{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T12:05:32Z","timestamp":1788264332322,"version":"build-2803163510"},"reference-count":46,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T00:00:00Z","timestamp":1687910400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Zurich"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Objectives: Quinolone resistance in Escherichia coli occurs mainly as a result of mutations in the quinolone-resistance-determining regions of gyrA and parC, which encode the drugs\u2019 primary targets. Mutational alterations affecting drug permeability or efflux as well as plasmid-based resistance mechanisms can also contribute to resistance, albeit to a lesser extent. Simplifying and generalizing complex evolutionary trajectories, low-level resistance towards fluoroquinolones arises from a single mutation in gyrA, while clinical high-level resistance is associated with two mutations in gyrA plus one mutation in parC. Both low- and high-level resistance can be detected phenotypically using nalidixic acid and fluoroquinolones such as ciprofloxacin, respectively. The aim of this study was to develop a decision tree based on disc diffusion data and to define epidemiological cut-offs to infer resistance mechanisms and to predict clinical resistance in E. coli. This diagnostic algorithm should provide a coherent genotype\/phenotype classification, which separates the wildtype from any non-wildtype and further differentiates within the non-wildtype. Methods: Phenotypic susceptibility of 553 clinical E. coli isolates towards nalidixic acid, ciprofloxacin, norfloxacin and levofloxacin was determined by disc diffusion, and the genomes were sequenced. Based on epidemiological cut-offs, we developed a QUInolone Resistance Mechanisms Inference Algorithm (QUIRMIA) to infer the underlying resistance mechanisms responsible for the corresponding phenotypes, resulting in the categorization as \u201csusceptible\u201d (wildtype), \u201clow-level resistance\u201d (non-wildtype) and \u201chigh-level resistance\u201d (non-wildtype). The congruence of phenotypes and whole genome sequencing (WGS)-derived genotypes was then assigned using QUIRMIA- and EUCAST-based AST interpretation. Results: QUIRMIA-based inference of resistance mechanisms and sequencing data were highly congruent (542\/553, 98%). In contrast, EUCAST-based classification with its binary classification into \u201csusceptible\u201d and \u201cresistant\u201d isolates failed to recognize and properly categorize low-level resistant isolates. Conclusions: QUIRMIA provides a coherent genotype\/phenotype categorization and may be integrated in the EUCAST expert rule set, thereby enabling reliable detection of low-level resistant isolates, which may help to better predict outcome and to prevent the emergence of clinical resistance.<\/jats:p>","DOI":"10.3390\/antibiotics12071119","type":"journal-article","created":{"date-parts":[[2023,6,29]],"date-time":"2023-06-29T00:41:45Z","timestamp":1687999305000},"page":"1119","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["QUIRMIA\u2014A Phenotype-Based Algorithm for the Inference of Quinolone Resistance Mechanisms in Escherichia coli"],"prefix":"10.3390","volume":"12","author":[{"given":"Frank","family":"Imkamp","sequence":"first","affiliation":[{"name":"Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elias","family":"Bodendoerfer","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Mancini","sequence":"additional","affiliation":[{"name":"Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,6,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"249","DOI":"10.2174\/1568026033452537","article-title":"Fluoroquinolones: Action and resistance","volume":"3","author":"Drlica","year":"2003","journal-title":"Curr. 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