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Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors. Molecules 2021; 26:molecules26051234. [PMID: 33669078 PMCID: PMC7956263 DOI: 10.3390/molecules26051234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.
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Weidlich D, Klostermeier D. Functional interactions between gyrase subunits are optimized in a species-specific manner. J Biol Chem 2020; 295:2299-2312. [PMID: 31953321 DOI: 10.1074/jbc.ra119.010245] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/03/2020] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase is a bacterial DNA topoisomerase that catalyzes ATP-dependent negative DNA supercoiling and DNA decatenation. The enzyme is a heterotetramer comprising two GyrA and two GyrB subunits. Its overall architecture is conserved, but species-specific elements in the two subunits are thought to optimize subunit interaction and enzyme function. Toward understanding the roles of these different elements, we compared the activities of Bacillus subtilis, Escherichia coli, and Mycobacterium tuberculosis gyrases and of heterologous enzymes reconstituted from subunits of two different species. We show that B. subtilis and E. coli gyrases are proficient DNA-stimulated ATPases and efficiently supercoil and decatenate DNA. In contrast, M. tuberculosis gyrase hydrolyzes ATP only slowly and is a poor supercoiling enzyme and decatenase. The heterologous enzymes are generally less active than their homologous counterparts. The only exception is a gyrase reconstituted from mycobacterial GyrA and B. subtilis GyrB, which exceeds the activity of M. tuberculosis gyrase and reaches the activity of the B. subtilis gyrase, indicating that the activities of enzymes containing mycobacterial GyrB are limited by ATP hydrolysis. The activity pattern of heterologous gyrases is in agreement with structural features present: B. subtilis gyrase is a minimal enzyme, and its subunits can functionally interact with subunits from other bacteria. In contrast, the specific insertions in E. coli and mycobacterial gyrase subunits appear to prevent efficient functional interactions with heterologous subunits. Understanding the molecular details of gyrase adaptations to the specific physiological requirements of the respective organism might aid in the development of species-specific gyrase inhibitors.
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Affiliation(s)
- Daniela Weidlich
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
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Klostermeier D. Why Two? On the Role of (A-)Symmetry in Negative Supercoiling of DNA by Gyrase. Int J Mol Sci 2018; 19:E1489. [PMID: 29772727 PMCID: PMC5983639 DOI: 10.3390/ijms19051489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 11/17/2022] Open
Abstract
Gyrase is a type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme consists of two GyrA and two GyrB subunits. It is believed to introduce negative supercoils into DNA by converting a positive DNA node into a negative node through strand passage: First, it cleaves both DNA strands of a double-stranded DNA, termed the G-segment, and then it passes a second segment of the same DNA molecule, termed the T-segment, through the gap created. As a two-fold symmetric enzyme, gyrase contains two copies of all elements that are key for the supercoiling reaction: The GyrB subunits provide two active sites for ATP binding and hydrolysis. The GyrA subunits contain two C-terminal domains (CTDs) for DNA binding and wrapping to stabilize the positive DNA node, and two catalytic tyrosines for DNA cleavage. While the presence of two catalytic tyrosines has been ascribed to the necessity of cleaving both strands of the G-segment to enable strand passage, the role of the two ATP hydrolysis events and of the two CTDs has been less clear. This review summarizes recent results on the role of these duplicate elements for individual steps of the supercoiling reaction, and discusses the implications for the mechanism of DNA supercoiling.
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Affiliation(s)
- Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany.
