Multicentre Evaluation of Cepheid Xpert® Research-Use-Only Panel for Molecular Rapid Detection of Gastrointestinal Pathogens

Rapid and accurate identification of enteric pathogens is essential for the management of acute infectious diarrhoeal diseases. Multiplex PCR panels have emerged as first-line screening tools to conventional stool culture by providing broad pathogen coverage and shorter turnaround times. This study evaluated the diagnostic performance of the Cepheid Xpert gastrointestinal (GI) research-use-only (RUO) panel in routine clinical practice across multiple European centres. A multicentre study was conducted in four hospitals across France, Germany and Italy. Stool specimens collected as part of routine care were tested using local standard-of-care (SoC) methods, including conventional stool culture, BDMax® Enteric Panels, or BioFire FilmArray® GI Panel, and subsequently analysed using the Cepheid Xpert GI RUO panel. A total of 11 bacterial, viral and parasitic enteropathogens were targeted. Discordant results underwent additional testing, and a consensus result based on a two-out-of-three agreement rule was used as the reference standard. Diagnostic performance metrics, agreement with SoC methods, microbiological findings and turnaround times were assessed. Of 508 samples, 115 (22.6%) were identified as positive for at least one pathogen according to the consensus result, including 12 samples with co-detection of more than one pathogen (10.4% of positive samples), resulting in a total of 128 pathogens detected. The most frequently detected pathogens were Campylobacter spp. (37 specimens), Norovirus (26 specimens), and Salmonella spp. (25 specimens). Compared with the consensus reference standard, Xpert achieved an overall sensitivity of 98% (95% CI: 94–100%), specificity of 100% (95% CI: 100–100%), positive predictive value of 95% (95% CI: 90–98%), and negative predictive value of 100% (95% CI: 100–100%). Sensitivity was ≥95% and specificity ≥99% for all evaluable targets. Agreement with routine diagnostic methods was high, with overall positive and negative percent agreements exceeding 90% and a Cohen’s kappa coefficient of 0.91. Median analytical turnaround time was 1 h 18 min for Xpert, compared with 3 h for BDMax, 1 h 15 min for BioFire and 48 h for conventional stool culture. The Cepheid Xpert GI (RUO) panel provided highly accurate detection of enteric pathogens across heterogeneous European diagnostic settings and reduced turnaround time by more than 95% compared with conventional stool culture. A future IVD version of this test could provide rapid and accurate detection of enteric pathogens for potential routine management of patients with suspected acute infectious gastroenteritis.