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Bové M, Kolpen M, Lichtenberg M, Bjarnsholt T, Coenye T. Adaptation of Pseudomonas aeruginosa biofilms to tobramycin and the quorum sensing inhibitor C-30 during experimental evolution requires multiple genotypic and phenotypic changes. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001278. [PMID: 36748633 PMCID: PMC9993117 DOI: 10.1099/mic.0.001278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In the present study we evaluated the fitness, antimicrobial susceptibility, metabolic activity, gene expression, in vitro production of virulence factors and in vivo virulence of experimentally evolved Pseudomonas aeruginosa PAO1. These strains were previously evolved in the presence of tobramycin and the quorum sensing inhibitor furanone C-30 (C-30) and carried mutations in mexT and fusA1. Compared to the wild-type (WT), the evolved strains show a different growth rate and different metabolic activity, suggesting they have an altered fitness. mexT mutants were less susceptible to C-30 than WT strains; they also show reduced susceptibility to chloramphenicol and ciprofloxacin, two substrates of the MexEF-OprN efflux pump. fusA1 mutants had a decreased susceptibility to aminoglycoside antibiotics, and an increased susceptibility to chloramphenicol. The decreased antimicrobial susceptibility and decreased susceptibility to C-30 was accompanied by a changed metabolic activity profile during treatment. The expression of mexE was significantly increased in mexT mutants and induced by C-30, suggesting that MexEF-OprN exports C-30 out of the bacterial cell. The in vitro production of virulence factors as well as virulence in two in vivo models of the strains evolved in the presence of C-30 was unchanged compared to the virulence of the WT. Finally, the evolved strains were less susceptible towards tobramycin (alone and combined with C-30) in an in vivo mouse model. In conclusion, this study shows that mutations acquired during experimental evolution of P. aeruginosa biofilms in the presence of tobramycin and C-30, are accompanied by an altered fitness, metabolism, mexE expression and in vitro and in vivo antimicrobial susceptibility.
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Affiliation(s)
- Mona Bové
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen N, Denmark
| | - Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.,Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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2
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Roemhild R, Schulenburg H. Evolutionary ecology meets the antibiotic crisis: Can we control pathogen adaptation through sequential therapy? EVOLUTION MEDICINE AND PUBLIC HEALTH 2019; 2019:37-45. [PMID: 30906555 PMCID: PMC6423369 DOI: 10.1093/emph/eoz008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/19/2019] [Indexed: 01/01/2023]
Abstract
The spread of antibiotic resistance is a global challenge that is fueled by evolution and ecological processes. Therefore, the design of new sustainable therapy should take account of these underlying processes—as proposed within the field of evolutionary medicine, yet usually not receiving the necessary attention from national and international health agencies. We here put the spotlight on a currently neglected treatment strategy: sequential therapy. Changes among antibiotics generate fluctuating selection conditions that are in general difficult to counter by any organism. We argue that sequential treatment designs can be specifically optimized by exploiting evolutionary trade-offs, for example collateral sensitivity and/or inducible physiological constraints, such as negative hysteresis, where pre-exposure to one antibiotic induces temporary hyper-sensitivity to another antibiotic. Our commentary provides an overview of sequential treatment strategies and outlines steps towards their further optimization.
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Affiliation(s)
- Roderich Roemhild
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel, Germany.,Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel, Germany.,Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, Germany
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3
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Podnecky NL, Fredheim EGA, Kloos J, Sørum V, Primicerio R, Roberts AP, Rozen DE, Samuelsen Ø, Johnsen PJ. Conserved collateral antibiotic susceptibility networks in diverse clinical strains of Escherichia coli. Nat Commun 2018; 9:3673. [PMID: 30202004 PMCID: PMC6131505 DOI: 10.1038/s41467-018-06143-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
There is urgent need to develop novel treatment strategies to reduce antimicrobial resistance. Collateral sensitivity (CS), where resistance to one antimicrobial increases susceptibility to other drugs, might enable selection against resistance during treatment. However, the success of this approach would depend on the conservation of CS networks across genetically diverse bacterial strains. Here, we examine CS conservation across diverse Escherichia coli strains isolated from urinary tract infections. We determine collateral susceptibilities of mutants resistant to relevant antimicrobials against 16 antibiotics. Multivariate statistical analyses show that resistance mechanisms, in particular efflux-related mutations, as well as the relative fitness of resistant strains, are principal contributors to collateral responses. Moreover, collateral responses shift the mutant selection window, suggesting that CS-informed therapies may affect evolutionary trajectories of antimicrobial resistance. Our data allow optimism for CS-informed therapy and further suggest that rapid detection of resistance mechanisms is important to accurately predict collateral responses.
