Biological safety

The microorganisms found in the food supply chain may be divided into three groups based on their health impacts:

• the first group includes indicator microorganisms, which presence in the production environment, food, water, or feed indicates hygiene problems;
  
• the second group includes the microorganisms which do not generally cause illnesses, but may cause health issues in certain conditions (such as improper storage of food);
  
• the third group includes those microorganisms which are hazardous to human health, i.e. pathogens.

The microbiology laboratories of LABRIS in Kuressaare, Tallinn, and Tartu have developed the capability to determine the most common hygiene- and safety-related microorganisms. The capability to determine rare pathogens has been concentrated to the Tartu laboratory.

Additional information:
Microbiology department
[email protected]
tel +372 738 6103 

The Tartu laboratory of LABRIS has introduced methods for detecting and characterisation rare bacterial food pathogens.

• Identification of Cronobacter spp. 
• Identification and quantification of Campylobacter spp.
• Identification of Vibrio parahaemolyticus
• Identification of Shigella spp. 
• Identification of pathogenic Yersinia enterocolitica 
• Identification of Shiga-toxin producing Escherichia coli (STEC) 
• Identification of enteropathogenic Escherichia coli (EPEC) 
• Identification of enterotoxigenic Escherichia coli (ETEC) 
• Identification of enteroaggregative Escherichia coli (EAEC) 
• Identification of enteroinvasive Escherichia coli (EIEC) 

In addition to the above, methods for the detection of coagulase-positive staphylococci (including Staphylococcus aureus), presumptive Bacillus cereus, and Clostridium perfringens have been introduced in the microbiology laboratories. Identification of those potentially hazardous microorganisms is also important, as they may produce toxins if food is stored in improper conditions.

The analysis of microorganisms is based on the methods of the International Organisation for Standardisation (ISO) and the official guidance materials of the sectoral reference laboratories of the European Union.

For the determination of other rare pathogens and/or toxins thereof, cooperation takes place with various EU laboratories and agencies.

Additional information:
Microbiology department
[email protected]
tel +372 738 6103 

Under Regulation (EU) No 2017/625 of the European Parliament and of the Council, national reference laboratories assist the state in investigating food-borne outbreaks. 

In the case of a suspected outbreak, the laboratories of LABRIS in Kuressaare, Tallinn, and Tartu have a permanent capacity to detect and quantify the most common food-borne pathogens such as Salmonella spp., Listeria monocytogenes, coagulase-positive staphylococci, presumptive Bacillus cereus, and Clostridium perfringens. 

The Tartu laboratory of LABRIS has also implemented methods for the detection of rare food pathogens in samples collected from primary production, food, feed, and the production environment. Salmonella spp., Yersinia enterocolitica, and pathogenic Escherichia coli are also detected by the real-time PCR method. For a number of pathogens, LABRIS is the only laboratory in Estonia that tests for these indicators.

Regional laboratories deliver pathogens isolated in the course of outbreak investigations to Tartu for confirmatory analyses. Confirmatory tests include further identification of isolates, serotyping, and a number of molecular biological tests. 

In the investigation of food-borne outbreaks, LABRIS cooperates with the Agriculture and Food Board and the Health Board. In collaboration with these authorities, it is possible to compare bacterial strains isolated from humans and food chain samples. This way, potential sources of outbreaks and transmission pathways are identified.

In the event of a food-borne outbreak, related analytical activities are coordinated by the microbiology department of LABRIS.

Additional information:
Microbiology department
[email protected]
tel +372 738 6103 

The Tartu laboratory of LABRIS has the capability for further identification and typing of microorganisms.

• Identification of bacteria with MALDI-TOF MS (matrix assisted laser desorption/ionization coupled with time-of-flight mass spectrometry).
• Serotyping. Conventional and molecular serotyping are used to identify serovars of Salmonella spp. Listeria monocytogenes, Escherichia coli, and Yersinia enterocolitica are serotyped using whole genome sequencing data.
• Determination of the pathogenic Yersinia enterocolitica ail gene
• Determination of toxin genes of Clostridium perfringes
• Species identification of Trichinella spp. and other parasites
• In the case of L. monocytogenes, Salmonella spp., pathogenic E. coli, Yersinia enterocolitica, Campylobacter spp., and other pathogens, whole genome sequencing (WGS)-based typing studies are used:
• to identify transmission routes and sources of food-borne outbreaks
• for the identification of the contamination of production lines by persistent strains
• for the detection of virulence and resistance genes 
• for the identification of Shiga toxin-producing Escherichia coli toxin subtypes and other virulence genes to assess the potential virulence of the pathogen
• for the detection of other Escherichia coli pathotypes (EPEC, EAEC, ETEC, EIEC)

Additional information:
Microbiology department
[email protected]
tel +372 738 6103 

The spectrum of the parasites spreading via contaminated food or water and the intermediate forms thereof is very wide. They are of different sizes from small single-cell organisms to forms which can be seen with the naked eye. Parasites may also have different life cycles. While some parasites use permanent hosts, others go through several phases of development, using different animals or humans as hosts.

LABRIS as the national reference laboratory for parasites has developed the capability to identify several food- or water-borne agents of parasitic diseases.

Additional information:
Department of bacteriology-pathology
[email protected]
+372 738 6139