Rapid and accurate eXDR screening: use Xpert Carba-R with FecalSwab

ABSTRACT

The FecalSwab® displays high performances for stool culture, but it was not assessed for carbapenemase-producing Enterobacterales (CPE) screening. We assess the performances of the Xpert Carba-R v2® with the FecalSwab®. Using a collection of 12 CPE strains, the limit of detection was assessed at 158 CFU/swab [interquartile range 93–589]. In 2019, 1540 swabs were included by 4 hospital laboratories, of which 39 (2.5%) yield an invalid result. Among the 1501 valid, 87 (5.8%) were positives by culture and PCR and 25 (1.7%) were discrepant: 7 PCR-negative culture-positive, and 18 PCR-positive culture-negative. Two PCR-positive culture-negative results involved non-Enterobacterales strains: a KPC-producing Acinetobacter baumannii and a KPC-producing Aeromonas spp. The overall percent agreement was 98.3% and the Kappa value was 0.88. FecalSwab® is an accurate sampling device for CPE screening. It allows performing all eXDR screening using a single swab, simplifying the sample collection, and improving the patient comfort. Regarding discrepant, we suggest combining a CPE screening by both culture and Xpert Carba-R v2® methods.

Introduction

Accurate identification of eXDR (emerging extensively drug-resistant organisms) carriers, that is, carbapenemase-producing Enterobacterales (CPE) and vancomycin-resistant enterococcus (VRE) carriers, is needed in order to implement eXDR-specific infection prevention and control (IPC) measures and avoid cross-transmission (Banach et al. 2018; Lepelletier et al. 2015; Magiorakos et al. 2017a). As the culture on selective media needs at least 24 to 48 hours, a rapid and robust method is required. The Xpert Carba-R v2
is a fully-integrated molecular method that provides accurate results within less an hour (Saliba et al. 2020). However, as it detects about 95% of all known carbapenemase genes and antimicrobial susceptibility testing is required, a culture remains needed (Dortet et al. 2017). Thus, rapid eXDR screening requires both a fullyintegrated molecular method and a conventional culture using selective media.

According to the manufacturer recommendations, Xpert Carba-R v2
should be performed on rectal or perirectal swabs sampled using the Transystem double swab (TDS) (Copan, Brescia, Italy). Consequently, at least 2 swabs are required in order to perform an eXDR (VRE plus CPE) screening. The FecalSwab
(Copan, Brescia, Italy) combines a flocked swab with 3 mL of Cary-Blair medium. It displays high performances for stool culture (Goneau et al. 2019). The accuracy of Xpert Carba-R v2
using FecalSwab
has never been assessed yet. In the present study, we aim to assess the limit of detection of the Xpert Carba-R v2
with the FecalSwab
and its performances in routine use.