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Liu C, Liu J, Lu Q, Wang P, Zou Q. The Mechanism of Tigecycline Resistance in Acinetobacter baumannii under Sub-Minimal Inhibitory Concentrations of Tigecycline. Int J Mol Sci 2024; 25:1819. [PMID: 38339095 PMCID: PMC10855123 DOI: 10.3390/ijms25031819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The presence of sub-minimal inhibitory concentration (sub-MIC) antibiotics in our environment is widespread, and their ability to induce antibiotic resistance is inevitable. Acinetobacter baumannii, a pathogen known for its strong ability to acquire antibiotic resistance, has recently shown clinical resistance to the last-line antibiotic tigecycline. To unravel the complex mechanism of A. baumannii drug resistance, we subjected tigecycline-susceptible, -intermediate, and -mildly-resistant strains to successive increases in sub-MIC tigecycline and ultimately obtained tigecycline-resistant strains. The proteome of both key intermediate and final strains during the selection process was analyzed using nanoLC-MS/MS. Among the more than 2600 proteins detected in all strains, we found that RND efflux pump AdeABC was associated with the adaptability of A. baumannii to tigecycline under sub-MIC pressure. qRT-PCR analysis also revealed higher expression of AdeAB in strains that can quickly acquire tigecycline resistance compared with strains that displayed lower adaptability. To validate our findings, we added an efflux pump inhibitor, carbonyl cyanide m-chlorophenyl hydrazine (CCCP), to the medium and observed its ability to inhibit tigecycline resistance in A. baumannii strains with quick adaptability. This study contributes to a better understanding of the mechanisms underlying tigecycline resistance in A. baumannii under sub-MIC pressure.
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Affiliation(s)
| | | | | | | | - Qinghua Zou
- Department of Microbiology, School of Basic Medical Sciences, Peking University, Beijing 100191, China; (C.L.); (J.L.); (Q.L.); (P.W.)
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2
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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3
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Meirelles LA, Perry EK, Bergkessel M, Newman DK. Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics. PLoS Biol 2021; 19:e3001093. [PMID: 33690640 PMCID: PMC7946323 DOI: 10.1371/journal.pbio.3001093] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Bacterial opportunistic human pathogens frequently exhibit intrinsic antibiotic tolerance and resistance, resulting in infections that can be nearly impossible to eradicate. We asked whether this recalcitrance could be driven by these organisms' evolutionary history as environmental microbes that engage in chemical warfare. Using Pseudomonas aeruginosa as a model, we demonstrate that the self-produced antibiotic pyocyanin (PYO) activates defenses that confer collateral tolerance specifically to structurally similar synthetic clinical antibiotics. Non-PYO-producing opportunistic pathogens, such as members of the Burkholderia cepacia complex, likewise display elevated antibiotic tolerance when cocultured with PYO-producing strains. Furthermore, by widening the population bottleneck that occurs during antibiotic selection and promoting the establishment of a more diverse range of mutant lineages, PYO increases apparent rates of mutation to antibiotic resistance to a degree that can rival clinically relevant hypermutator strains. Together, these results reveal an overlooked mechanism by which opportunistic pathogens that produce natural toxins can dramatically modulate the efficacy of clinical antibiotics and the evolution of antibiotic resistance, both for themselves and other members of clinically relevant polymicrobial communities.
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Affiliation(s)
- Lucas A. Meirelles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Elena K. Perry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Megan Bergkessel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
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4
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Sun J, Wang B, Warden AR, Cui D, Ding X. Overcoming Multidrug-Resistance in Bacteria with a Two-Step Process to Repurpose and Recombine Established Drugs. Anal Chem 2019; 91:13562-13569. [DOI: 10.1021/acs.analchem.9b02690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiahui Sun
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Boqian Wang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Antony R. Warden
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Center for Intelligent Instrument for Diagnosis and Therapy, Thin Film and Microfabrication Key Laboratory of Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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5
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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6
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El Meouche I, Dunlop MJ. Heterogeneity in efflux pump expression predisposes antibiotic-resistant cells to mutation. Science 2019; 362:686-690. [PMID: 30409883 DOI: 10.1126/science.aar7981] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 06/07/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022]
Abstract
Antibiotic resistance is often the result of mutations that block drug activity; however, bacteria also evade antibiotics by transiently expressing genes such as multidrug efflux pumps. A crucial question is whether transient resistance can promote permanent genetic changes. Previous studies have established that antibiotic treatment can select tolerant cells that then mutate to achieve permanent resistance. Whether these mutations result from antibiotic stress or preexist within the population is unclear. To address this question, we focused on the multidrug pump AcrAB-TolC. Using time-lapse microscopy, we found that cells with higher acrAB expression have lower expression of the DNA mismatch repair gene mutS, lower growth rates, and higher mutation frequencies. Thus, transient antibiotic resistance from elevated acrAB expression can promote spontaneous mutations within single cells.
