Genomic paradigms for food-borne enteric pathogen analysis at the USFDA: case studies highlighting method utility,...

Area of Science:

• Food safety microbiology
• Genomic technologies
• Pathogen surveillance

Background:

• Food-borne bacterial pathogens pose significant public health risks.
• Traditional methods for pathogen characterization are often slow and lack specificity.
• Genomic technologies offer rapid and precise strain identification for improved food safety.

Purpose of the Study:

• To examine the utility of optical genome mapping and DNA microarray genotyping in food-borne pathogen outbreak analysis.
• To review best practices and limitations of these genomic technologies for pathogen differentiation.
• To consider the future integration of these methods with whole genome sequencing for enhanced surveillance.

Main Methods:

• Optical genome mapping for assessing genomic architecture.
• DNA microarray genotyping for evaluating gene content.
• Comparative analysis of outbreak strain subtyping and trace-back capabilities.

Main Results:

• Both optical mapping and microarrays provide rapid, highly specific strain characterizations for food-borne pathogens.
• Integration of these technologies enhances high-resolution scrutiny of genomic landscapes, exemplified by Shiga toxin-producing Escherichia coli (STEC) and Salmonella enterica.
• Whole genome sequencing offers single nucleotide resolution, enabling refined microarray designs and targeted approaches for strain-specific fingerprinting.

Conclusions:

• Optical mapping and microarrays are valuable tools for food-borne pathogen outbreak analysis and food safety.
• Future integration with whole genome sequencing will further refine pathogen differentiation and surveillance capabilities.
• These advanced genomic approaches are crucial for modern risk control and ensuring a safe food supply.