Guidance document for WGS-laboratory procedures
Contributors
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1.
Istituto Superiore di Sanità
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2.
Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail
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3.
National Institute for Public Health and the Environment
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4.
Technical University of Denmark
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5.
Swedish Veterinary Agency
- 6. Swedish Food Agency - Livsmedelsverket
Description
The use of whole genome sequencing (WGS) for diagnostics and surveillance of pathogenic microorganisms is becoming more and more widespread. Common applications include the identification of pathogens (bacteria, viruses, and parasites), investigation of antimicrobial resistance (AMR) determinants, virulence gene detection and investigations of outbreaks.
The availability of high quality DNA is a prerequisite for the successful application of WGS methodologies. In this regard, efficient DNA extraction is strongly influenced by the nature of the pathogen and by the possibility to use in vitro culture systems prior to it. In the case of uncultivable pathogens (e.g., most parasites), enrichment procedures are needed to purify the target organisms from the outnumbering number of unrelated organisms, including the host.
This guidance document provides a list of the available Standard Operating Procedures (SOPs) or Laboratory Operating Procedures (LOPs) for nucleic acid extraction, to validate the performances and suitability for the NRLs network. In addition, information was sought on procedures that can potentially reduce the time from culture to sequencing, using different library preparation and sequencing kits.
Files
Biorisks EURLs WG on NGS - Del3-Guidance document for WGS-laboratory procedures-Caccio-20210322-v1.pdf
Files
(3.8 MB)
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