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4
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Hartmann S, Gubaev A, Klostermeier D. Binding and Hydrolysis of a Single ATP Is Sufficient for N-Gate Closure and DNA Supercoiling by Gyrase. J Mol Biol 2017; 429:3717-3729. [PMID: 29032205 DOI: 10.1016/j.jmb.2017.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 11/19/2022]
Abstract
Topoisomerases catalyze the relaxation, supercoiling, catenation, and decatenation of DNA. Gyrase is a bacterial topoisomerase that introduces negative supercoils into DNA in an ATP-dependent reaction. The enzyme consists of two GyrB subunits, containing the ATPase domains, and two GyrA subunits. Nucleotide binding to gyrase B GyrB causes closing of the N-gate in gyrase, which orients bound DNA for supercoiling. N-gate re-opening after ATP hydrolysis, at the end of the supercoiling reaction, resets the enzyme for subsequent catalytic cycles. Gyrase binds and hydrolyzes two ATP molecules per catalytic cycle. Here, we dissect the role of these two binding and hydrolysis events using gyrase with one ATP-binding- and hydrolysis-deficient subunit, or with one binding-competent, but hydrolysis-deficient ATPase domain. We show that binding of a single ATP molecule induces N-gate closure. Gyrase that can only bind and hydrolyze a single ATP undergoes opening and closing of the N-gate in synchrony with ATP hydrolysis, and promotes DNA supercoiling under catalytic conditions. In contrast, gyrase that can bind two ATP molecules, but hydrolyzes only one, only supercoils DNA under stoichiometric conditions. Here, ATP bound to the hydrolysis-deficient subunit keeps the N-gate closed after hydrolysis of the other ATP and prevents further turnovers. Gyrase with only one functional ATPase domain hydrolyzes ATP with a similar rate to wild-type, but its supercoiling efficiency is reduced. Binding and hydrolysis of the second ATP may thus ensure efficient coupling of the nucleotide cycle with the supercoiling reaction by stabilizing the closed N-gate and by acting as a timer for N-gate re-opening.
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Affiliation(s)
- Simon Hartmann
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Airat Gubaev
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany.
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Hartmann S, Weidlich D, Klostermeier D. Single-Molecule Confocal FRET Microscopy to Dissect Conformational Changes in the Catalytic Cycle of DNA Topoisomerases. Methods Enzymol 2016; 581:317-351. [PMID: 27793284 DOI: 10.1016/bs.mie.2016.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Molecular machines undergo large-scale conformational changes during their catalytic cycles that are linked to their biological functions. DNA topoisomerases are molecular machines that interconvert different DNA topoisomers and resolve torsional stress that is introduced during cellular processes that involve local DNA unwinding. DNA gyrase catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. During its catalytic cycle, gyrase undergoes large-scale conformational changes that drive the supercoiling reaction. These conformational changes can be followed by single-molecule Förster resonance energy transfer (FRET). Here, we use DNA gyrase from Bacillus subtilis as an illustrative example to present strategies for the investigation of conformational dynamics of multisubunit complexes. We provide a brief introduction into single-molecule FRET and confocal microscopy, with a focus on practical considerations in sample preparation and data analysis. Different strategies in the preparation of donor-acceptor-labeled molecules suitable for single-molecule FRET experiments are outlined. The insight into the mechanism of DNA supercoiling by gyrase gained from single-molecule FRET experiment is summarized. The general strategies described here can also be applied to investigate conformational changes and their link to biological function of other multisubunit molecular machines.
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Affiliation(s)
- S Hartmann
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany
| | - D Weidlich
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany
| | - D Klostermeier
- Institute for Physical Chemistry, University of Muenster, Muenster, Germany.
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Gubaev A, Weidlich D, Klostermeier D. DNA gyrase with a single catalytic tyrosine can catalyze DNA supercoiling by a nicking-closing mechanism. Nucleic Acids Res 2016; 44:10354-10366. [PMID: 27557712 PMCID: PMC5137430 DOI: 10.1093/nar/gkw740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/20/2016] [Accepted: 08/12/2016] [Indexed: 01/10/2023] Open
Abstract
The topological state of DNA is important for replication, recombination and transcription, and is regulated in vivo by DNA topoisomerases. Gyrase introduces negative supercoils into DNA at the expense of ATP hydrolysis. It is the accepted view that gyrase achieves supercoiling by a strand passage mechanism, in which double-stranded DNA is cleaved, and a second double-stranded segment is passed through the gap, converting a positive DNA node into a negative node. We show here that gyrase with only one catalytic tyrosine that cleaves a single strand of its DNA substrate can catalyze DNA supercoiling without strand passage. We propose an alternative mechanism for DNA supercoiling via nicking and closing of DNA that involves trapping, segregation and relaxation of two positive supercoils. In contrast to DNA supercoiling, ATP-dependent relaxation and decatenation of DNA by gyrase lacking the C-terminal domains require both tyrosines and strand passage. Our results point towards mechanistic plasticity of gyrase and might pave the way for finding novel and specific mechanism-based gyrase inhibitors.