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Affiliation(s)
- Imane El Meouche
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA.,School of Engineering, University of Vermont, Burlington, VT 05405, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA. .,School of Engineering, University of Vermont, Burlington, VT 05405, USA
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7
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Matthews H, Duffy CW, Merrick CJ. Checks and balances? DNA replication and the cell cycle in Plasmodium. Parasit Vectors 2018; 11:216. [PMID: 29587837 PMCID: PMC5872521 DOI: 10.1186/s13071-018-2800-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/19/2018] [Indexed: 01/10/2023] Open
Abstract
It is over 100 years since the life-cycle of the malaria parasite Plasmodium was discovered, yet its intricacies remain incompletely understood - a knowledge gap that may prove crucial for our efforts to control the disease. Phenotypic screens have partially filled the void in the antimalarial drug market, but as compound libraries eventually become exhausted, new medicines will only come from directed drug development based on a better understanding of fundamental parasite biology. This review focusses on the unusual cell cycles of Plasmodium, which may present a rich source of novel drug targets as well as a topic of fundamental biological interest. Plasmodium does not grow by conventional binary fission, but rather by several syncytial modes of replication including schizogony and sporogony. Here, we collate what is known about the various cell cycle events and their regulators throughout the Plasmodium life-cycle, highlighting the differences between Plasmodium, model organisms and other apicomplexan parasites and identifying areas where further study is required. The possibility of DNA replication and the cell cycle as a drug target is also explored. Finally the use of existing tools, emerging technologies, their limitations and future directions to elucidate the peculiarities of the Plasmodium cell cycle are discussed.
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Affiliation(s)
- Holly Matthews
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, ST55BG, Keele, UK
| | - Craig W Duffy
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, ST55BG, Keele, UK
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Staffordshire, ST55BG, Keele, UK.
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8
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Zhang WH, Zhang CZ, Liu ZJ, Gu XX, Li W, Yang L, Liu YH, Zeng ZL, Jiang HX. In VitroDevelopment of Ciprofloxacin Resistance ofSalmonella entericaSerovars Typhimurium, Enteritidis, and Indiana Isolates from Food Animals. Microb Drug Resist 2017; 23:687-694. [DOI: 10.1089/mdr.2016.0119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wen-Hui Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Chuan-Zhen Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Zhi-Jie Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Xi-Xi Gu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Wan Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Ling Yang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Zhen-Ling Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
| | - Hong-Xia Jiang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University (SCAU), Guangzhou, China
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9
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Lee AH, Fidock DA. Evidence of a Mild Mutator Phenotype in Cambodian Plasmodium falciparum Malaria Parasites. PLoS One 2016; 11:e0154166. [PMID: 27100094 PMCID: PMC4839739 DOI: 10.1371/journal.pone.0154166] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/09/2016] [Indexed: 12/22/2022] Open
Abstract
Malaria control efforts have been continuously stymied by drug-resistant strains of Plasmodium falciparum, which typically originate in Southeast Asia prior to spreading into high-transmission settings in Africa. One earlier proposed explanation for Southeast Asia being a hotbed of resistance has been the hypermutability or "Accelerated Resistance to Multiple Drugs" (ARMD) phenotype, whereby multidrug-resistant Southeast Asian parasites were reported to exhibit 1,000-fold higher rates of resistance to unrelated antimalarial agents when compared to drug-sensitive parasites. However, three recent studies do not recapitulate this hypermutability phenotype. Intriguingly, genome sequencing of recently derived multidrug-resistant Cambodian isolates has identified a high proportion of DNA repair gene mutations in multidrug-resistant parasites, suggesting their potential role in shaping local parasite evolution. By adapting fluctuation assays for use in P. falciparum, we have examined the in vitro mutation rates of five recent Cambodian isolates and three reference laboratory strains. For these studies we also generated a knockout parasite line lacking the DNA repair factor Exonuclease I. In these assays, parasites were typed for their ability to acquire resistance to KAE609, currently in advanced clinical trials, yielding 13 novel mutations in the Na+/H+-ATPase PfATP4, the primary resistance determinant. We observed no evidence of hypermutability. Instead, we found evidence of a mild mutator (up to a 3.4-fold increase in mutation rate) phenotype in two artemisinin-resistant Cambodian isolates, which carry DNA repair gene mutations. We observed that one such mutation in the Mismatch Repair protein Mlh1 contributes to the mild mutator phenotype when modeled in yeast (scmlh1-P157S). Compared to basal rates of mutation, a mild mutator phenotype may provide a greater overall benefit for parasites in Southeast Asia in terms of generating drug resistance without incurring detrimental fitness costs.
