Genes of concern

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.
Your path to approved studies — what happens after you contact us?
WHAT YOU DO:
1.
Contact us
Take the first step and reach out to Biosafe.
WHAT WE DO:
2.
Personalised Kick-off Meeting
Biosafe clarifies your objectives and expectations.
WHAT YOU DO:
3.
Accept the quote & provide background info
Customize our services to your unique needs.
WHAT WE DO:
4.
Clear shipment instructions
We’ve got the playbook for shipping biological samples safely.
WHAT YOU DO:
5.
Send your samples
Send your samples to Biosafe. You can also send us Whole Genome Sequencing (WGS) data.
WHAT WE DO:
6.
Comprehensive DNA sequencing and analysis service
Biosafe processes, analyses the WGS data and drafts a comprehensive report.
WHAT YOU DO:
7.
Review the WGS and bioinformatics report
We will perfect the final EFSA-compliant report with your feedback.
WHAT WE DO:
8.
Continuous support with authorities
Biosafe’s got your back, addressing post-submission queries or if any issues emerge.
Contact us

Jenny Makkonen
Project Manager, PhD
+35840 5474 110
jenny.makkonen@biosafe.fi

Daniel Blande
Bioinformatician, PhD
+35840 506 8086
daniel.blande@biosafe.fi

Lars Granlund
Project Manager
+358 40 5061 244
lars.granlund@biosafe.fi

Minna Voutilainen
Bioinformatician
+358 40 5050 913
minna.voutilainen@biosafe.fi
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