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Improved detection of gastrointestinal pathogens using generalised sample processing and amplification panels.

Shoo Peng Siah1, Juan Merif, Kiran Kaur

  • 11Genetic Signatures, c/o Virology Research Laboratories, Prince of Wales Hospital, Randwick 2Microbiology Division, SEALS, Prince of Wales Hospital, Randwick 3Virology Division, SEALS Microbiology, Prince of Wales, Randwick 4Department of Microbiology & Infectious Diseases, Pacific Laboratory Medicine Services, Royal North Shore Hospital, St Leonards 5Microbiology Department, St Vincent's Hospital, Darlinghurst 6General Microbiology, CIDMLS, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.

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Multiplex real-time PCR panels offer a streamlined approach for diagnosing gastrointestinal infections. This method rapidly identifies multiple pathogens, including bacteria, viruses, and protozoa, from stool samples with high accuracy.

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Area of Science:

  • Clinical microbiology
  • Molecular diagnostics
  • Infectious disease

Background:

  • Accurate and rapid diagnosis of gastrointestinal infections is crucial for effective patient management.
  • Conventional diagnostic methods can be time-consuming and may not detect all causative agents, especially in mixed infections.

Purpose of the Study:

  • To develop and validate multiplex real-time PCR panels for the simultaneous detection of various gastrointestinal pathogens.
  • To streamline the diagnostic workflow for gastrointestinal diseases using universal sample preparation.

Main Methods:

  • Development of four multiplex real-time PCR panels for bacterial, viral, protozoan, and Clostridium difficile detection.
  • Testing of 487 characterized stool samples and 81 clinical samples using the developed panels.
  • Comparison of PCR panel performance against conventional methods and gold standards.

Main Results:

  • Improved sensitivity for protozoan detection and identification of 16 additional mixed infections compared to conventional methods.
  • Achieved 100% sensitivity for Clostridium difficile detection, identifying hypervirulent strains like ribotype 027.
  • Bacterial and viral panels performed comparably to conventional methods, with results available in 3 hours.

Conclusions:

  • Multiplex real-time PCR with universal sample preparation enables streamlined and rapid diagnosis of gastrointestinal pathogens.
  • The panels enhance pathogen characterization in stool samples, aiding in better clinical decision-making.
  • This approach offers a significant advancement in the molecular diagnostics of infectious gastroenteritis.