Frontiers in cellular and infection microbiology · 2025
Detection of β-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay.
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Ivagnes Vittorio, De Maio Flavio, Baccani Ilaria, Antonelli Alberto, Menchinelli Giulia, Rosato Roberto, Cafaro Giordana, Santarelli Giulia, Falletta Federico, D'Inzeo Tiziana, Sanguinetti Maurizio, Spanu Teresa, De Angelis Giulia, Rossolini Gian Maria, Posteraro Brunella
Аннотация
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 bla KPC, bla VIM, bla NDM, bla IMP, bla OXA-23-like, bla OXA-48-like, bla SHV-ESBL, bla CTX-M-1/9 group, and bla CMY-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.
RESULTS: 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 bla SHV-ESBL gene but true positive for a bla KPC 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 bla CMY-2 -like (n=6), bla OXA-23-like (n=5), and bla SHV-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.
CONCLUSION: 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.
METHODS: Simulated (n=146) and clinical (n=106) GN-PBC samples were tested for bla KPC, bla VIM, bla NDM, bla IMP, bla OXA-23-like, bla OXA-48-like, bla SHV-ESBL, bla CTX-M-1/9 group, and bla CMY-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.
RESULTS: 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 bla SHV-ESBL gene but true positive for a bla KPC 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 bla CMY-2 -like (n=6), bla OXA-23-like (n=5), and bla SHV-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.
CONCLUSION: 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.