Evaluation of Xpert® Carba-R Assay Performance from FecalSwab™ Samples

Background/Objectives: The emergence and spread of carbapenemase-producing Enterobacterales (CPE) represents a significant challenge prompting the need to optimize diagnostic tools to detect CPE carriers. The Xpert® Carba-R assay (Cepheid, Sunnyvale, CA, USA), a Real-Time PCR-based test, can detect the blaKPC, blaVIM, blaOXA-48, blaNDM and blaIMP carbapenemase genes directly from rectal swabs. This study assessed the performance of the Xpert® Carba-R assay using FecalSwab™ (Copan, Brescia, Italy), a liquid-based collection device. Methods: The first part of the study aimed to establish the FecalSwabTM volume which gave the most similar Ct values to those obtained by the Transystem™ double swab (Copan). The best volume was then used to assess the limit of detection (LoD) for each target and compare the accuracy of different FecalSwabTM storage conditions (room temperature or 4 °C after 16 h compared to T0). Results: The results indicated that using 200 µL of the FecalSwab™ medium provided reliable Ct values, with the lowest number of invalid samples compared to traditional methods. The average LoDs for different carbapenemases ranged from 4.7 × 103 to 6.8 × 103 CFU/mL. FecalSwab™ showed a better performance after 16 h at room temperature compared to storage at 4 °C. Conclusions: This study supports single sampling with the FecalSwab™ medium for both molecular and cultural methods, for the potential optimization of CPE screening.