Bioinformatics services at Biosafe provide genome-based safety assessments of microorganisms. Usually, we start with DNA isolation and carry out genome assembly and annotation after sequencing. A pipeline has been developed in-house to obtain the needed information from the genome in a cost-effective manner. As bioinformatics is a fast-developing field, no exact methods are recommended by EFSA or by other authorities. Biosafe closely monitors possible changes in the requirements and if so, we adjust the pipeline without delay.
Unequivocal taxonomic identification at the species level is a crucial requirement. It is also essential for granting the QPS (qualified presumption of safety) status for a microorganism. Sometimes the taxonomic analysis leads to the description of a new species.
Genes of concern are searched for from the genome. These include putative antimicrobial resistance genes as well as those related to toxicity and pathogenicity.
EFSA recommends certain identity, similarity and coverage thresholds for those genes that should be reported and assessed. Usually, we assess genome safety in parallel with microbial testing. Phenotypic tests, such as antimicrobial susceptibility, help interpret the data, e.g, if the antimicrobial resistance can be linked to the presence of a known resistance gene.
For genetically modified microorganisms, we describe the genetic modifications in detail. Secondary metabolite biosynthesis clusters are searched for and assessed case-by-case.
Biosafe has assessed hundreds of genomes and has gained valuable knowledge about the characteristics of common industrial microorganisms, and what can be expected and not expected during the hazard identification step. The study reports include expert data interpretation in the light of current scientific knowledge and are ready to be delivered to the authorities as is.