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Affiliation(s)
- Andrew H. Lee
- Department of Microbiology and Immunology, Columbia University, New York, New York, United States of America
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
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10
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Komp Lindgren P, Higgins PG, Seifert H, Cars O. Prevalence of hypermutators among clinical Acinetobacter baumannii isolates. J Antimicrob Chemother 2015; 71:661-5. [PMID: 26660878 PMCID: PMC4743697 DOI: 10.1093/jac/dkv378] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/17/2015] [Indexed: 01/24/2023] Open
Abstract
Objectives The objectives of this study were to study the presence of mutators in a set of Acinetobacter baumannii isolates and to explore whether there is a correlation between mutation rates and antibiotic resistance. Methods The variation in mutation rate was evaluated for 237 clinical A. baumannii isolates by determining the frequency of their mutation to rifampicin resistance. For each isolate, the antibiotic resistance profile was determined by disc diffusion and/or Etest. Isolates were divided into susceptible, resistant and MDR groups according to their resistance to five groups of different antibiotics. A comparison between differences in mutation frequency (f) and strain-specific factors was performed. Results Of the 237 isolates 32%, 18% and 50% were classified as susceptible, resistant and MDR, respectively. The f of rifampicin resistance varied between 2.2 × 10−10 and 1.2 × 10−6. Of the strains under investigation, 16% had an ≥2.5- to 166-fold higher f. The presence of mutators (definition ≥2.5-fold increase in f compared with ATCC 19606) in the MDR group (22%) was significantly higher (P < 0.05) than that in the susceptible and resistant groups (11% and 7%, respectively). Furthermore, f was significantly higher in the MDR group compared with that in the susceptible and resistant groups. Conclusions The facts that 26 of 37 mutator isolates (70%) in the population were MDR and that there was a significantly higher general f in isolates exhibiting an MDR profile suggest that hypermutability can be of advantage for the organism in a selective environment with extensive exposure to antimicrobials.
