Periodic Reporting for period 1 - SafeFood (Tracing allergenic plants in food products)
Reporting period: 2019-08-05 to 2021-08-04
SafeFood aimed to develop a protocol to implement the cutting-edge Nanopore sequencing technology for rapid, on-site identification of contaminants such as allergenic plant ingredients and bacteria in complex, multi-ingredient food or pharmaceutical products.
Enriching the mixture of DNA has always been the most challenging aspect of generating data for molecular biology. PCR and target sequencing are examples of enrichment. For the first time in sequencing history, enrichment can be done bioinformatically. Bioinformatical enrichment reduces costs and the time spend in the lab. However, little is known on the performance, applications, and limitations of such methods.
During this action, a protocol for the identification of contaminants using third generation sequencing and selective sequencing was developed to contribute to safer food and pharmaceutical industries.
Enriching the mixture of DNA has always been the most challenging aspect of generating data for molecular biology. PCR and target sequencing are examples of enrichment. For the first time in sequencing history, enrichment can be done bioinformatically. Bioinformatical enrichment reduces costs and the time spend in the lab. However, little is known on the performance, applications, and limitations of such methods.
During this action, a protocol for the identification of contaminants using third generation sequencing and selective sequencing was developed to contribute to safer food and pharmaceutical industries.
During the action, we tested the performance of selective sequencing to detect contaminants based on a set of dilutions of reference material. Selective sequencing coupled with third-generation sequencing showed good application for target species that are represented at one to five percent in the total available DNA. However, when is concentrations are below 0.1%, the method does perform below shotgun sequencing. In combination with other methods such as CRISPR/Cas9, selective sequencing could show higher performance. The combination of CRISPR/Cas9 and selective sequencing are promising, but concluding results are not yet available due to delays in the development of the guide RNA for the CRISPR/Cas9. Comparisons with standard methods were inconclusive.
The protocol developed here can enrich any species provided that reference material is available. It is a versatile and extremely quick tool to detect contaminants, with identifications available within 24 hours. The protocol includes standard DNA extraction, library prep sequencing, and bioinformatic analyses.
The protocol developed here can enrich any species provided that reference material is available. It is a versatile and extremely quick tool to detect contaminants, with identifications available within 24 hours. The protocol includes standard DNA extraction, library prep sequencing, and bioinformatic analyses.
One of the main missions of Quality Control solutions is to make a more secure food industry and increase the quality of the products in the food and the pharmaceutical chains. This responsibility is not to be underestimated and it is a crucial task if we want to safeguard the safety of foods and medicines. Contaminants in industrial processes are very challenging to detect and identify at timescales allowing swift interventions. This project made a small but valuable contribution to this mammoth task. Although the project’s objectives were quite specific, they contribute to developing new protocols for food safety.