Strain-level identification of bacteria persisting in food and in food processing facilities: when do two isolates represent the same strain and which tools identify a strain?

Strain-level identification informs decisions on whether two isolates represent the same strain and is used in investigations of outbreaks of foodborne disease. The same concept has only rarely been applied to nonpathogenic microbes in food or food processing facilities. Strain-level monitoring of food microbes requires definitions and tools that have only partially been developed. The review defines the concept of ‘microbial strains’ to guide the tracking of strains in food and food processing facilities. In addition, we discuss whole genome sequencing (WGS) and single-nucleotide polymorphism (SNP) calling as suitable tools for strain identification. Limitations of WGS and SNP analysis are also examined. Food spoilage causes food waste and fermented foods and probiotic foods are widely consumed. Therefore, strain identification and tracking of the food-associated microbes address a potential approach to eradicate pathogens and spoilage organisms in processing facilities and to ensure the quality of fermented foods and probiotic foods. • Genome sequences allow strain-level identification of microbes in food. • The definition of a strain depends on the context. • SNP calling requires high-quality genome sequences. • The accuracy of SNPs depends on the sequencing platform and the SNP pipeline.