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Affiliation(s)
- Patricia Komp Lindgren
- Department of Medical Sciences, Section of Infectious Diseases, University of Uppsala, 75105 Uppsala, Sweden
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, 50935 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, 50935 Cologne, Germany
| | - Otto Cars
- Department of Medical Sciences, Section of Infectious Diseases, University of Uppsala, 75105 Uppsala, Sweden
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11
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Rodríguez-Rojas A, Makarova O, Rolff J. Antimicrobials, stress and mutagenesis. PLoS Pathog 2014; 10:e1004445. [PMID: 25299705 PMCID: PMC4192597 DOI: 10.1371/journal.ppat.1004445] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/03/2014] [Indexed: 12/05/2022] Open
Abstract
Cationic antimicrobial peptides are ancient and ubiquitous immune effectors that multicellular organisms use to kill and police microbes whereas antibiotics are mostly employed by microorganisms. As antimicrobial peptides (AMPs) mostly target the cell wall, a microbial ‘Achilles heel’, it has been proposed that bacterial resistance evolution is very unlikely and hence AMPs are ancient ‘weapons’ of multicellular organisms. Here we provide a new hypothesis to explain the widespread distribution of AMPs amongst multicellular organism. Studying five antimicrobial peptides from vertebrates and insects, we show, using a classic Luria-Delbrück fluctuation assay, that cationic antimicrobial peptides (AMPs) do not increase bacterial mutation rates. Moreover, using rtPCR and disc diffusion assays we find that AMPs do not elicit SOS or rpoS bacterial stress pathways. This is in contrast to the main classes of antibiotics that elevate mutagenesis via eliciting the SOS and rpoS pathways. The notion of the ‘Achilles heel’ has been challenged by experimental selection for AMP-resistance, but our findings offer a new perspective on the evolutionary success of AMPs. Employing AMPs seems advantageous for multicellular organisms, as it does not fuel the adaptation of bacteria to their immune defenses. This has important consequences for our understanding of host-microbe interactions, the evolution of innate immune defenses, and also sheds new light on antimicrobial resistance evolution and the use of AMPs as drugs. Cationic antimicrobial peptides are ancient and ubiquitous immune effectors that multicellular organisms use to kill and police microbes, whilst antibiotics are mostly employed by microorganisms. Here we provide a new hypothesis to explain this widespread adoption of antimicrobial peptides. We show that cationic antimicrobial peptides (AMPs) do not increase bacterial mutagenesis, as they do not elicit bacterial stress pathways. Those stress pathways increase the mutation rate when bacteria are treated with antibiotics. Employing AMPs hence seems advantageous for multicellular organisms, as it does not fuel the adaptation of bacteria to their immune defenses. This has important consequences for our understanding of host-microbe interactions, the evolution of innate immune defenses, and also sheds new light on antimicrobial resistance evolution and the use of AMPs as drugs.
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Affiliation(s)
| | - Olga Makarova
- Evolutionary Biology, Institute for Biology, Free University Berlin, Berlin, Germany
| | - Jens Rolff
- Evolutionary Biology, Institute for Biology, Free University Berlin, Berlin, Germany
- * E-mail:
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12
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Abstract
Human use of antibiotics has driven the selective enrichment of pathogenic bacteria resistant to clinically used drugs. Traditionally, the selection of resistance has been considered to occur mainly at high, therapeutic levels of antibiotics, but we are now beginning to understand better the importance of selection of resistance at low levels of antibiotics. The concentration of an antibiotic varies in different body compartments during treatment, and low concentrations of antibiotics are found in sewage water, soils, and many water environments due to natural production and contamination from human activities. Selection of resistance at non-lethal antibiotic concentrations (below the wild-type minimum inhibitory concentration) occurs due to differences in growth rate at the particular antibiotic concentration between cells with different tolerance levels to the antibiotic. The minimum selective concentration for a particular antibiotic is reached when its reducing effect on growth of the susceptible strain balances the reducing effect (fitness cost) of the resistance determinant in the resistant strain. Recent studies have shown that resistant bacteria can be selected at concentrations several hundred-fold below the lethal concentrations for susceptible cells. Resistant mutants selected at low antibiotic concentrations are generally more fit than those selected at high concentrations but can still be highly resistant. The characteristics of selection at low antibiotic concentrations, the potential clinical problems of this mode of selection, and potential solutions will be discussed.
