Molecular techniques for detection of foodborne bacteria

Food poisoning is the leading cause of hospitalization worldwide. The European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control reported around 360,000 hospitalizations due to confirmed foodborne infections and nearly 500 fatal cases in the European Union in 2016. Collective food poisoning outbreaks (CFTIs) are reportable. They correspond to at least two cases presenting the same symptoms and having the same food origin. On average, 1,380 outbreaks of CFTI are reported in France every year, affecting more than 12,000 people, 5% of whom are hospitalized. When a CFTI is reported to the Regional Health Agency and the Departmental Directorate for Population Protection, the suspected foodstuffs are analyzed to determine the pathogens responsible. However, the true incidence of food-borne infections is severely underestimated for many reasons, including misdiagnosis, lack of systematic testing for many bacterial agents, under-reporting (particularly of minor outbreaks) and incorrect sample collection.

Bacterial control of food is a crucial food safety issue. The importance of this practice is illustrated on the European market by pathogen detection kits, which accounted for 4 billion euros in 2018. They are expected to reach 6.5 billion euros by 2025. Epidemics caused by bacteria share a common symptomatology (diarrhea, fever, vomiting), making it difficult to identify the causal agent. Among bacterial infections, salmonellosis, campylobacteriosis and shiga toxin-producing Escherichia coli are responsible for the vast majority of illnesses, hospitalizations and deaths. Although listeriosis is not common, with Listeria monocytogenes having a lower prevalence than Campylobacter or Salmonella, it is one of the most fatal food-borne illnesses, with a fatal outcome in around 37% of cases.

Bacterial detection and enumeration methods for food matrices are traditionally based on bacterial culture on agar plates. These methods are sensitive and selective, but not well suited to the needs of the food industry and control agencies due to the long analysis times and high costs involved. Two to three days are needed to obtain the first results, and confirmation of the specific pathogen can take over a week. Time is a crucial parameter in the detection of food-borne pathogens. Other methods, such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassays and agglutination tests, are faster, taking 1-2 days to produce results. However, they are not sufficiently selective, as they are based on the use of antibodies that can produce cross-reactivity and false-positive results. As a result, molecular analysis methods based on the detection of nucleic acids (DNA or RNA) are emerging as the methods of choice. They enable pathogens to be...