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Summary

High-throughput sequencing (HTS) offers advanced microbial typing for food safety. While promising for foodborne pathogen surveillance and outbreak investigations, challenges in data analysis and standardization remain.

Keywords:
bacteria and virusesfungi and parasitesmetagenomicsmetataxonomicsmicrobial profilingoutbreak investigationsurveillancewhole genome sequencing

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Area of Science:

  • Food safety science
  • Microbial genomics
  • Public health surveillance

Background:

  • High-throughput sequencing (HTS) is a leading technology for microbial typing in clinical settings.
  • Its application in foodborne pathogen monitoring and outbreak investigations is still developing.

Purpose of the Study:

  • To review the literature on HTS for food pathogen surveillance.
  • To assess the current status and future potential of HTS in improving food safety and reducing outbreak impacts.
  • To identify challenges and opportunities for HTS implementation in food analysis.

Main Methods:

  • Comprehensive literature review of published studies on HTS for bacterial, viral, and eukaryotic food pathogens.
  • Analysis of HTS application in food surveillance, epidemiological, and outbreak investigations.
  • Identification of technological and bioinformatic bottlenecks.

Main Results:

  • HTS technology and bioinformatics advancements have outpaced data analysis capabilities.
  • Obstacles include sample processing, nucleic acid extraction, standardized protocols, and curated reference databases.
  • Despite challenges, significant progress in HTS capacity and application range has been observed over the last decade.

Conclusions:

  • HTS holds immense potential for enhancing food safety and outbreak response.
  • Addressing challenges in data interpretation, standardization, and database development is crucial.
  • International collaborations are driving efforts to overcome obstacles and foster future progress in HTS applications for foodborne pathogen management.