Short communicationInterference with swine DNA limits applicability of a fish PCR system in foodstuff

- A fish PCR system was characterized for its performance with various fish species.
- Suitability of the PCR system for sensitive fish DNA detection was demonstrated.
- The PCR system was inhibited by the presence of swine DNA.
- PCR inhibition was due to sequence similarities with a porcine gene.
- Use of the PCR for allergen detection in foodstuff is not recommended.

Ingestion of fish may exert severe health effects in food-allergic individuals. Sensitive analytical methods are required for the surveillance of the obligation to label fish as a potentially allergenic ingredient in foodstuff. Recently a sensitive multi-copy PCR method has been published to detect a broad spectrum of fish species by amplification of the mitochondrial 12S rRNA gene. The performance of this method in real-life samples also containing DNA from other sources such as plants or animals has not been studied yet. The applicability domain of the PCR, especially for allergen detection, is therefore still unclear. Here we assessed the ability of the PCR system to detect fish in a background of excess animal and plant DNA. The results demonstrate satisfying performance with various fish species but pronounced PCR inhibition by swine DNA. Subsequent analyses revealed homology of one PCR primer to the swine 12S rRNA gene, causing competition during the PCR reaction and thus raising the limit of detection by two orders of magnitude. In conclusion, the tested PCR system is suited for fish detection in plant matrices, but not in matrices containing excess animal, especially swine, DNA. Application of the PCR system for allergen detection is therefore not recommended.