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Affiliation(s)
- Nicole L Podnecky
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Elizabeth G A Fredheim
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Kloos
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Adam P Roberts
- Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9037, Tromsø, Norway
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
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4
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Hu Y, Miller M, Zhang B, Nguyen TT, Nielsen MK, Aroian RV. In vivo and in vitro studies of Cry5B and nicotinic acetylcholine receptor agonist anthelmintics reveal a powerful and unique combination therapy against intestinal nematode parasites. PLoS Negl Trop Dis 2018; 12:e0006506. [PMID: 29775454 PMCID: PMC5979042 DOI: 10.1371/journal.pntd.0006506] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/31/2018] [Accepted: 05/08/2018] [Indexed: 01/21/2023] Open
Abstract
Background The soil-transmitted nematodes (STNs) or helminths (hookworms, whipworms, large roundworms) infect the intestines of ~1.5 billion of the poorest peoples and are leading causes of morbidity worldwide. Only one class of anthelmintic or anti-nematode drugs, the benzimidazoles, is currently used in mass drug administrations, which is a dangerous situation. New anti-nematode drugs are urgently needed. Bacillus thuringiensis crystal protein Cry5B is a powerful, promising new candidate. Drug combinations, when properly made, are ideal for treating infectious diseases. Although there are some clinical trials using drug combinations against STNs, little quantitative and systemic work has been performed to define the characteristics of these combinations in vivo. Methodology/Principal findings Working with the hookworm Ancylostoma ceylanicum-hamster infection system, we establish a laboratory paradigm for studying anti-nematode combinations in vivo using Cry5B and the nicotinic acetylcholine receptor (nAChR) agonists tribendimidine and pyrantel pamoate. We demonstrate that Cry5B strongly synergizes in vivo with both tribendimidine and pyrantel at specific dose ratios against hookworm infections. For example, whereas 1 mg/kg Cry5B and 1 mg/kg tribendimidine individually resulted in only a 0%-6% reduction in hookworm burdens, the combination of the two resulted in a 41% reduction (P = 0.020). Furthermore, when mixed at synergistic ratios, these combinations eradicate hookworm infections at doses where the individual doses do not. Using cyathostomin nematode parasites of horses, we find based on inhibitory concentration 50% values that a strongylid parasite population doubly resistant to nAChR agonists and benzimidazoles is more susceptible or “hypersusceptible” to Cry5B than a cyathostomin population not resistant to nAChR agonists, consistent with previous Caenhorhabditis elegans results. Conclusions/Significance Our study provides a powerful means by which anthelmintic combination therapies can be examined in vivo in the laboratory. In addition, we demonstrate that Cry5B and nAChR agonists have excellent combinatorial properties—Cry5B combined with nAChR agonists gives rise to potent cures that are predicted to be recalcitrant to the development of parasite resistance. These drug combinations highlight bright spots in new anthelmintic development for human and veterinary animal intestinal nematode infections. Intestinal nematodes are roundworm parasites of humans and animals, causing significant morbidity in both. In humans, these parasites are leading causes of morbidity in children, e.g., causing growth stunting, cognitive impairment, and malnutrition. Few drugs are used to treat these parasites in humans and animals and there is increasing evidence that the drugs are losing efficacy and/or have low efficacy. Infectious diseases are best treated with drug combinations and not single drugs. However, there has been little work to characterize in detail how various anti-nematode drugs combine. Here we establish a new laboratory model to study anti-nematode drug combinations using the human hookworm Ancylostoma ceylanicum infection in hamsters. We show that two classes of anti-nematode drugs, Cry5B and the nicotinic acetylcholine receptor agonists tribendimidine and pyrantel, combine (synergize) in a way that is more powerful at specific drug ratios than predicted from their individual impacts. Furthermore, when combined at these ratios, these combinations completely eliminated parasites at doses where normally neither drug has that effect. Horse parasites resistant to pyrantel also appear to be hypersensitive (more sensitive than wild-type parasites) to Cry5B. These characteristics predict that combinations of Cry5B with tribendimidine or pyrantel will be extremely effective therapeutically and relatively recalcitrant to the development of parasite resistance.
