Research project
36 | monthsGMS_TRADITFOOD

Genome-based microbiological safety assessment of traditional italian foods

Related toSpoke 03

Principal investigators
Daniela Bassi,Pier Sandro Cocconcelli,
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Highlights

Task involved

Task 3.1.1.

Standard protocols (ISO), whole genome sequencing (WGS), computational methodologies, and MetaOmic approaches (metagenomics, metatrascriptomics, metabolomics, lipidomics, culturomics and phenomics) will be applied for the identification and characterization of the new and (re)-emerging chemical and biological hazards in traditional products, related to climate changes, microbial evolution, and modifications in the manufacturing processes. Omics techniques will also be applied to study factors affecting the survival and the stress resistance mechanisms of pathogens and antimicrobial resistant (AMR) bacteria during food processing and shelf life. In addition, a CAD-based automatic feature recognition procedure will be developed for hygienic design of food machinery, as a prerequisite for GMP in food production.

Task 3.1.4

A guideline of actual risks and benefits for the food chain will be realised to promote an independent point of view. Safety of bacteria derived from genome editing (GE) by using intragenesis and synthetic biology will be assessed using model organisms. The RA will be conducted considering deliberate release for food production or for fermentations in confined environments. WGS approaches for RA of GE-strains will be applied. Lab-scale models to study the fate of GE- bacteria and their DNA will be developed following recent EFSA indications.

Project deliverables

D3.1.1.1.

Database of WGS data of foodborne pathogens (M24)

D3.1.1.2.

Omics protocols to evaluate food safety

D3.1.1.3.

Report on RA of Italian traditional foods (M36)

D3.1.1.4.

Identification of AMR risk factors in food products

D3.1.1.5.

Report on consolidated RA workflows for the identification, prioritisation, and characterization of (re)emerging risks

D3.1.4.1.

Systematic review on GMO and NBT practical case studies (M36)

D3.1.4.2.

Completion of risk assessment of GE bacteria (M36)

Interaction with other spokes

State of the art

The microbiological risk assessment (MRA) is a main component of the EU strategy for food safety. In the last years the classical methodologies for MRA, based on epidemiological data and physiological characterization of isolate strains, has been complemented with genomics and, more recently, metagenomics and other omics approaches. Although genomic analyses are already embedded in the risk assessment procedures, these has been rarely applied to the study of traditional food. Moreover, the currently used approaches present limitations, e.g. in the antimicrobial resistance (AMR) genes identification (intrinsic versus acquired resistances) and virulence characterization.

Operation plan

UNICATT will contribute to the culture collection of ONFOODS, composed by relevant microbial strains, for which the whole genome sequencing (WGS) is available or will be elucidated during ONFOODS activities. Data (origin, phenotypic and molecular characterization, WGS, annotation) will be included in the database. UNICATT will focus on traditional Italian foods of animal origin (cheese and meat products), including protected denomination of origin (PDO) foods. Pathogens (e.g. STEC, B. cereus, Salmonella, L. monocytogenes) and potential pathogens (e.g. enterococci) will be isolated, WGS determined and analysed, focusing identification, virulence determinants, AMR genes (intrinsic/acquired), mobile genetic island and environmental adaptation factors. Phylogenomics analysis will be performed on the strains isolated from the different units and traditional foods. Innovative approach will be used in the WGS analysis overcoming the existing limitations in the identification of intrinsic or acquired AMR and significant virulence factors.

Expected results

The main aim is the WGS-based risk assessment of the pathogenic bacteria from the traditional Italian foods, a fundamental step to design risk mitigation strategies to reduce the risks associated with newly identified, emerging and re-emerging risks (e.g. STEC in raw milk cheese, Salmonella in dry fermented sausages). The omic approaches and the comparison of strains included in the database also with those isolated from other sources, including the clinical samples, will provide a better knowledge of the features (virulence, AMR and environmental adaption) of strains from traditional foods. Moreover, bioinformatic analyses for safety assessment will be constructed to ensure error-free diagnostics and thorough wet-lab procedures will be carried out to validate WGS assessment.