Next Generation Sequencing (NGS) of Bacteria – A New Tool for Food Microbiology

Next Generation Sequencing (NGS) as an Alternative to Classical Typing Techniques

Decreasing costs and analysis times for Next Generation Sequencing (NGS) approaches make this technology more and more attractive for the applications also in food analysis. Especially for microbial issues concerning food safety and food quality, Whole Genome Sequencing (WGS) of bacteria and fungi as well as Microbiota Screening and Metagenomics approaches are modern innovative analytical solutions.

Genomic Pathogen Surveillance (GPS) – A Guide for Pathogenic Contaminations

Contaminations of food products with pathogenic microorganisms can cause severe problems for food companies. They can end up in product recalls or even outbreaks with infected consumers. Three stages of contamination can be defined for the food industry:

Single pathogen finding in a production process, no contaminated product in the market so far.
Recurring findings in production processes (e.g. same production site, different places; different productions sites of the same company), no contaminated product in the market so far.
The contaminated product is already in the market, a recall becomes necessary, possibly already infected consumers.

The service „Genomic Pathogen Surveillance (GPS)“ from Eurofins Genomics can analytically support the concerned industry in all stages of pathogen contamination.

WGS of the pathogenic bacterial strains and the subsequent comparison of their genomes provide insight into their genetic relationship. Differences/similarities can be easily shown in tables and phylogenetic trees. Taking additional meta-information like e.g. date and place of finding into consideration, the source of contamination can be narrowed down and finally identified. In the case of outbreaks with infected consumers, the genome sequences of the pathogenic strains isolated from patients can be compared with those found in productions sites. Companies or their suppliers can be finally identified or excluded as source of the outbreak.

„Genomic Pathogen Surveillance (GPS)” can therefore help to find answers to the following questions:

Do all my contaminations derive from the same source?
Is my contamination involved in/responsible for a current outbreak?

Official laboratories like e.g. the Robert Koch Institute in Germany or the US Food & Drug Administration (FDA) already apply Whole Genome Sequencing (WGS) for bacterial strain characterisation. Classical typing techniques (e.g. PFGE, MLVA, MLST) will be replaced step by step by WGS in the next years. „Genomic Pathogen Surveillance (GPS)“ from Eurofins enables the food industry to lift their in-house microbial analysis on the same modern analytical level and facilitates discussions with authorities in crisis situations.

Whole Genome Sequencing as Tool for Authenticity Control of Production Strains

WGS cannot only be used in the case of microbial contamination issues. Besides that it can be a useful tool for a full characterisation of valuable productions strains. The knowledge of the whole genome sequence leads to a unique definition of the production strain. This can be very helpful in case of e.g. patent infringement issues.

Which kind of Microflora contains my Sample? ⇒ Microbiota Screening and Metagenomics

The analysis of complex bacterial or fungal mixed populations is also possible by NGS. The Microbiota Screening Services from Eurofins Genomics enable an insight into the microflora of e.g. food and environmental samples as well as fermentation processes by the use of so called barcoding regions in the bacterial resp. fungal DNA. This Microbiota Screening Service enables an identification of bacteria and fungi on species or genus level. The more comprehensive Metagenomics Service analyses the total DNA of a complex sample containing bacterial/fungal mixed populations by NGS and allows an identification of even strains and subspecies. Both approaches are independent of microbial enrichment steps and therefore include and identify also non-cultivable microorganisms.

For more information on NGS please feel free to contact us.