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Affiliation(s)
- Yan Hu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Melanie Miller
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Bo Zhang
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Thanh-Thanh Nguyen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Martin K. Nielsen
- Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
| | - Raffi V. Aroian
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
- * E-mail:
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Affiliation(s)
- Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
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6
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Hickman RA, Munck C, Sommer MOA. Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs. Front Microbiol 2017; 8:893. [PMID: 28596757 PMCID: PMC5442168 DOI: 10.3389/fmicb.2017.00893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/03/2017] [Indexed: 12/18/2022] Open
Abstract
Understanding the evolutionary processes that lead to antibiotic resistance can help to achieve better treatment strategies. Yet, little is known about the dynamics of the resistance alleles during adaptation. Here, we use population sequencing to monitor genetic changes in putative resistance loci at several time-points during adaptive evolution experiments involving five different antibiotic conditions. We monitor the mutational spectra in lineages evolved to be resistant to single antibiotics [amikacin (AMK), chloramphenicol (CHL), and ciprofloxacin (CIP)], as well as antibiotic combinations (AMK + CHL and CHL + CIP). We find that lineages evolved to antibiotic combinations exhibit different resistance allele dynamics compared with those of single-drug evolved lineages, especially for a drug pair with reciprocal collateral sensitivity. During adaptation, we observed interfering, superimposing and fixation allele dynamics. To further understand the selective forces driving specific allele dynamics, a subset of mutations were introduced into the ancestral wild type enabling differentiation between clonal interference and negative epistasis.
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Affiliation(s)
- Rachel A Hickman
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
| | - Christian Munck
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
| | - Morten O A Sommer
- Bacterial Synthetic Biology, Novo Nordisk Foundation, Center for Biosustainability, Technical University of DenmarkKongens Lyngby, Denmark
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7
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Jahn LJ, Munck C, Ellabaan MMH, Sommer MOA. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes. Front Microbiol 2017; 8:816. [PMID: 28553265 PMCID: PMC5425606 DOI: 10.3389/fmicb.2017.00816] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 12/01/2022] Open
Abstract
Antibiotic resistance is a global threat to human health, wherefore it is crucial to study the mechanisms of antibiotic resistance as well as its emergence and dissemination. One way to analyze the acquisition of de novo mutations conferring antibiotic resistance is adaptive laboratory evolution. However, various evolution methods exist that utilize different population sizes, selection strengths, and bottlenecks. While evolution in increasing drug gradients guarantees high-level antibiotic resistance promising to identify the most potent resistance conferring mutations, other selection regimes are simpler to implement and therefore allow higher throughput. The specific regimen of adaptive evolution may have a profound impact on the adapted cell state. Indeed, substantial effects of the selection regime on the resulting geno- and phenotypes have been reported in the literature. In this study we compare the geno- and phenotypes of Escherichia coli after evolution to Amikacin, Piperacillin, and Tetracycline under four different selection regimes. Interestingly, key mutations that confer antibiotic resistance as well as phenotypic changes like collateral sensitivity and cross-resistance emerge independently of the selection regime. Yet, lineages that underwent evolution under mild selection displayed a growth advantage independently of the acquired level of antibiotic resistance compared to lineages adapted under maximal selection in a drug gradient. Our data suggests that even though different selection regimens result in subtle genotypic and phenotypic differences key adaptations appear independently of the selection regime.
