Whole Genome Sequencing of Listeria monocytogenes and the Consequences for Food Manufacturers and Retailers
Dec 2019. Recent food recalls triggered by evidence of Listeria monocytogenes (L. mono) underline the need for reliable quality assurance measures to control a Listeria risk. For you as a food business operator, whole genome sequencing gives you the opportunity to get to the bottom of the cause of an infection in your facility. Ideally, you can trace a contamination back to the supplier or compare it with previous cases in the company. This makes it possible to draw conclusions about carry-overs or entries into the plant.
Consequences of Listeria in Foodstuffs
L. mono occur ubiquitously, i.e. they are omnipresent and are transmitted throughout the entire production chain. In food production, they occur both in raw materials and, above all, as recontamination germs.
They can lead to serious, even fatal, infections, especially in risk groups. For this reason, YOPIs (young, old, pregnant, immunocompromised) must play a very important role in the risk assessment of the process chain and the end product. The group most affected by listeriosis in the EU in 2017 was the elderly over 84 years of age. The mortality rate in this age group was 24%; across all age groups, the mortality rate was 9%. [EFSA Journal 2018;16(12):5500, ISSN: 1831-4732]
Listeria monocytogenes are usually psychrotrophic, which means that they multiply even in the cold, and can pose a risk to food at temperatures as low as around 2 - 4 °C. This important point plays a decisive role in the calculation of the best-before date.
Currently, the authorities are directly linking human listeriosis diseases, which originate from food-borne outbreaks of L. mono, with products and environmental samples.
So far, the relationships between case and (potential) sources have only been communicated between authorities or in specialist publications, but not for the general public as in the recent cases in the media. What are the consequences for retailers? What awaits food manufacturers?
Whole Genome Sequencing
The generic term "next generation sequencing" (NGS) refers to high-throughput sequencing technologies. One option is whole genome sequencing (WGS), in which the entire genome is sequenced.
The serotyping of L. mono is a classical method to further identify a found microbiological strain. The additional step of sequencing the whole genome of a bacterium is similar to creating a DNA profile of a human in forensics. The exact identification of the complete bacterial DNA sequence (i.e. the sequence of the bases in the deoxyribonucleic acid) makes it the unique fingerprint of a bacterium. For L. mono this means that its genome is completely registered with 2.88 million individual bases.
In contrast, in PCR methods (polymerase chain reaction), such as the microbiological qualitative detection of L. mono, only short partial DNA sequences are compared and evaluated.
Setup of Databases
The data collected during whole genome sequencing is stored in databases and can be used for further evaluation. Currently, different types are used, e.g:
- Publicly accessible, such as the GenomeTrakr der FDA
- Official, not observable
- Private, individually created for customers
The RKI (Robert Koch Institute) gathers L. mono isolates from human infections, the BfR (Federal Institute for Risk Assessment) collects corresponding isolates from product or environmental samples (sponges/swabs). Further national reference laboratories for L. mono within the EU capture data in a comparable form.
The method currently used by RKI and BfR, which was also used in the current media-effective cases, is the so-called Listeria monocytogenes cgMLST method (core genome multilocus sequence typing).
On the basis of whole genome sequencing, 1,701 gene sequences are bioinformatically evaluated and compared with the data of a public database, so that a complex type can be indicated as the result, which may already have been published in publications of the RKI (e.g. CT1248, Sieber case) or by the EFSA (European Food Safety Authority) / ECDC (European Centre for Disease Prevention and Control). There are currently about 9,000 complex types publicly known, which are being expanded very regularly and currently in large numbers.
Benefits of Sequencing
Where a link is established between specific strains and defined foods and, if applicable, environmental samples, it is possible to identify the source of different foods in relation to specific human infections.
The method can also be used in the private sector to reliably identify a source of contamination in the production plant or to limit contamination in the end product to raw materials and suppliers as part of supply chain control.
Conclusion
With the technical prerequisites, it is possible today to establish a direct connection between human cases of disease, products, companies and thus also trading companies with high precision and only very slight restrictions. Public communication plays a considerable role and must be taken into account in the risk management of every company.
Eurofins is your secure partner who can deliver the fastest and most reliable results with the appropriate diagnostics. In addition, Eurofins can provide guidance and support in the creation or verification of listeria monitoring. The Listeria monocytogenes cgMLST methodology is a completely new addition to Eurofins Germany's portfolio. It can be carried out directly after the detection/isolation of the strain or from frozen strains (-80°C). In addition to classical cultural methods, accredited PCR or immunologically based rapid detection methods are also available for food matrices and environmental samples.