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Affiliation(s)
- Airat Gubaev
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Daniela Weidlich
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
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7
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Structural Dynamics and Mechanochemical Coupling in DNA Gyrase. J Mol Biol 2016; 428:1833-45. [PMID: 27016205 DOI: 10.1016/j.jmb.2016.03.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/16/2016] [Accepted: 03/15/2016] [Indexed: 11/22/2022]
Abstract
Gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex. Here we present a current understanding of mechanochemical coupling in this essential molecular machine, with a focus on recent diverse biophysical approaches that have revealed details of molecular architectures, new conformational intermediates, structural transitions modulated by ATP binding, and the influence of mechanics on motor function. Recent single-molecule assays have also illuminated the reciprocal relationships between supercoiling and transcription, an illustration of mechanical interactions between gyrase and other molecular machines at the heart of chromosomal biology.
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Luan G, Bao G, Lin Z, Li Y, Chen Z, Li Y, Cai Z. Comparative genome analysis of a thermotolerant Escherichia coli obtained by Genome Replication Engineering Assisted Continuous Evolution (GREACE) and its parent strain provides new understanding of microbial heat tolerance. N Biotechnol 2015; 32:732-8. [DOI: 10.1016/j.nbt.2015.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 11/15/2022]
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Hearnshaw SJ, Chung TTH, Stevenson CEM, Maxwell A, Lawson DM. The role of monovalent cations in the ATPase reaction of DNA gyrase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:996-1005. [PMID: 25849408 PMCID: PMC4388272 DOI: 10.1107/s1399004715002916] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/10/2015] [Indexed: 11/25/2022]
Abstract
Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.
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Affiliation(s)
- Stephen James Hearnshaw
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - Terence Tsz-Hong Chung
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - David Mark Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
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Gubaev A, Klostermeier D. Reprint of "The mechanism of negative DNA supercoiling: a cascade of DNA-induced conformational changes prepares gyrase for strand passage". DNA Repair (Amst) 2014; 20:130-141. [PMID: 24974097 DOI: 10.1016/j.dnarep.2014.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/03/2014] [Accepted: 01/13/2014] [Indexed: 01/04/2023]
Abstract
DNA topoisomerases inter-convert different DNA topoisomers in the cell. They catalyze the introduction or relaxation of DNA supercoils, as well as catenation and decatenation. Members of the type I topoisomerase family cleave a single strand of their double-stranded DNA substrate, whereas enzymes of the type II family cleave both DNA strands. Bacterial DNA gyrase, a type II topoisomerase, catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. Gyrase is not present in humans, and constitutes an attractive drug target for the treatment of bacterial and parasite infections. DNA supercoiling by gyrase is believed to occur by a strand passage mechanism, in which one segment of the double-stranded DNA substrate is passed through a (transient) break in a second segment. This mechanism requires the coordinated opening and closing of three protein interfaces, so-called gates, to ensure the directionality of strand passage toward negative supercoiling. Single molecule fluorescence resonance energy transfer experiments are ideally suited to investigate conformational changes during the catalytic cycle of DNA topoisomerases. In this review, we summarize the current knowledge on the cascade of DNA- and nucleotide-induced conformational changes in gyrase that lead to strand passage and negative supercoiling of DNA. We discuss how these conformational changes couple ATP hydrolysis to DNA supercoiling in gyrase, and how the common mechanistic principle of coordinated gate opening and closing is modulated to allow for the catalysis of different reactions by different type II topoisomerases.