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Affiliation(s)
- Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Christian Munck
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkHørsholm, Denmark
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8
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Andersson D, Hughes D, Kubicek-Sutherland J. Mechanisms and consequences of bacterial resistance to antimicrobial peptides. Drug Resist Updat 2016; 26:43-57. [DOI: 10.1016/j.drup.2016.04.002] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
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9
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Reales-Calderon JA, Blanco P, Alcalde-Rico M, Corona F, Lira F, Hernando-Amado S, Bernardini A, Sánchez MB, Martínez JL. Use of phenotype microarrays to study the effect of acquisition of resistance to antimicrobials in bacterial physiology. Res Microbiol 2016; 167:723-730. [PMID: 27106258 DOI: 10.1016/j.resmic.2016.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/03/2016] [Accepted: 04/07/2016] [Indexed: 01/17/2023]
Abstract
It is widely accepted that the acquisition of resistance to antimicrobials confers a fitness cost. Different works have shown that the effect of acquiring resistance in bacterial physiology may be more specific than previously thought. Study of these specific changes may help to predict the outcome of resistant organisms in different ecosystems. In addition to changing bacterial physiology, acquisition of resistance either increases or reduces susceptibility to other antimicrobials. In the current article, we review recent information on the effect of acquiring resistance upon bacterial physiology, with a specific focus on studies using phenotype microarray technology.
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Affiliation(s)
- Jose A Reales-Calderon
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Paula Blanco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Manuel Alcalde-Rico
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Felipe Lira
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - Alejandra Bernardini
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - María B Sánchez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
| | - José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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Munck C, Gumpert HK, Wallin AIN, Wang HH, Sommer MOA. Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci Transl Med 2015; 6:262ra156. [PMID: 25391482 DOI: 10.1126/scitranslmed.3009940] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Resistance arises quickly during chemotherapeutic selection and is particularly problematic during long-term treatment regimens such as those for tuberculosis, HIV infections, or cancer. Although drug combination therapy reduces the evolution of drug resistance, drug pairs vary in their ability to do so. Thus, predictive models are needed to rationally design resistance-limiting therapeutic regimens. Using adaptive evolution, we studied the resistance response of the common pathogen Escherichia coli to 5 different single antibiotics and all 10 different antibiotic drug pairs. By analyzing the genomes of all evolved E. coli lineages, we identified the mutational events that drive the differences in drug resistance levels and found that the degree of resistance development against drug combinations can be understood in terms of collateral sensitivity and resistance that occurred during adaptation to the component drugs. Then, using engineered E. coli strains, we confirmed that drug resistance mutations that imposed collateral sensitivity were suppressed in a drug pair growth environment. These results provide a framework for rationally selecting drug combinations that limit resistance evolution.
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Affiliation(s)
- Christian Munck
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Heidi K Gumpert
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Annika I Nilsson Wallin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Morten O A Sommer
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
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Hughes D, Andersson DI. Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms. Nat Rev Genet 2015; 16:459-71. [DOI: 10.1038/nrg3922] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Phenotypic Suppression of Streptomycin Resistance by Mutations in Multiple Components of the Translation Apparatus. J Bacteriol 2015; 197:2981-8. [PMID: 26148717 DOI: 10.1128/jb.00219-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/02/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The bacterial ribosome and its associated translation factors are frequent targets of antibiotics, and antibiotic resistance mutations have been found in a number of these components. Such mutations can potentially interact with one another in unpredictable ways, including the phenotypic suppression of one mutation by another. These phenotypic interactions can provide evidence of long-range functional interactions throughout the ribosome and its functional complexes and potentially give insights into antibiotic resistance mechanisms. In this study, we used genetics and experimental evolution of the thermophilic bacterium Thermus thermophilus to examine the ability of mutations in various components of the protein synthesis apparatus to suppress the streptomycin resistance phenotypes of mutations in ribosomal protein S12, specifically those located distant from the streptomycin binding site. With genetic selections and strain constructions, we identified suppressor mutations in EF-Tu or in ribosomal protein L11. Using experimental evolution, we identified amino acid substitutions in EF-Tu or in ribosomal proteins S4, S5, L14, or L19, some of which were found to also relieve streptomycin resistance. The wide dispersal of these mutations is consistent with long-range functional interactions among components of the translational machinery and indicates that streptomycin resistance can result from the modulation of long-range conformational signals. IMPORTANCE The thermophilic bacterium Thermus thermophilus has become a model system for high-resolution structural studies of macromolecular complexes, such as the ribosome, while its natural competence for transformation facilitates genetic approaches. Genetic studies of T. thermophilus ribosomes can take advantage of existing high-resolution crystallographic information to allow a structural interpretation of phenotypic interactions among mutations. Using a combination of genetic selections, strain constructions, and experimental evolution, we find that certain mutations in the translation apparatus can suppress the phenotype of certain antibiotic resistance mutations. Suppression of resistance can occur by mutations located distant in the ribosome or in a translation factor. These observations suggest the existence of long-range conformational signals in the translating ribosome, particularly during the decoding of mRNA.
