Work

Diagnostic performance of the direct stool Xpert Carba-R assay in active surveillance of carbapenemase-producing enterobacterales

Year: 2025

Type: article

Abstract: The Xpert Carba-R assay allows direct identification of major carbapenemase genes from stools, offering faster results than culture-based methods. This study aimed to evaluate the diagnostic performance of the Xpert Carba-R assay for detecting CPE colonization and assess gene-level concordance between direct stool and cultured samples. Between March and December 2023, two rectal swabs were collected from high-risk patients, those admitted to the intensive care unit or with prior hospitalization—at a tertiary care hospital. One swab was analyzed using the direct stool Xpert Carba-R assay, and the other underwent conventional culture techniques. Diagnostic performance was evaluated against culture-based detection, and concordance of carbapenemase gene identification between direct stool and culture isolate results was assessed. Among 4,120 screened patients, 107 (2.5%) were colonized with CPE. The direct stool Xpert assay showed a sensitivity of 97.2% and specificity of 99.1% for CPE detection. Concordance analysis showed an overall agreement of 64.1% (Cohen’s kappa coefficient = 0.456). Discordance occurred in 52 cases (35.9%), primarily due to multiple gene detections in direct stool samples that were not confirmed in cultural isolates. The positive predictive value varied significantly by gene: bla KPC showed 90.8%, bla NDM 52.6%, bla OXA-48 50.0%, while bla IMP-1 showed 0%, with none of the nine bla IMP-1 detections from stool samples confirmed in corresponding cultured isolates. The Xpert Carba-R assay is a reliable tool for direct CPE detection from stool samples, though discordance with culture-based testing, particularly for bla IMP-1 —should be considered in clinical interpretation.

Source: Antimicrobial Resistance and Infection Control

DOI: 10.1186/s13756-025-01642-2

Authors: Cheon-Hoo Jun, Si-Ho Kim, Hyoung Tae Kim, Yu Mi Wi

Institutions: Samsung Changwon Hospital, Sungkyunkwan University

Language: English

Topic: Antibiotic Resistance in Bacteria

Subfield: Molecular Medicine

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $3,290