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Updated: Jul 3, 2025
A High-throughput Platform for the Screening of Salmonella spp./Shigella spp.
Published on: November 7, 2018
Comparative evaluation of the detection rate, workflow and associated costs of a multiplex PCR panel versus
J Ambrosius-Eichner1,2, M Hogardt1,2, A Berger2,3
1Institute of Medical Microbiology and Infection Control, Goethe University Frankfurt, University Hospital, Frankfurt, Germany.
Abstract:
Introduction. Infectious gastroenteritis is a common reason for consulting a physician. Although most cases of gastrointestinal illness are self-limiting, the identification of the etiologic pathogen by stool specimen analysis is important in cases of more severe illness and for epidemiological reasons.Due to the broad range of causative pathogens, the conventional examination of a stool specimen is labour-intensive and usually requires different diagnostic methods. Multiplex PCR tests [e.g. BioFire Gastrointestinal (GI) Panel] allow the rapid detecting of up to 22 pathogens in one test.Hypothesis. Using a multiplex PCR panel to test stool specimens for infectious gastroenteritis pathogens can improve the detection rate, reduce the time-to-result and hands-on time and lower the costs of a microbiology laboratory.Aim. This study was aimed at evaluating the detection rate, the workflow and associated costs of stool specimen management using the BioFire GI Panel versus conventional methods.Methodology. Stool specimens were evaluated prospectively during the routine operation. Pathogen detection rate, hands-on time, time-to-result and material and personnel costs were determined for the BioFire GI Panel and conventional methods-the latter based on physician request and excluding viral testing.Results. Analysing 333 specimens collected between 2019 and 2020, the detection rate of enteropathogens was significantly higher with a positivity rate of 39.9 % using the multiplex PCR panel compared with 15.0 % using the conventional methods. The BioFire GI Panel presented results in a median time of 2.2 h compared with 77.5 h for culture and 22.1 h for antigen testing, noting that no tests were performed at weekends except for toxinogenic Clostridioides difficile. Based on list prices, the BioFire GI Panel was nine times more expensive compared with conventional methods, whereas hands-on-time was significantly lower using the BioFire GI Panel.Conclusion. Multiplex PCR panels are valuable tools for laboratory identification of infectious agents causing diarrhoea. The higher costs of such a multiplex PCR panel might be outweighed by the higher detection rate, ease of handling, rapid results and most likely improved patient management. However, these panels do not provide information on antimicrobial susceptibility testing. Therefore, if this is necessary for targeted therapy or if outbreak monitoring and control is required, specimens must still be cultured.
Insights
Multiplex PCR panels significantly increase infectious gastroenteritis pathogen detection rates and speed up results compared to conventional methods. While more expensive upfront, these panels offer improved efficiency and patient management, though they don't replace culture for antimicrobial susceptibility testing.
Area of Science:
- Clinical Microbiology
- Infectious Diseases
- Molecular Diagnostics
Background:
- Infectious gastroenteritis is a common clinical concern, often requiring stool specimen analysis for pathogen identification, especially in severe cases or for epidemiological surveillance.
- Conventional stool analysis is labor-intensive and employs diverse methods for detecting a wide range of pathogens.
- Multiplex PCR panels, such as the BioFire GI Panel, offer rapid detection of numerous pathogens simultaneously.
Purpose of the Study:
- To evaluate the BioFire GI Panel's performance against conventional methods in terms of pathogen detection rate, workflow efficiency, and cost.
- To assess the impact of multiplex PCR on laboratory diagnostics for infectious gastroenteritis.
Main Methods:
- Prospective evaluation of stool specimens during routine laboratory operations.
- Comparison of pathogen detection rates, hands-on time, time-to-result, and costs between the BioFire GI Panel and conventional diagnostic methods (excluding viral testing).
- Analysis of 333 specimens collected between 2019 and 2020.
Main Results:
- The multiplex PCR panel achieved a significantly higher enteropathogen detection rate (39.9%) compared to conventional methods (15.0%).
- The BioFire GI Panel yielded results in a median of 2.2 hours, drastically faster than conventional methods (culture: 77.5 hours; antigen testing: 22.1 hours).
- Despite a higher cost per test (nine times more expensive based on list prices), the BioFire GI Panel significantly reduced hands-on time.
Conclusions:
- Multiplex PCR panels are valuable for identifying infectious diarrhea agents, offering higher detection rates and faster results.
- The increased cost of multiplex PCR may be offset by improved workflow, efficiency, and potential for better patient management.
- Conventional culture methods remain essential for antimicrobial susceptibility testing and outbreak surveillance when required.