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Pál C, Papp B, Lázár V. Collateral sensitivity of antibiotic-resistant microbes. Trends Microbiol 2015; 23:401-7. [PMID: 25818802 DOI: 10.1016/j.tim.2015.02.009] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/09/2015] [Accepted: 02/23/2015] [Indexed: 11/15/2022]
Abstract
Understanding how evolution of microbial resistance towards a given antibiotic influences susceptibility to other drugs is a challenge of profound importance. By combining laboratory evolution, genome sequencing, and functional analyses, recent works have charted the map of evolutionary trade-offs between antibiotics and have explored the underlying molecular mechanisms. Strikingly, mutations that caused multidrug resistance in bacteria simultaneously enhanced sensitivity to many other unrelated drugs (collateral sensitivity). Here, we explore how this emerging research sheds new light on resistance mechanisms and the way it could be exploited for the development of alternative antimicrobial strategies.
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Affiliation(s)
- Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
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14
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Gimode WR, Kiboi DM, Kimani FT, Wamakima HN, Burugu MW, Muregi FW. Fitness cost of resistance for lumefantrine and piperaquine-resistant Plasmodium berghei in a mouse model. Malar J 2015; 14:38. [PMID: 25627576 PMCID: PMC4336485 DOI: 10.1186/s12936-015-0550-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/06/2015] [Indexed: 01/12/2023] Open
Abstract
Background The evolution of drug-resistant parasites is a major hindrance to malaria control, and thus understanding the behaviour of drug-resistant mutants is of clinical relevance. The study aimed to investigate how resistance against lumefantrine (LU) and piperaquine (PQ), anti-malarials used as partner drugs in artemisinin-based combination therapy (ACT), impacts parasite fitness. This is important since resistance to ACT, the first-line anti-malarial regimen is increasingly being reported. Methods The stability of Plasmodium berghei ANKA strain that was previously selected for LU and PQ resistance was evaluated using the 4-day assay and established infection test in mice. Fitness cost of resistance was determined by comparing parasites proliferation rates in absence of drug pressure for the drug-exposed parasites between day 4 and 7 post-infection (pi), relative to the wild-type. Statistical analysis of data to compare mean parasitaemia and growth rates of respective parasite lines was carried out using student’s t-test and one-way analysis of variance, with significance level set at p<0.05. Results During serial passaging in the absence of the drug, the PQ-resistant parasite maintained low growth rates at day 7 pi (mean parasitaemia, 5.6% ± 2.3) relative to the wild-type (28.4% ± 6.6), translating into a fitness cost of resistance of 80.3%. Whilst resistance phenotype for PQ was stable, that of LU was transient since after several serial passages in the absence of drug, the LU-exposed line assumed the growth patterns of the wild-type. Conclusions The contrasting behaviour of PQ- and LU-resistance phenotypes support similar findings which indicate that even for drugs within the same chemical class, resistance-conferred traits may vary on how they influence parasite fitness and virulence. Resistance-mediating polymorphisms have been associated with less fit malaria parasites. In the absence of drug pressure in the field, it is therefore likely that the wild-type parasite will out-compete the mutant form. This implies the possibility of reintroducing a drug previously lost to resistance, after a period of suspended use. Considering the recent reports of high failure rates associated with ACT, high fitness cost of resistance to PQ is therefore of clinical relevance as the drug is a partner in ACT.
