[Real-time rectal swab Xpert Carba-R assay for early warning of CRO bloodstream infection in patients undergoing hematopoietic stem cell transplant: a clinical feasibility study].

Abstract

Objective: This study aimed to analyze the homology between carbapenem-resistant organisms (CRO) intestinal colonization strains and bloodstream infection (BSI) strains in patients undergoing hematopoietic stem cell transplantation (HSCT), confirming the clinical use of the real-time rectal swab Xpert Carba-R assay, and investigate its feasibility in early warning of BSI. Methods: Drug-resistant strains obtained from rectal swabs and blood culture samples of patients undergoing the same HSCT from January 2021 to December 2021 were collected and analyzed. The homology of the CRO intestinal colonization and BSI strains was confirmed using strain identification, antimicrobial resistance phenotyping, whole genome sequencing (WGS), multilocus sequence typing (MLST), and carbapenemase type identification. Rectal swab cultures and the real-time rectal swab Xpert Carba-R assay were conducted concurrently on patients with HSCT from August 2021 to August 2022. The accuracy of the real-time rectal swab Xpert Carba-R assay was confirmed with the sequencing results of polymerase chain reaction amplification products of the carbapenemase gene from purified colonies as a reference standard. Results: This study included 24 CRO strains from 10 patients undergoing HSCT, including 14 intestinal colonizers and 10 CRO-BSI strains. The results revealed that the CRO intestinal colonization strains and CRO-BSI strains from the same patient and their carbapenemase genes were almost identical. Additionally, WGS revealed that CRO intestinal colonization and CRO-BSI strains from the same patient were more closely related than strains from different patients. Additionally, this study included 488 rectal swab specimens from 184 patients undergoing HSCT, with CRO detection rates of 16.4% for rectal swab culture and 18.4% for the real-time rectal swab Xpert Carba-R assay. The overall sensitivity, specificity, and positive and negative predictive values of the real-time rectal swab Xpert Carba-R assay were 96.6%, 72.8%, 90.6%, and 88.9%, respectively. Conclusions: A high degree of homology was found between the CRO intestinal colonization strains and the CRO-BSI strains in patients undergoing HSCT. The real-time rectal swab Xpert Carba-R assay is a reliable and convenient method for detecting common carbapenemase genes, serving as an alternative to rectal swab culture for early warning of CRO-BSI.