Standardisation and validation of metagenomics methods for the detection of foodborne zoonoses, antimicrobial resistance and emerging threats.
Novel sequencing technologies have a huge potential for the unbiased characterization of the microbial and viral content of human, animal, and food samples. The potential advantages for human and animal health research are the rapid identification of novel pathogens, the characterization of complete microbial communities, and the tracking of origins, sources and transmission pathways of infections. Here, we focus on the potential development of catch-all diagnostics through sequencing of all RNA and DNA in samples, so called metagenomic sequencing. Metagenomic analysis is increasingly used to identify possible causes of unexplained disease outbreaks, to complement routine diagnostic evaluation, and to study the role of the microbiome and virome in health and disease. However, translating these promising technological developments into diagnostic tools for veterinary and public health laboratories requires careful validation, which is the focus of the current proposal. METASTAVA aims to evaluate the potential use of metagenomic analysis to the public and animal health reference laboratory by targeted collection of reference data and reference materials (WP1), by generating focused analytical validation data (WP3), and by proposing criteria and tools for a robust quality assurance (QA) of metagenomic workflows from sample selection to interpretation of result (WP2). The proposal will use hepatitis E virus (HEV), norovirus (NoV), zoonotic pox viruses, antibiotic resistant bacteria and Shigatoxigenic Escherichia coli (STEC), also known as verotoxigenic E. coli (VTEC) as model pathogens in developing the methods and reference datasets. We will address the following key objectives: (1) Develop a set of reference data for the model pathogens, representing most common sample types, (2) Develop harmonized workflows for the generation and analysis of metagenomic data fitting to a defined diagnostic scope for the model pathogens, (3) Develop a validation protocol for metagenomic diagnostics (including quality assurance and robustness testing), (4) provide analytical validation data on targeted pathogens and sample matrices to guide the diagnostic interpretation of metagenomics. In short, where ongoing initiatives invest in the development and standardization of metagenomics sequencing and data analysis tool sets, METASTAVA wants to bring metagenomics closer to the diagnostic laboratory.