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Affiliation(s)
- Winnie R Gimode
- Department of Biochemistry and Biotechnology, Kenyatta University, P.O. Box 43844, Nairobi, Kenya.
| | - Daniel M Kiboi
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62 000, Nairobi, Kenya.
| | - Francis T Kimani
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute (KEMRI), P.O. Box 54840, Nairobi, Kenya.
| | - Hannah N Wamakima
- Centre for Traditional Medicine and Drug Research, Kenya Medical Research Institute (KEMRI), P.O. Box 54840, Nairobi, Kenya.
| | - Marion W Burugu
- Department of Biochemistry and Biotechnology, Kenyatta University, P.O. Box 43844, Nairobi, Kenya.
| | - Francis W Muregi
- Directorate of Research and Development, Mount Kenya University, P.O. Box 342-01000, Thika, Kenya.
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15
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Lázár V, Nagy I, Spohn R, Csörgő B, Györkei Á, Nyerges Á, Horváth B, Vörös A, Busa-Fekete R, Hrtyan M, Bogos B, Méhi O, Fekete G, Szappanos B, Kégl B, Papp B, Pál C. Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network. Nat Commun 2014; 5:4352. [PMID: 25000950 PMCID: PMC4102323 DOI: 10.1038/ncomms5352] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 06/09/2014] [Indexed: 12/29/2022] Open
Abstract
Understanding how evolution of antimicrobial resistance increases resistance to other drugs is a challenge of profound importance. By combining experimental evolution and genome sequencing of 63 laboratory-evolved lines, we charted a map of cross-resistance interactions between antibiotics in Escherichia coli, and explored the driving evolutionary principles. Here, we show that (1) convergent molecular evolution is prevalent across antibiotic treatments, (2) resistance conferring mutations simultaneously enhance sensitivity to many other drugs and (3) 27% of the accumulated mutations generate proteins with compromised activities, suggesting that antibiotic adaptation can partly be achieved without gain of novel function. By using knowledge on antibiotic properties, we examined the determinants of cross-resistance and identified chemogenomic profile similarity between antibiotics as the strongest predictor. In contrast, cross-resistance between two antibiotics is independent of whether they show synergistic effects in combination. These results have important implications on the development of novel antimicrobial strategies. Understanding how evolution of antimicrobial resistance increases resistance to other drugs is of key importance. Here, Lazar et al. build a map of cross-resistance interactions between antibiotics in Escherichia coli and show that chemical and genomic similarities are good predictors of bacterial cross-resistance.
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Affiliation(s)
- Viktória Lázár
- 1] Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary [2]
| | - István Nagy
- 1] Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary [2]
| | - Réka Spohn
- 1] Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary [2]
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Ádám Györkei
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Horváth
- Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Andrea Vörös
- Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Róbert Busa-Fekete
- MTA-SZTE Research Group on Artificial Intelligence, Tisza Lajos krt 103., H-6720 Szeged, Hungary
| | - Mónika Hrtyan
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Bogos
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Szappanos
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Kégl
- Linear Accelerator Laboratory, University of Paris-Sud, CNRS, Orsay 91898, France
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
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16
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Lázár V, Pal Singh G, Spohn R, Nagy I, Horváth B, Hrtyan M, Busa-Fekete R, Bogos B, Méhi O, Csörgő B, Pósfai G, Fekete G, Szappanos B, Kégl B, Papp B, Pál C. Bacterial evolution of antibiotic hypersensitivity. Mol Syst Biol 2013; 9:700. [PMID: 24169403 PMCID: PMC3817406 DOI: 10.1038/msb.2013.57] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/25/2013] [Indexed: 12/15/2022] Open
Abstract
The evolution of resistance to a single antibiotic is frequently accompanied by increased resistance to multiple other antimicrobial agents. In sharp contrast, very little is known about the frequency and mechanisms underlying collateral sensitivity. In this case, genetic adaptation under antibiotic stress yields enhanced sensitivity to other antibiotics. Using large-scale laboratory evolutionary experiments with Escherichia coli, we demonstrate that collateral sensitivity occurs frequently during the evolution of antibiotic resistance. Specifically, populations adapted to aminoglycosides have an especially low fitness in the presence of several other antibiotics. Whole-genome sequencing of laboratory-evolved strains revealed multiple mechanisms underlying aminoglycoside resistance, including a reduction in the proton-motive force (PMF) across the inner membrane. We propose that as a side effect, these mutations diminish the activity of PMF-dependent major efflux pumps (including the AcrAB transporter), leading to hypersensitivity to several other antibiotics. More generally, our work offers an insight into the mechanisms that drive the evolution of negative trade-offs under antibiotic selection.
