ORIGINAL RESEARCH article
Front. Cell. Infect. Microbiol.
Sec. Clinical Microbiology
Volume 15 - 2025 | doi: 10.3389/fcimb.2025.1597700
Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay
Provisionally accepted
Vittorio Ivagnes1
Flavio De Maio2
Ilaria Baccani3
Alberto Antonelli3Giulia Menchinelli2Roberto Rosato1
Giordana Cafaro2
Giulia Santarelli2Federico Falletta1Tiziana D'Inzeo1
MAURIZIO SANGUINETTI1,2*Teresa Spanu2
Giulia De Angelis1,2*
Gian Maria Rossolini3
Brunella Posteraro1,2- 1Catholic University of the Sacred Heart, Milano, Italy
- 2Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- 3Università di Firenze, Firenze, Italy
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Background: Accurate detection of β-lactam resistance genes in bloodstream infections is critical for guiding antimicrobial therapy. This study evaluates the Alifax Gram-negative resistance (GNR) microchip assay for detecting β-lactam resistance genes directly from positive blood cultures (PBCs) for Gram-negative (GN) bacteria, including Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii.Methods: Simulated (n=146) and clinical (n=106) GN-PBC samples were tested for blaKPC, blaVIM, blaNDM, blaIMP, blaOXA-23-like, blaOXA-48-like, blaSHV-ESBL, blaCTX-M-1/9 group, and blaCMY-2-like genes using the GNR microchip assay. Whole-genome sequencing (WGS) served as the reference assay for simulated samples and, selectively, for clinical samples. The bioMérieux BioFire Blood Culture Identification 2 (BCID2) panel assay was used as a comparator for clinical samples.The GNR microchip assay correctly identified 203 (99.5%) of 204 β-lactam resistance genes in simulated samples. One sample tested false negative for a blaSHV-ESBL gene but true positive for a blaKPC gene. In clinical samples, GNR results were concordant with BCID2 for 113 (100%) of 113 genes included in both assays. Additionally, the GNR assay detected blaCMY-2-like (n=6), blaOXA-23-like (n=5), and blaSHV-ESBL (n=2), which are not targeted by BCID2, all confirmed by WGS. In two β-lactam-resistant P. aeruginosa samples but negative by the GNR assay, WGS confirmed the absence of acquired β-lactam resistance genes, suggesting alternative resistance mechanisms.The GNR microchip assay demonstrated high concordance and broader β-lactam resistance gene coverage compared to BCID2, supporting its potential role in routine diagnostics. Further validation in larger, prospective studies is warranted.
Keywords: antimicrobial resistance, β-lactamase, GNR microchip assay, Gram-Negative Bacteria, molecular detection, positive blood cultures
Received: 21 Mar 2025; Accepted: 07 May 2025.
Copyright: © 2025 Ivagnes, De Maio, Baccani, Antonelli, Menchinelli, Rosato, Cafaro, Santarelli, Falletta, D'Inzeo, SANGUINETTI, Spanu, De Angelis, Rossolini and Posteraro. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
MAURIZIO SANGUINETTI, Catholic University of the Sacred Heart, Milano, Italy
Giulia De Angelis, Catholic University of the Sacred Heart, Milano, Italy
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