For many years, classical microbiology has been the fundamental pillar for the control and characterization of foodborne pathogens. The application of these methodologies have reduced the prevalence of those pathogens in the food production chain and protect the consumer. Despite being robust and widely validated techniques for which there are a large number of standardized working protocols, the information these methods provide is limited. Also, different techniques have to be used for isolation, identification, determination of antimicrobial resistance or virulence. This consumes an extensive amount of time and resources. Furthermore, these techniques do not allow the phylogenetic relationships of the different bacteria isolated to be determined, which is particularly important in the management of foodborne outbreaks. This requires the use of molecular techniques. In this sense, the development of next generation sequencing a new window of opportunity in the control and characterization of foodborne pathogens.

Whole genome sequencing allows us to obtain complete information of a sequenced strain in a single analysis. By combining this technique with bioinformatics tools, it is possible to obtain genome functionality, antimicrobial resistance, virulence, as well as to perform a precise tracking of foodborne outbreaks through phylogenetic analysis. On the other hand, RNA-seq is a useful tool to study the behavior of foodborne pathogens under different conditions of the food chain and to understand their resistance mechanisms. But next generation sequencing should not only be seen as a characterization tool. In addition, metagenomics can be applied to the development of new methods for the detection of foodborne pathogens. Therefore, the development of studies in this field will allow us to have a better knowledge of foodborne pathogens and the development of more efficient control methods. Therefore, the application of this technology will result in more effective consumer protection.

This Research Topic welcomes Original Research, Mini Review, Review and Method manuscripts on topics related, but not limited to, the following areas:

• Whole genome sequencing of foodborne pathogens;

• Metagenomics for detection and characterization of foodborne pathogens;

• Development of next generation sequencing methods for foodborne pathogen detection in food products;

• Transcriptomic studies to determine the behavior of foodborne pathogens under food chain conditions.

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Frontiers in Microbiology

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