Whole genome sequencing (WGS) provides a comprehensive view for assessing the safety of a microorganism, which can be complemented with phenotypic tests. Thanks to databases dedicated to listing antimicrobial resistance genes, virulence factors and toxin genes, as well as secondary metabolites, bioinformatics can be used to search these from sequencing data. For regulatory purposes, EFSA is leading the path in guiding applicants on how to analyse and report the data. Special attention is paid to preventing the spread of antimicrobial resistance genes through horizontal gene transfer. This is explained in the Statement on how to interpret the QPS qualification on ‘acquired antimicrobial resistance genes’. Our experts have implemented the requirements in our analysis pipeline and we are constantly updating it when new requirements are published.

Other genes of concern, i.e. virulence or toxin production -related genes, are similarly searched against up-to-date databases. Full pathways leading to the production of antimicrobial compounds or other types of secondary metabolites can also be searched. Targeted searches are feasible as well: Biosafe uses appropriate databases or searches information from literature to identify any gene or pathway you require.

When microorganisms are used as active substances in plant protection, the analysis of genes of concern differ from other regulated products. Regulation 283/2013 sets out the data requirements for active substances, and Regulation 546/2011 sets out uniform principles for evaluation and authorisation of plant protection products. To support the interpretation of the provisions of the regulations, Commission has published a more practical guidance. The SANTE/2020/12260 and SANCO/2020/12258 guidance documents deal with antimicrobial resistance and secondary metabolites, respectively. Biosafe is familiar in these requirements and uses the appropriate reporting templates.

 

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