Related Experiment Video
Updated: Apr 4, 2026
Detection of Helicobacter pylori Infection and Antibiotic Resistance via Stool Quantitative Polymerase Chain Reaction Analysis
Published on: May 16, 2025
Comparative Evaluation of Broad-Panel PCR Assays for the Detection of Gastrointestinal Pathogens in Pediatric
Zhengming Gu1, Haiqing Zhu1, Alicia Rodriguez1
1Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
Abstract:
Broadly multiplexed molecular amplification assays offer an unprecedented ability to diagnose gastrointestinal infection in immunocompromised patients. However, little data are available to compare the performance of such systems in this population. A total of 436 stool samples were collected from 199 predominantly immunocompromised pediatric oncology patients. Remnant samples were tested in parallel with the use of the premarket (investigational use only) versions of two broadly multiplexed PCR assays (BioFire and Luminex), and the results of samples corresponding to the first episode per patient were compared with those from laboratory-developed molecular assays, culture, and antigen detection. Overall performance of the multiplexed systems was comparable, with BioFire and Luminex detecting 94 and 99 positives (P = 0.34), respectively. Stratifying by analyte, BioFire assay detected 51 samples positive for Clostridium difficile, whereas Luminex assay detected 60 (P = 0.01). Biofire and Luminex detected 28 and 38 norovirus-positive samples (P = 0.002), respectively. Astrovirus- and adenovirus-positive samples were detected in higher numbers by in-house PCR than by BioFire; the same was observed for adenovirus with Luminex. Differences observed with other analytes were minimal, did not reach statistical significance, or lacked the numbers needed to detect a difference between systems. Broadly multiplexed PCR offers an effective means of detecting a variety of gastrointestinal pathogens in pediatric oncology patients, with assay performance comparable among the tests examined.
Insights
Broadly multiplexed PCR assays effectively diagnose gastrointestinal infections in immunocompromised children. Performance of BioFire and Luminex systems was comparable for detecting common pathogens.
Area of Science:
- Clinical microbiology
- Molecular diagnostics
- Pediatric oncology
Background:
- Gastrointestinal infections pose significant risks for immunocompromised patients, particularly those undergoing cancer treatment.
- Broadly multiplexed molecular amplification assays offer rapid and comprehensive pathogen detection but require performance evaluation in specific patient populations.
- Limited data exist comparing the diagnostic accuracy of different multiplexed PCR systems in immunocompromised pediatric oncology patients.
Purpose of the Study:
- To compare the performance of two broadly multiplexed PCR assays (BioFire and Luminex) for diagnosing gastrointestinal infections in immunocompromised pediatric oncology patients.
- To evaluate the diagnostic yield of these investigational assays against established laboratory methods, including in-house PCR, culture, and antigen detection.
Main Methods:
- A total of 436 stool samples were collected from 199 immunocompromised pediatric oncology patients.
- Samples were tested in parallel using premarket versions of the BioFire and Luminex multiplexed PCR assays.
- Results were compared with laboratory-developed molecular assays, culture, and antigen detection for the first episode per patient.
Main Results:
- Overall performance of the BioFire and Luminex assays was comparable, detecting 94 and 99 positive cases, respectively (P = 0.34).
- Significant differences were observed for specific analytes: Luminex detected more Clostridium difficile (60 vs. 51, P = 0.01) and norovirus (38 vs. 28, P = 0.002) cases than BioFire.
- In-house PCR detected more astrovirus and adenovirus cases than BioFire, and more adenovirus cases than Luminex.
Conclusions:
- Broadly multiplexed PCR assays are effective tools for identifying a range of gastrointestinal pathogens in pediatric oncology patients.
- The performance of the BioFire and Luminex multiplexed PCR systems is comparable overall, with some analyte-specific variations.
- These molecular assays provide a valuable diagnostic approach for managing gastrointestinal infections in this vulnerable patient group.
