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

Aaron M. Walsh, Fiona Crispie, Kareem Daari, Orla O’Sullivan, Jennifer C Martin, Cornelius T. Arthur, Marcus J Claesson, Karen P Scott, Paul D. Cotter

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66 Citations (Scopus)
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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.
Original languageEnglish
Article numbere01144-17
Number of pages28
JournalApplied and Environmental Microbiology
Volume83
Issue number16
Early online date16 Jun 2017
DOIs
Publication statusPublished - Aug 2017

Bibliographical note

ACKNOWLEDGMENTS
We thank the researchers at the Animal Research Institute (Accra, Ghana) for their help with sample collection, storage, and processing.

This research was funded by Science Foundation Ireland in the form of a center grant (APC Microbiome Institute grant SFI/12/RC/2273). Research in the Cotter laboratory is also funded by Science Foundation Ireland through grant 11/PI/1137. O.O. is funded by Science Foundation Ireland through a Starting Investigator Research Grant (grant 13/SIRG/2160). K.D. is a PhD student funded by the Ghana Educational Trust Fund. The Rowett Institute receives funding from the Scottish Government (RESAS). The Rowett Institute receives funding from the Scottish Government strategic research portfolio (RAFE).

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