Background: Detection of gastrointestinal (GI) pathogens (bacteria, parasites and/or viruses) by conventional methods is time-consuming, requires strong technical experience, and lacks sensitivity. Several rapid multiplex PCRs (mPCR) have been recently developed to improve their identification and their relative performances should be evaluated. The aim of the study was to assess the performance of 3 rapid mPCR GI assays (BIOFIRE® FILMARRAY® Gastrointestinal Panel [bioMérieux], QIAstat-Dx® gastrointestinal [Qiagen] and Novodiag® gastrointestinal panel [Mobidiag] – bacteria search only).
Materials/methods: Enteric pathogens were detected in the stools using the 3 mPCR kits and conventional methods (standard stool culture, GenXpert PCR [Cepheid] for Clostridioides difficile, parasitological stool examination and/or in-house PCR). The patients enrolled were adults consulting for digestive disorders in the emergency department or the infectious diseases department of Bichat hospital (Paris). We used a composite gold standard taking into account either the conventional method or the positivity of 2 out of 3 mPCR.
Results: 85 stools were studied, including 77 collected prospectively from April to September 2019 and 8 stored at -80 °C. Prevalence of bacterial pathogens was 47.1% (n=40) including C. difficile at 9.4% (n=8). Prevalence of parasites and viruses were respectively 12.9% (n=11) and 2.4% (n=2). For bacteria detection, 95.7% (732/765) of the overall results and 73.5% (36/49) of positive results were concordant between the 3 mPCRs. We observe a concordance between BIOFIRE® FILMARRAY® and QIAstat-Dx® for parasites and viruses, at 99.4% (338/340) and 99.8% (424/425) of overall results and 90.9% (10/11) and 100.0% (2/2) of positive results, respectively. Performances of the three kits are detailed in the table below. The discrepancies in Yersinia sp. detection were explained because Novodiag® only detects toxigenic Yersinia sp. whose absence was confirmed by the national reference center (NRC). Discrepancies in the detection of Campylobacter sp. were also investigated by the corresponding NRC.
Conclusions: All tested rapid molecular methods have identified more enteric pathogens than conventional methods. Although some discrepancies have been identified, the 3 mPCR assays showed good agreements.
Table. Results of conventional methods and the 3 multiplex PCR BIOFIRE® FILMARRAY® Gastrointestinal Panel [bioMérieux], QIAstat-Dx® gastrointestinal [Qiagen] and Novodiag® gastrointestinal Panel [Mobidiag]
(Se = Sensitivity, Sp = Specifivity)