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Affiliation(s)
- Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Gajinder Pal Singh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Réka Spohn
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - István Nagy
- Genomics Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Horváth
- Genomics Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Mónika Hrtyan
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Róbert Busa-Fekete
- Linear Accelerator Laboratory, University of Paris-Sud, CNRS, Orsay, France
| | - Balázs Bogos
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - György Pósfai
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Szappanos
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Kégl
- Linear Accelerator Laboratory, University of Paris-Sud, CNRS, Orsay, France
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
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17
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The antibiotic resistome: challenge and opportunity for therapeutic intervention. Future Med Chem 2012; 4:347-59. [PMID: 22393941 DOI: 10.4155/fmc.12.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite the relevance of infectious disease as main causes of human morbidity and mortality, the development of new antibacterials is not among the highest priorities for pharmaceutical companies. Regulatory and economic issues, together with the lack of novel targets, might justify the reduced rate of discovery of new antimicrobials. With the increasing number of antibiotic resistant pathogens, the mechanisms of resistance appear as appealing alternatives for developing new drugs. Defining the elements that contribute to the characteristic phenotype of susceptibility to antibiotics of a given bacterial species, will serve to find those targets. Recent information on the elements forming part of bacterial intrinsic resistomes and on the inhibitors of resistance currently under development are presented. The possibility of developing new therapeutic procedures based on the administration, together with antibiotics of specific metabolic intermediates capable of increasing the susceptibility to antibiotics by altering bacterial physiology, are also discussed.
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18
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Abstract
In recent years, emerging and reemerging pathogens resistant to nearly all available antibiotics are on the rise. This limits the availability of effective antibiotics to treat infections, thus it is imperative to develop new drugs. The accumulation of alarmones guanosine tetraphosphate and guanosine pentaphosphate, collectively known as (p)ppGpp, is a global response of bacteria to environmental stress. (p)ppGpp has been documented to be involved in the resistance to beta-lactam and peptide antibiotics. Proposed mechanisms of action include occupation of drug targets, regulation of the expression of virulence determinants, and modification of protein activities. (p)ppGpp analogs might counteract these actions. Several such entities are being tested as new antibiotics. Further insights into the mechanisms of (p)ppGpp-mediated drug resistance might facilitate the discovery and development of novel antibiotics.
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Affiliation(s)
- Jun Wu
- Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, China
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19
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Andersson DI, Hughes D. Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 2010; 8:260-71. [PMID: 20208551 DOI: 10.1038/nrmicro2319] [Citation(s) in RCA: 1435] [Impact Index Per Article: 102.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most antibiotic resistance mechanisms are associated with a fitness cost that is typically observed as a reduced bacterial growth rate. The magnitude of this cost is the main biological parameter that influences the rate of development of resistance, the stability of the resistance and the rate at which the resistance might decrease if antibiotic use were reduced. These findings suggest that the fitness costs of resistance will allow susceptible bacteria to outcompete resistant bacteria if the selective pressure from antibiotics is reduced. Unfortunately, the available data suggest that the rate of reversibility will be slow at the community level. Here, we review the factors that influence the fitness costs of antibiotic resistance, the ways by which bacteria can reduce these costs and the possibility of exploiting them.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BOX 582, SE-751 23, Uppsala, Sweden.
