Practice Abstract - Research and innovation

Sampling and testing for pathogens in food: finding the needle in a haystack and the impact of the food microbiome

To evaluate the constraints in pathogen sampling and detection, focusing on how intrinsic and extrinsic factors affect enrichment-based recovery and how molecular methods can improve pathogen detection. 

Outcome: 

  • Low contamination: Regulatory absence testing requires detecting low cell numbers. Enrichment increase cell concentration to detectable levels, but unevenly distribution and small sample sizes limit detection probability. 
  • Physiological status: Processing and storage can induce sublethal injury. Recovery during enrichment is strain- and history-dependent; prolonged lag phases may prevent cells from reaching detection thresholds, increasing false negatives. 
  • Food microbiome: Pathogens are a small fraction of total microbiota. Nonselective enrichment may allow competitors to suppress growth, while selective enrichment may inhibit competitors but extend lag or reduce recovery of stressed cells. 
  • Biological variability: Intraspecies and single-cell heterogeneity affect growth and recovery, and selective enrichment may bias subtype detection. 
  • Molecular detection: PCR, RT-PCR, CRISPR, and sequencing reduce time-to-detection and improve specificity but remain enrichment-dependent for low-level contamination. Limitations include detection of DNA from dead cells, matrix inhibition, low sensitivity, and limited multipathogen detection. 
  • Metagenomics: Shotgun and long-read sequencing enable untargeted detection, but low-abundance pathogens may be missed, and distinguishing pathogenic from nonpathogenic strains requires deep sequencing. 

Recommendations: Quasi-metagenomics (i.e, sequencing of enriched cultures) combines enrichment with high-throughput analysis to improve sensitivity and multipathogen detection. Optimization of enrichment is critical for unbiased recovery. 

Combining optimized unselective enrichment with molecular and sequencing methods offers improved detection capabilities.

Source Project
Future-Proofing Food: Transforming Risk Analysis for a better and more adaptive food system
Ongoing | 2022-2026
Main funding source
Horizon Europe (EU Research and Innovation Programme)
Geographical location
Netherlands, Italy, Hungary, Greece, Austria, France, Ireland, Denmark, Germany, Belgium, Austria, United Kingdom
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