The Project #METASTAVA
Start: | 1 January 2018 |
Duration: | 2 Years |
Domain: | Foodborne Zoonoses |
Keywords: | Next generation sequencing (NGS), metagenomics, method validation, diagnostics, quality assurance |
Contact: | Steven Van Borm (Sciensano) |
METASTAVA: Standardisation and validation of metagenomics methods for the detection of foodborne zoonoses, antimicrobial resistance and emerging threats
The objectives of METASTAVA were to evaluate the potential use of metagenomic analysis to the public health reference laboratory by (i) targeted collection of reference data and reference materials, (ii) generating focused validation data, and (iii) proposing criteria and tools for a robust quality assurance (QA) of metagenomic workflows from sample selection for interpretation of results.
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. 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 was the focus of this project.
METASTAVA focused on using metagenomic analysis for robust diagnostics. The project identified several important gaps in our knowledge of NGS and metagenomics that needed to be filled by the:
- 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).
Project Outputs and Outcomes
The METASTAVA project addressed the identified gaps and used 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.
Overall, METASTAVA standardised and validated metagenomics methods/guidelines for the detection of foodborne zoonoses, antimicrobial resistance and emerging threats in diagnostic laboratories. This project has helped to ensure that the diagnostic use of metagenomic methods for pathogen detection are made more accessible to public health, veterinary health and food sector laboratories.
Please read the project impact brochure, for more information on METASTAVA’s outputs and outcomes.
It is also available on Zenodo.
Project Assets
Chi-Wai Chan, M,. Roy, S., Bonifacio, J., Zhang, YY., Chhabra, P., Chan, JCM., Celma, C., Igoy, MA., Lau SL., Mohammad, KN., Vinjé, J., Vennema, H., Breuer, J., Koopmans, M., de Graaf, M. (2021). Detection of Norovirus Variant GII.4 Hong Kong in Asia and Europe, 2017-2019. Emerging Infectious Diseases. 27(1), pp 283- 293. DOI: https://doi.org/10.3201/eid2701.203351
Sikkema, RS., Pas, SD., Nieuwenhuijse, DF., O’Toole, A., Verweij, JJ., van der Linden, A., Chestakova, I., Schapendonk, C., Pronk, M., Lexmond, P., Bestebroer, T., Overmars, RJ., van Nieuwkoop, S., van den Bijllaardt, W., Bentvelsen RG., van Rijen, MML., Buiting, AGM., van Oudheusden, AJG., Diederen, BM., Bergmans, AMC., van der Eijk, A., Molenkamp, R., Rambaut, A., Timen, A., Kluytmans, JAJW., Oude Munnink, BB., Kluytmans van den Bergh, MFQ., Koopmans, MPG. (2021). COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study. The Lancet: Infectious Disease. 20(11), p1273-1280. DOI: https://doi.org/10.1016/S1473-3099(20)30527-2
Izquierdo-Lara, R,, Elsinga, G., Heijnen, L., et al. (2021). Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium. Emerging Infectious Diseases. 27(5), 1405-1415. DOI: https://doi.org/10.3201/eid2705.204410
Van Borm, S., Vanneste, K., Fu, Q. et al. (2020). Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea. Virus Genes 56, 696–704. DOI: https://doi.org/10.1007/s11262-020-01791-z
Oude Munnink, BB., Nieuwenhuijse, DF., Stein, M., O’Toole, A., Haverkate, M., Mollers, M., Kamga, SK., Schapendonk, C., Pronk, M., Lexmond, P., van der Linden, A., Bestebroer, T., Chestakova, I., Overmars, RJ., van Nieuwkoop, S., Molenkamp, R., van der Eijk, AA,. Geurtsvan Kessel, C., Vennema, H., Meijer, A., Rambaut, A., van Dissel, J., Sikkema, RS., Timen, A., Koopmans, M. (2020). Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nature Medicine. 26, p 1405–1410. DOI: https://doi.org/10.1038/s41591-020-0997-y
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