Jolien D’aes from Sciensano, Belgium presented at the Nanopore Community Meeting 2021 on “Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing.” They explained that Sciensano is the Belgian science institute for food and animal safety. They monitor GMO-derived fermentation products. They may contain antimicrobial genes as resistance markers. Regulation prohibits the presence of these organisms in final products. D’aes noted that they have detected these organisms by PCR and also in some cases isolated organisms. For this study, they performed short and long de novo assembly. They performed hybrid assembly with Unicycler. The hybrid assembly with Hybrid SPAdes indicated that the construct had integrated. With Canu assembly of long reads only, the story was again different. Each assembler produced a different result with respect to the location of the construct. Next, they performed BLAST searches of the long reads. They found that the pUB110 sequence. They then filtered reads visualized. Most of the reads seem to be concatemers. This confirmed that the output of the long reads was not an artifact. Further, they found a subset of reads supporting the integration into the host genome. D’aes concluded that concatemers and unstable integration of the plasmid was detected by long-read sequencing. This approach is useful for characterizing genetically modified organisms in products that may come into contact with humans.
