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Standardisation and validation of metagenomics methods for the detection of foodborne zoonoses, antimicrobial resistance and emerging threats (METASTAVA)

Published 2017-11-16

The consortium consists of 6 European institutions: Veterinary andAgrochemical Research Center (CODA-CERVA) and Scientific Institute of Public Health (WIV-ISP) in Belgium, Friedrich-Loeffler-Institut (FLI) in Germany, French Agency for Food, Environmental and Occupational Health &Safety (ANSES) in France, CVI-NCOH-EMC in The Netherlands and National Veterinary Institute (SVA) in Sweden, and is coordinated by Dr Van Borm at CODA-CERVA.

Novel sequencing technologies have a huge potentialfor the unbiased characterization of the microbial and viral content of human, animal,and food samples. The potential advantages for human and animal health researchare the rapid identification of novel pathogens, the characterization ofcomplete microbial communities, and the tracking of origins, sources andtransmission pathways of infections. Here, we focus on the potentialdevelopment of catch-all diagnostics through sequencing of all RNA and DNA insamples, so called metagenomic sequencing. Metagenomic analysis is increasinglyused to identify possible causes of unexplained disease outbreaks, tocomplement routine diagnostic evaluation, and to study the role of themicrobiome and virome in health and disease. However, translating thesepromising technological developments into diagnostic tools for veterinary andpublic health laboratories requires careful validation, which is the focus ofthe current proposal. METASTAVA aims to evaluate the potential use ofmetagenomic analysis to the public health reference laboratory by targetedcollection of reference data and reference materials (WP1), by generatingfocused validation data (WP3), and by proposing criteria for a robust qualityassurance (QA) for metagenomics workflows from sample selection tointerpretation of result (WP2). The proposal will use hepatitis E virus (HEV),norovirus (NoV), zoonotic pox viruses, antibiotic resistant bacteria andShigatoxigenic Escherichia coli(STEC), also known as verotoxigenic E.coli (VTEC) as model pathogens in developing the methods and referencedatasets. We will address the following key objectives: (1) Develop a set ofreference data for the model pathogens, representing most common sample types,(2) Develop harmonized workflows for the generation and analysis of metagenomicdata fitting to a defined diagnostic scope for the model pathogens, (3) Developa validation protocol for metagenomic diagnostics (including quality assessmentand robustness testing).