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20
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Kempf I, Zeitouni S. [The cost of antibiotic resistance: analysis and consequences]. ACTA ACUST UNITED AC 2009; 60:e9-14. [PMID: 19942376 DOI: 10.1016/j.patbio.2009.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 10/27/2009] [Indexed: 11/16/2022]
Abstract
Antimicrobial resistance, either by mutation or acquisition of resistance determinants harbored by mobile genetic elements, may confer a biological cost for the bacteria. This biological cost can be evaluated by comparing the resistant mutant to the wild susceptible strain, in the absence of antibiotic selection. This fitness cost can affect the growth rate in vitro or the survival in the host or in the environment or the virulence capacity. Various studies have evidenced this cost, either in vitro or in vivo, in different analysis models. However, bacteria can evolve and adapt to reduce this cost, by compensatory mutations or fine regulation of resistance expression. This compensatory evolution allows resistant bacteria to persist even in the absence of antibiotic selection pressure.
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Affiliation(s)
- I Kempf
- Unite´ mycoplasmologie-bacteriologie, Zoopole-les-Croix, 22440 Ploufragan, France.
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21
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Garénaux A, Guillou S, Ermel G, Wren B, Federighi M, Ritz M. Role of the Cj1371 periplasmic protein and the Cj0355c two-component regulator in the Campylobacter jejuni NCTC 11168 response to oxidative stress caused by paraquat. Res Microbiol 2008; 159:718-26. [PMID: 18775777 DOI: 10.1016/j.resmic.2008.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 08/03/2008] [Indexed: 10/21/2022]
Abstract
Campylobacter jejuni is a microaerophilic pathogen representing one of the major causes of bacterial enteritis in humans. The oxidative stress response after exposure to paraquat, a strong oxidising agent, was analysed by two-dimensional protein electrophoresis and Maldi-ToF mass spectrometry. Oxidative stress and redox-related proteins were overexpressed: FldA flavodoxin and a pyruvate-flavodoxin oxidoreductase encoded by cj1476c. No increase in SodB expression was observed. An additional quantitative RT-PCR analysis showed an increase in katA but not in sodB expression. However, the sodB mutant was very sensitive to paraquat, its basal expression level being essential for oxidative stress resistance. Proteins related to iron homeostasis (Cft and a non-haem iron protein encoded by cj0012c) and general stress response (FusA and MreB) were found overexpressed. Interestingly, a two-component regulator encoded by cj0355c was differentially expressed in the presence of paraquat and could play a role in induction of the C. jejuni oxidative stress response. Virulence factors (CadF, FlaA and a VacJ homolog encoded by cj1371) were also found overexpressed under oxidative stress conditions and a cj1371 mutant showed increased sensitivity to paraquat, suggesting that the Cj1371 periplasmic protein could play a role in C. jejuni oxidative stress resistance.
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Affiliation(s)
- Amélie Garénaux
- UMR-INRA 1014 SECALIM ENVN/ENITIAA, Ecole Nationale Vétérinaire de Nantes, Route de Gachet-La Chantrerie, BP 40706, 44307 Nantes cedex 03, France.
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22
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Abstract
The ribosome is one of the main antibiotic targets in the cell. Recent years brought important insights into the mode of interaction of antibiotics with the ribosome and mechanisms of antibiotic action. Ribosome crystallography provided a detailed view of the interactions between antibiotics and rRNA. Advances in biochemical techniques let us better understand how the binding of small organic molecules can interfere with functions of an enzyme four orders of magnitude larger than the inhibitor. These and other achievements paved the way for the development of new ribosome-targeting antibiotics, some of which have already entered medical practice. The recent progress, problems and new directions of research of ribosome-targeting antibiotics are discussed in this review.
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Affiliation(s)
- Tanel Tenson
- Institute of Technology, University of Tartu, Estonia.
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