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Affiliation(s)
- Airat Gubaev
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
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Gubaev A, Klostermeier D. The mechanism of negative DNA supercoiling: a cascade of DNA-induced conformational changes prepares gyrase for strand passage. DNA Repair (Amst) 2014; 16:23-34. [PMID: 24674625 DOI: 10.1016/j.dnarep.2014.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/03/2014] [Accepted: 01/13/2014] [Indexed: 11/29/2022]
Abstract
DNA topoisomerases inter-convert different DNA topoisomers in the cell. They catalyze the introduction or relaxation of DNA supercoils, as well as catenation and decatenation. Members of the type I topoisomerase family cleave a single strand of their double-stranded DNA substrate, whereas enzymes of the type II family cleave both DNA strands. Bacterial DNA gyrase, a type II topoisomerase, catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. Gyrase is not present in humans, and constitutes an attractive drug target for the treatment of bacterial and parasite infections. DNA supercoiling by gyrase is believed to occur by a strand passage mechanism, in which one segment of the double-stranded DNA substrate is passed through a (transient) break in a second segment. This mechanism requires the coordinated opening and closing of three protein interfaces, so-called gates, to ensure the directionality of strand passage toward negative supercoiling. Single molecule fluorescence resonance energy transfer experiments are ideally suited to investigate conformational changes during the catalytic cycle of DNA topoisomerases. In this review, we summarize the current knowledge on the cascade of DNA- and nucleotide-induced conformational changes in gyrase that lead to strand passage and negative supercoiling of DNA. We discuss how these conformational changes couple ATP hydrolysis to DNA supercoiling in gyrase, and how the common mechanistic principle of coordinated gate opening and closing is modulated to allow for the catalysis of different reactions by different type II topoisomerases.
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Affiliation(s)
- Airat Gubaev
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
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Shoji H, Shirakura T, Fukuchi K, Takuma T, Hanaki H, Tanaka K, Niki Y. A molecular analysis of quinolone-resistant Haemophilus influenzae: validation of the mutations in Quinolone Resistance-Determining Regions. J Infect Chemother 2014; 20:250-5. [PMID: 24480551 DOI: 10.1016/j.jiac.2013.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/19/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
The mechanism of quinolone-resistance is considered to be amino acid mutations in the type II topoisomerase. We validated the genetic mechanisms of quinolone resistance in Haemophilus influenzae. We obtained 29 H. influenzae strains from a nationwide surveillance program in Japan (including 11 quinolone-resistant strains [moxifloxacin: MFLX or levofloxacin MIC ≥2 μg/ml]). We analyzed the sequences of the Quinolone Resistance-Determining Regions (QRDRs) in GyrA, GyrB, ParC and ParE. Furthermore, we induced resistance in susceptible strains by exposing them to quinolone, and investigated the relationship between mutations in the QRDRs and the MICs. Five amino acid substitutions in GyrA (at Ser84 and Asp88) and ParC (at Gly82, Ser84 and Glu88) were found to be closely related to the MICs. The strains with a MFLX MIC of 0.125-1 and 2-4 μg/ml had one and two mutations, respectively. The strains with a MFLX MIC of ≥8 μg/ml had three or more mutations. The strains with induced resistance with MFLX MICs of 0.5-1 and ≥2 μg/ml also had one and two mutations, respectively. We confirmed that these five mutations strongly contribute to quinolone resistance and found that the degree of resistance is related to the number of the mutations. In addition, the three strains of 18 susceptible strains (16.7%) also had a single mutation. These strains may therefore be in the initial stage of quinolone resistance. Currently, the frequency of quinolone-resistant H. influenzae is still low. However, as has occurred with β-lactams, an increase in quinolone use may lead to more quinolone-resistant strains.
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Affiliation(s)
- Hisashi Shoji
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan.
| | - Tetsuro Shirakura
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan
| | - Kunihiko Fukuchi
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan
| | - Takahiro Takuma
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan
| | - Hideaki Hanaki
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan
| | - Kazuo Tanaka
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan
| | - Yoshihito Niki
- Showa University, School of Medicine, Department of Medicine, Division of Clinical Infectious Diseases, 1-5-8, Hatanodai, Shinagawa, Tokyo, Japan
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