Molecular Detection and Typing of Foodborne Bacterial Pathogens: A Review

Abstract

In most developed countries a sharp increase in foodborne intoxications occurs since the last decade. Amongst the bacterial pathogens, the incidence rate is highest for Campylobacter jejuni and Salmonella spp. Nucleid acid based identification and detection methods have been developed for nearly all bacterial pathogens, based on probes in hybridisation assays or primers in PCR, NASBA or RT-PCR assays. As targets for molecular identification, virulence genes, the rRNA gene region or other specific sequences can be used and several commercialised systems are already available. For the (direct) detection of pathogens in food products, several problems may be encountered: PCR inhibition by food components, contamination in sensitive PCR assays, detection of living as well as dead cells. The latter problem can be solved by using mRNA as amplification target, but for routine applications the combination of a short culturing period with a less sensitive PCR is more suitable. Direct quantification of pathogens is possible with quantitative competitive PCR using an internal standard or with kinetic quantitative PCR (TaqMan or LightCycler commercial system).In bacterial typing, distinct types, strains or clones within a pathogenic bacterial species are differentiated which is important in epidemiological studies of foodborne outbreaks but also in the “from stable to table” investigation of the whole food production chain. Compared to the classical phenotypic typing techniques, molecular typing techniques have several advantages such as general applicability and a high discriminatory power. The currently available molecular techniques can be classified according to their working principle in PCR-mediated typing techniques (RAPD, rep-PCR), typing techniques combining PCR with restriction analysis (e.g.flaA typing of C. jejuni), typing techniques based on chromosomal restriction fragment length polymorphisms (e.g. ribotyping, pulsed field gel electrophoresis or PFGE), typing techniques combining restriction digestion with selective amplification (AFLP), and plasmid analysis. Both PFGE and AFLP are proposed as likely candidates for a uniform definite molecular typing approach using appropriate software for cluster analysis and database storing of the fingerprints. For Salmonella, two typing levels can be proposed: the first important level corresponds with the serovar level and the second level can be performed by classical phage typing or molecular typing revealing clonal lineage or strain level. Several molecular techniques have a serovar dependent discriminatory power with the greatest challenge presented by the highly clonal serovar Salmonella enteritidis.KeywordsListeria MonocytogenesMolecular TypingFoodborne PathogenPhage TypingRestriction Fragment Length PolymorphismThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.