Preparing a laboratory for the use of high-throughput sequencing as routine diagnostic test: general and technical requirements

Authors: LEBAS, BENECICTE - UNIVERSITY OF LIEGE; ADAMS, IAN - FERA SCIENCE LTD.; AI RWAHNIH, MAHER - UNIVERSITY OF CALIFORNIA, DAVIS; BAEYEN, STEVE - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; BILODEAU, GUILLAUME - CANADIAN FOOD INSPECTION AGENCY; BLOUIN, ARNAUD - UNIVERSITY OF LIEGE; BOONHAM, NEIL - UNIVERSITY OF NEWCASTLE; BRUINSMA, MAAIKE - NAKTUINBOUW; CANDRESSE, THIERRY - FRENCH NATIONAL INSTITUTE FOR AGRICULTURAL RESEARCH; CHANDELIER, ANNE - WALLOON AGRICULTURAL RESEARCH CENTER; DE JONGHE, KRIS - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; FOX, ADRIAN - FERA SCIENCE LTD.; GAAFAR, YAHYA - JULIUS KUHN INSTITUTE; GENTIT, PASCAL - FRENCH AGENCY FOR FOOD, ENVIRONMENTAL AND OCCUPATIONAL HEALTH & SAFETY (ANSES); HAEGEMANS, ANNELIES - FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; HO, WELLCOME - MINISTRY FOR PRIMARY INDUSTRIES; HURTADO-GONZALES, OSCAR; JONKERS, WILFRIED - BEJO SEEDS; KREUZE, JAN - INTERNATIONAL POTATO CENTER; KUTJNAK, DENIS - NATIONAL INSTITUTE OF BIOLOGY; LANDA, BLANCA - INSTITUTO DE AGRICULTURA; LEITE VICENTE, CLAUDIA - INSTITUTO NACIONAL DE INVESTIGAÇÃO AGRÁRIA E VETERINÁRIA; LIEFTING, LIA - MINISTRY FOR PRIMARY INDUSTRIES; LIU, MINGXIN - UNIVERSITY OF TASMANIA; MACLOT, FRANCOIS - UNIVERSITY OF LIEGE; WIGHT-MALAPI, MARTHA; MAREE, HANAO - STELLENBOSCH UNIVERSITY; MARTONI, FRANCESCO - AGRICULTURE VICTORIA; MEHLE, NATASA - NATIONAL INSTITUTE OF BIOLOGY; MINAFRA, ANGELANTONIO - INSTITUTE FOR SUSTAINABLE AGRICULTURE; MOLLOV, DIMITRE; MOREIRA, ADRIANA - FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS (FAO); NAKHLA, MARK - ANIMAL AND PLANT HEALTH INSPECTION SERVICE (APHIS); PETTER, FRANCOISE - EUROPEAN AND MEDITERRANEAN PLANT PROTECTION ORGANIZATION(EPPO); PONCHART, JULIEN - BEEODIVERSITY; RAE, ROBBIE - LIVERPOOL UNIVERSITY; REMENANT, BENOIT - FRENCH AGENCY FOR FOOD, ENVIRONMENTAL AND OCCUPATIONAL HEALTH & SAFETY (ANSES); RIVERA, YAZMIN; RODONI, BRENDAN - AGRICULTURE VICTORIA; ROENHORST, ANNELIEN - NETHERLANDS FOOD AND CONSUMER PRODUCTION SAFETY AUTHORITY(NVWA); ROLLIN, JOHAN - UNIVERSITY OF LIEGE; SALDARELLI, PASQUALE - INSTITUTE FOR SUSTAINABLE AGRICULTURE; SANTALA, JOHANNA - FINNISH FOOD SAFETY AUTHORITY; SPADARO, DAVIDE - UNIVERSITY OF TURIN; SOUZA-RICHARDS, ROSA - INTERNATIONAL SEED FEDERATION; SULTIMANIS, STEFANIE - INNOVATION, SCIENCE AND ECONOMIC DEVELOPMENT CANADA; VAN DER VLUGT, RENE - WAGENINGEN UNIVERSITY; TAMISIER, LUCIE - UNIVERSITY OF LIEGE; TRONTIN, CHARLOTTE - EUROPEAN AND MEDITERRANEAN PLANT PROTECTION ORGANIZATION(EPPO); WETZEL, THIERRY - GERMAN INSTITUTE OF PLANT NUTRITION; ZIEBELL, HEIKO - JULIUS KUHN INSTITUTE; MASSART, SEBASTIEN - UNIVERSITY OF LIEGE

Submitted to: European Plant Protection Organization Bulletin
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2022
Publication Date: 8/8/2022
Citation: Lebas, B., Adams, I., Ai Rwahnih, M., Baeyen, S., Bilodeau, G., Blouin, A., Boonham, N., Bruinsma, M., Candresse, T., Chandelier, A., De Jonghe, K., Fox, A., Gaafar, Y., Gentit, P., Haegemans, A., Ho, W., Hurtado-Gonzales, O.P., Jonkers, W., Kreuze, J., Kutjnak, D., Landa, B., Leite Vicente, C., Liefting, L., Liu, M., Maclot, F., Wight-Malapi, M., Maree, H., Martoni, F., Mehle, N., Minafra, A., Mollov, D.S., Moreira, A., Nakhla, M., Petter, F., Ponchart, J., Rae, R., Remenant, B., Rivera, Y., Rodoni, B., Roenhorst, A., Rollin, J., Saldarelli, P., Santala, J., Spadaro, D., Souza-Richards, R., Sultimanis, S., Van Der Vlugt, R., Tamisier, L., Trontin, C., Wetzel, T., Ziebell, H., Massart, S. 2022. Preparing a laboratory for the use of high-throughput sequencing as routine diagnostic test: general and technical requirements. European Plant Protection Organization Bulletin. https://doi.org/10.1111/epp.12863.
DOI: https://doi.org/10.1111/epp.12863

Interpretive Summary: High-throughput sequencing (HTS) is the most advanced diagnostic technology for plant pests and pathogens. However, HTS is the most complex diagnostics method. The use of specialized equipment, requirements of highly skilled and trained personnel and the interpretation of data are some of the main challenges. In this paper we addressed all aspects of the HTS protocols. The manuscript’s points are on nucleic acid extraction, sample preparation, sequencing, data analysis, pathogen identification, and data application. HTS use for diagnostics and regulatory purposes is widely discussed. The general and technical recommendations using HTS as a routine diagnostic test presented here can be applied for the detection and identification of any plant pest by plant health diagnostic laboratories serving diagnostics, industry, or regulatory entities.

Technical Abstract: High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous sequencing and identification of potentially any organisms present in a sample. Because of the growing interest in applying HTS for routine diagnostics in plant health laboratories, there is a need for guidelines on how to prepare the laboratory for adopting HTS testing. This paper describes general and technical recommendations to guide these laboratories on the complex process of HTS test adoption. This guide is relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants, protozoan, viroids, viruses or weeds) from any type of matrices (e.g. pure microbial culture, plant tissue, soil, water) regardless of the type of HTS technologies (e.g. amplicon sequencing, shotgun sequencing) and their application (e.g. surveillance programme, phytosanitary certification, crop protection). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics to enable broader applications in all plant health fields.