Standardisation and validation of metagenomics methods for the detection of foodborne zoonoses, antimicrobial resistance and emerging threats (METASTAVA)
METASTAVA aims to evaluate the potential use of metagenomic analysis to the public health reference laboratory by targeted collection of reference data and reference materials, by generating focused validation data, and by proposing criteria for a robust quality assurance for metagenomics workflows from sample selection to interpretation of result.
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 health reference laboratory by targeted
collection of reference data and reference materials (WP1), by generating
focused validation data (WP3), and by proposing criteria for a robust quality
assurance (QA) for metagenomics 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:
- Develop a set of
reference data for the model pathogens, representing most common sample types,
- Develop harmonized workflows for the generation and analysis of metagenomic
data fitting to a defined diagnostic scope for the model pathogens,
- Develop a validation protocol for metagenomic diagnostics (including quality assessment and robustness testing).