The use of next generation sequencing for improving food safety: Translation into practice.
Balamurugan Jagadeesan,Peter Gerner-Smidt,Marc W. Allard,Sébastien Leuillet,Anett Winkler,Yinghua Xiao,Samuel Chaffron,Jos M.B.M. van der Vossen,Silin Tang,Mitsuru Katase,Peter McClure,Bon Kimura,Lay Ching Chai,John W. Chapman,Kathleen Grant +14 more
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TLDR
The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges, and how to critically interpret results and place them in a broader context.About:
This article is published in Food Microbiology.The article was published on 2019-06-01 and is currently open access. It has received 193 citations till now. The article focuses on the topics: Metagenomics & Food safety.read more
Citations
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
Outbreak of Listeriosis in South Africa Associated with Processed Meat.
Juno Thomas,N. Govender,Kerrigan McCarthy,Linda Erasmus,Tim Doyle,Mushal Allam,Arshad Ismail,Ntsieni Ramalwa,Phuti Sekwadi,Genevie Ntshoe,A.M. Shonhiwa,Vivien Essel,Nomsa P. Tau,Shannon L. Smouse,Hlengiwe M Ngomane,Bolele Disenyeng,Nicola Page,Nelesh P. Govender,Adriano Duse,Robert W. Stewart,Teena Thomas,Deon Mahoney,Mathieu Tourdjman,Olivier Disson,Pierre Thouvenot,Mylène M. Maury,Alexandre Leclercq,Marc Lecuit,Anthony M. Smith,Lucille Blumberg +29 more
TL;DR: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons.
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IoT, Big Data, and Artificial Intelligence in Agriculture and Food Industry
TL;DR: In this article , the authors present an overview of IoT, big data, and artificial intelligence (AI), and their disruptive role in shaping the future of agri-food systems, including greenhouse monitoring, intelligent farm machines, and drone-based crop imaging.
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Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms
Kostas Koutsoumanis,Ana Allende,Avelino Alvarez-Ordóñez,Declan Bolton,Sara Bover-Cid,Marianne Chemaly,Robert Davies,Alessandra De Cesare,Friederike Hilbert,Roland Lindqvist,Maarten Nauta,Luísa Peixe,Giuseppe Ru,Marion Simmons,Panagiotis N. Skandamis,Elisabetta Suffredini,Claire Jenkins,Burkhard Malorny,Ana Sofia Ribeiro Duarte,Mia Torpdahl,Maria Teresa Da Silva Felicio,Beatriz Guerra,Mirko Rossi,Lieve Herman +23 more
TL;DR: WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management.
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Typing methods based on whole genome sequencing data
Laura Uelze,Josephine Grützke,Maria Borowiak,Jens A. Hammerl,Katharina Juraschek,Carlus Deneke,Simon H. Tausch,Burkhard Malorny +7 more
TL;DR: The relevant approaches for phylogenomic studies for outbreak studies are described and an overview of selected tools for the characterization of foodborne pathogens based on WGS data are given.
References
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