Development of a high-throughput real-time PCR system for detection of enzootic pathogens in pigs

Nicole Bakkegård Goecke*, Charlotte Kristiane Hjulsager, Jesper Schak Krog, Kerstin Skovgaard, Lars Erik Larsen

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


Respiratory and intestinal diseases in pigs can have significant negative influence on productivity and animal welfare. A wide range of real-time PCR (rtPCR) assays are used in our laboratory (National Veterinary Institute, Technical University of Denmark) for pathogen detection, and PCR analyses are performed on traditional rtPCR platforms in which a limited number of samples can be analyzed per day given limitations in equipment and personnel. To mitigate these restrictions, rtPCR assays have been optimized for the high-throughput rtPCR BioMark platform (Fluidigm). Using this platform, we developed a high-throughput detection system that can be used for simultaneous examination of 48 samples with detection specificity for 18 selected respiratory and enteric viral and bacterial pathogens of high importance to Danish pig production. The rtPCR assays were validated and optimized to run under the same reaction conditions using a BioMark 48.48 dynamic array (DA) integrated fluidic circuit chip, and the sensitivity and specificity were assessed by testing known positive samples. Performance of the 48.48DA was similar to traditional rtPCR analysis, and the specificity of the 48.48DA was high. Application of the high-throughput platform has resulted in a significant reduction in cost and working hours and has provided production herds with a new innovative service with the potential to facilitate the optimal choice of disease control strategies such as vaccination and treatment.

Original languageEnglish
JournalJournal of Veterinary Diagnostic Investigation
Issue number1
Pages (from-to)51-64
Publication statusPublished - 2020


  • Bacteria
  • Detection
  • High-throughput
  • Porcine pathogens
  • Real-time PCR
  • Viruses

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