METASTAVA: Standardisation and validation of metagenomics methods for the detection of foodborne zoonoses, antimicrobial resistance and emerging threats
|Start:||1 January 2018|
|Keywords:||Next generation sequencing (NGS), metagenomics, method validation, diagnostics, quality assurance|
|Contact:||Steven Van Borm (Sciensano)|
The Project #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 and tools for a robust quality assurance (QA) of metagenomic workflows from sample selection to interpretation of result .
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. Currently, standardisation of metagenomics data generation and analysis tools is being sufficiently covered by other ongoing initiatives (including COMPARE). However, translating these promising technological developments into diagnostic tools for veterinary and public health laboratories requires careful validation, which is the focus of this project.
In order to use Metagenomic analysis for robust diagnostics, METASTAVA identified several important gaps in our knowledge of NGS and metagenomics that must be filled:
- Development of a set of reference data for the model pathogens, representing most common sample types
- Development of harmonized workflows for the generation and analysis of metagenomic data fitting to a defined diagnostic scope for the model pathogens
- Development of a validation protocol for metagenomic diagnostics (including quality assurance and robustness testing).
The METASTAVA project is addressing the identified gaps and using hepatitis E virus (HEV), norovirus (NoV), zoonotic pox viruses, antibiotic resistant bacteria and Shigatoxigenic Escherichia coli (STEC), as model pathogens in developing the methods and reference datasets.
In short, where ongoing initiatives invest in the standardization of metagenomics tool sets, METASTAVA wants to bring metagenomics to the diagnostic laboratory.
Van Borm, S., Fu, Q.,Winand, R.,Vanneste, K., Hakhverdyan, M., Höper, D., Vandenbussche, F. Evaluation of a commercial exogenous internal process control for diagnostic RNA virus metagenomics from different animal clinical samples. (2020). Journal of Virological Methods, 283. DOI: https://doi.org/10.1016/j.jviromet.2020.113916