Metagenomics for pathogen surveillance

We are bombarded by media about yet another Listeria or Salmonella contaminated food batch, which has to be recalled from supermarkets. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, compromises our ability to scale-up such efforts. Traditional microbiological food safety monitoring relies on targeted detection of pathogens or safety indicator organisms in food1,2. It requires involvement of variety of culture methods to select specific species from complex food matrices.

Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.

Metagenomics—the interrogation of genetic material from a sample containing multiple species—could enable culture-free methods and workflows for the detection of known and unknown viruses, bacteria and fungi. Metagenomic studies are often either done using a targeted amplicon approach that is based on marker genes (for example, 16S rRNA gene sequencing) or shotgun metagenomic sequencing to probe the entire genetic content of a sample. Metagenomic sequencing of samples can also enable the detection of virulence and resistance determinants outside their genome contexts. With improvements in ease of analysis and cost, the majority of bio-surveillance efforts across various sectors would benefit from the adoption of metagenomic approaches.


1. Carolissen, V. Principles and Guidelines for the Establishment and Application of Microbiological Criteria Related to Foods CAC/GL 21-1997, Codex Alimentarius 6 (FAO and WHO, 1997).

2. Principle and Guidelines for the Conduct of Microbiological Risk Assessment CAC/GL 30-1999, Amendments 2012, 2014, Codex Alimentarius 7 (FAO and WHO, 1999).

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