! en
dc.internal.licenseacceptance Yes en
dc.internal.IRISemailaddress m.claesson@ucc.ie en


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