CRISPR-Based Typing and Next-Generation Tracking Technologies

Rodolphe Barrangou, Edward G. Dudley

Research output: Contribution to journalReview articlepeer-review

57 Scopus citations


Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology-based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.

Original languageEnglish (US)
Pages (from-to)395-411
Number of pages17
JournalAnnual Review of Food Science and Technology
StatePublished - Feb 28 2016

All Science Journal Classification (ASJC) codes

  • Food Science


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