{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T02:20:47Z","timestamp":1782872447748,"version":"3.54.5"},"reference-count":38,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T00:00:00Z","timestamp":1748908800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Accurate detection of \u03b2-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 \u03b2-lactam resistance genes directly from positive blood cultures (PBCs) for Gram-negative (GN) bacteria, including Enterobacterales, <jats:italic>Pseudomonas aeruginosa<\/jats:italic>, and <jats:italic>Acinetobacter baumannii<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Simulated (n=146) and clinical (n=106) GN-PBC samples were tested for <jats:italic>bla<\/jats:italic><jats:sub>KPC<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>VIM<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>NDM<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>IMP<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>OXA-23<\/jats:sub>-like, <jats:italic>bla<\/jats:italic><jats:sub>OXA-48<\/jats:sub>-like, <jats:italic>bla<\/jats:italic><jats:sub>SHV<\/jats:sub>-ESBL, <jats:italic>bla<\/jats:italic><jats:sub>CTX-M-1\/9<\/jats:sub> group, and <jats:italic>bla<\/jats:italic><jats:sub>CMY-2<\/jats:sub>-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 bioM\u00e9rieux BioFire Blood Culture Identification 2 (BCID2) panel assay was used as a comparator for clinical samples.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The GNR microchip assay correctly identified 203 (99.5%) of 204 \u03b2-lactam resistance genes in simulated samples. One sample tested false negative for a <jats:italic>bla<\/jats:italic><jats:sub>SHV<\/jats:sub>-ESBL gene but true positive for a <jats:italic>bla<\/jats:italic><jats:sub>KPC<\/jats:sub> 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<jats:italic><jats:sub>CMY-2<\/jats:sub><\/jats:italic>-like (n=6), <jats:italic>bla<\/jats:italic><jats:sub>OXA-23<\/jats:sub>-like (n=5), and <jats:italic>bla<\/jats:italic><jats:sub>SHV<\/jats:sub>-ESBL (n=2), which are not targeted by BCID2, all confirmed by WGS. In two \u03b2-lactam-resistant <jats:italic>P. aeruginosa<\/jats:italic> samples but negative by the GNR assay, WGS confirmed the absence of acquired \u03b2-lactam resistance genes, suggesting alternative resistance mechanisms.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The GNR microchip assay demonstrated high concordance and broader \u03b2-lactam resistance gene coverage compared to BCID2, supporting its potential role in routine diagnostics. Further validation in larger, prospective studies is warranted.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2025.1597700","type":"journal-article","created":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T05:22:54Z","timestamp":1748928174000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Detection of \u03b2-lactam resistance genes in Gram-negative bacteria from positive blood cultures using a microchip-based molecular assay"],"prefix":"10.3389","volume":"15","author":[{"given":"Vittorio","family":"Ivagnes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Flavio","family":"De Maio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilaria","family":"Baccani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Antonelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Menchinelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Rosato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giordana","family":"Cafaro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Santarelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federico","family":"Falletta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiziana","family":"D\u2019Inzeo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maurizio","family":"Sanguinetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Spanu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"De Angelis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gian Maria","family":"Rossolini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brunella","family":"Posteraro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,6,3]]},"reference":[{"key":"B1","unstructured":"Welcome inside innovation\n          \n          \n          \n          2024"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00082-25","article-title":"Evaluation of phenotypic and genotypic methods for detecting KPC variants","volume":"3","author":"Benhadid-Brahmi","year":"2025","journal-title":"Antimicrob. 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