Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay
BackgroundAccurate 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 G...
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| author | Vittorio Ivagnes Flavio De Maio Ilaria Baccani Alberto Antonelli Giulia Menchinelli Roberto Rosato Giordana Cafaro Giulia Santarelli Federico Falletta Tiziana D’Inzeo Tiziana D’Inzeo Maurizio Sanguinetti Maurizio Sanguinetti Teresa Spanu Giulia De Angelis Giulia De Angelis Gian Maria Rossolini Gian Maria Rossolini Brunella Posteraro Brunella Posteraro |
| author_facet | Vittorio Ivagnes Flavio De Maio Ilaria Baccani Alberto Antonelli Giulia Menchinelli Roberto Rosato Giordana Cafaro Giulia Santarelli Federico Falletta Tiziana D’Inzeo Tiziana D’Inzeo Maurizio Sanguinetti Maurizio Sanguinetti Teresa Spanu Giulia De Angelis Giulia De Angelis Gian Maria Rossolini Gian Maria Rossolini Brunella Posteraro Brunella Posteraro |
| author_sort | Vittorio Ivagnes |
| collection | DOAJ |
| description | BackgroundAccurate 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.MethodsSimulated (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.ResultsThe 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.ConclusionThe 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. |
| format | Article |
| id | doaj-art-ea5ca696230b4767836e4594be969b73 |
| institution | Kabale University |
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| publishDate | 2025-06-01 |
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| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-ea5ca696230b4767836e4594be969b732025-08-20T03:25:59ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-06-011510.3389/fcimb.2025.15977001597700Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assayVittorio Ivagnes0Flavio De Maio1Ilaria Baccani2Alberto Antonelli3Giulia Menchinelli4Roberto Rosato5Giordana Cafaro6Giulia Santarelli7Federico Falletta8Tiziana D’Inzeo9Tiziana D’Inzeo10Maurizio Sanguinetti11Maurizio Sanguinetti12Teresa Spanu13Giulia De Angelis14Giulia De Angelis15Gian Maria Rossolini16Gian Maria Rossolini17Brunella Posteraro18Brunella Posteraro19Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Medicina Sperimentale e Clinica, Università di Firenze, Florence, ItalyDipartimento di Medicina Sperimentale e Clinica, Università di Firenze, Florence, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyDipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyDipartimento di Medicina Sperimentale e Clinica, Università di Firenze, Florence, ItalyStruttura Organizzativa Dipartimentale (SOD) Microbiologia e Virologia, Azienda Ospedaliera Universitaria Careggi, Florence, ItalyDipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, ItalyUnità Operativa “Medicina di Precisione in Microbiologia Clinica”, Direzione Scientifica, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, ItalyBackgroundAccurate 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.MethodsSimulated (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.ResultsThe 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.ConclusionThe 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.https://www.frontiersin.org/articles/10.3389/fcimb.2025.1597700/fullantimicrobial resistanceβ-lactamaseGNR microchip assayGram-negative bacteriamolecular detectionpositive blood cultures |
| spellingShingle | Vittorio Ivagnes Flavio De Maio Ilaria Baccani Alberto Antonelli Giulia Menchinelli Roberto Rosato Giordana Cafaro Giulia Santarelli Federico Falletta Tiziana D’Inzeo Tiziana D’Inzeo Maurizio Sanguinetti Maurizio Sanguinetti Teresa Spanu Giulia De Angelis Giulia De Angelis Gian Maria Rossolini Gian Maria Rossolini Brunella Posteraro Brunella Posteraro Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay Frontiers in Cellular and Infection Microbiology antimicrobial resistance β-lactamase GNR microchip assay Gram-negative bacteria molecular detection positive blood cultures |
| title | Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay |
| title_full | Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay |
| title_fullStr | Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay |
| title_full_unstemmed | Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay |
| title_short | Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay |
| title_sort | detection of β lactam resistance genes in gram negative bacteria from positive blood cultures using a microchip based molecular assay |
| topic | antimicrobial resistance β-lactamase GNR microchip assay Gram-negative bacteria molecular detection positive blood cultures |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1597700/full |
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