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Affiliation(s)
- Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
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13
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Occurrence of weak mutators among avian pathogenic Escherichia coli (APEC) isolates causing salpingitis and peritonitis in broiler breeders. Vet Microbiol 2014; 168:141-7. [DOI: 10.1016/j.vetmic.2013.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 09/19/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022]
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14
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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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15
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Swick MC, Evangelista MA, Bodine TJ, Easton-Marks JR, Barth P, Shah MJ, Bormann Chung CA, Stanley S, McLaughlin SF, Lee CC, Sheth V, Doan Q, Hamill RJ, Steffen D, Becnel LB, Sucgang R, Zechiedrich L. Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates. PLoS One 2013; 8:e65961. [PMID: 23824211 PMCID: PMC3688849 DOI: 10.1371/journal.pone.0065961] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 05/03/2013] [Indexed: 11/20/2022] Open
Abstract
Current efforts to understand antibiotic resistance on the whole genome scale tend to focus on known genes even as high throughput sequencing strategies uncover novel mechanisms. To identify genomic variations associated with antibiotic resistance, we employed a modified genome-wide association study; we sequenced genomic DNA from pools of E. coli clinical isolates with similar antibiotic resistance phenotypes using SOLiD technology to uncover single nucleotide polymorphisms (SNPs) unanimously conserved in each pool. The multidrug-resistant pools were genotypically similar to SMS-3-5, a previously sequenced multidrug-resistant isolate from a polluted environment. The similarity was evenly spread across the entire genome and not limited to plasmid or pathogenicity island loci. Among the pools of clinical isolates, genomic variation was concentrated adjacent to previously reported inversion and duplication differences between the SMS-3-5 isolate and the drug-susceptible laboratory strain, DH10B. SNPs that result in non-synonymous changes in gyrA (encoding the well-known S83L allele associated with fluoroquinolone resistance), mutM, ligB, and recG were unanimously conserved in every fluoroquinolone-resistant pool. Alleles of the latter three genes are tightly linked among most sequenced E. coli genomes, and had not been implicated in antibiotic resistance previously. The changes in these genes map to amino acid positions in alpha helices that are involved in DNA binding. Plasmid-encoded complementation of null strains with either allelic variant of mutM or ligB resulted in variable responses to ultraviolet light or hydrogen peroxide treatment as markers of induced DNA damage, indicating their importance in DNA metabolism and revealing a potential mechanism for fluoroquinolone resistance. Our approach uncovered evidence that additional DNA binding enzymes may contribute to fluoroquinolone resistance and further implicate environmental bacteria as a reservoir for antibiotic resistance.
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Affiliation(s)
- Michelle C. Swick
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael A. Evangelista
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
| | - Truston J. Bodine
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeremy R. Easton-Marks
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Biomedical Informatics Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Patrick Barth
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Minita J. Shah
- Life Technologies, Beverly, Massachusetts, United States of America
| | | | - Sarah Stanley
- Life Technologies, Beverly, Massachusetts, United States of America
| | | | - Clarence C. Lee
- Life Technologies, Beverly, Massachusetts, United States of America
| | - Vrunda Sheth
- Life Technologies, Beverly, Massachusetts, United States of America
| | - Quynh Doan
- Life Technologies, Foster City, California, United States of America
| | - Richard J. Hamill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Steffen
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Biomedical Informatics Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lauren B. Becnel
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Biomedical Informatics Group, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
- * E-mail: (RS); (LZ)
| | - Lynn Zechiedrich
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (RS); (LZ)
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16
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Wang S, Wang Y, Shen J, Wu Y, Wu C. Polymorphic mutation frequencies in clinical isolates of Staphylococcus aureus: the role of weak mutators in the development of fluoroquinolone resistance. FEMS Microbiol Lett 2013; 341:13-7. [PMID: 23330696 DOI: 10.1111/1574-6968.12085] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/08/2013] [Indexed: 11/28/2022] Open
Abstract
The polymorphic mutation frequencies for 154 Staphylococcus aureus isolates from Chinese bovine clinical mastitis cases were investigated. We found that nearly 29% of the isolates presented as weak mutators, while only two (1.3%) strong mutators were detected. Of the 15 weak mutators that exhibited ciprofloxacin resistance phenotypes, only one isolate was found to be mutS deficient. All of the ciprofloxacin-resistant isolates had the classic ciprofloxacin resistance mutations at codon 80 within the ParC subunit of topoisomerase IV and codon 84/88 within the GyrA subunit of DNA gyrase. The proportion of ciprofloxacin-resistant isolates among the weak mutators (34.1%) was significantly higher than that found in the normomutators (11.4%) and hypomutators (0%) (P < 0.001, Fisher's exact test), suggesting a positive correlation between weak mutators and ciprofloxacin resistance.
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Affiliation(s)
- Shaochen Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
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17
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Selection of resistance at lethal and non-lethal antibiotic concentrations. Curr Opin Microbiol 2012; 15:555-60. [DOI: 10.1016/j.mib.2012.07.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 11/23/2022]
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18
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Andersson DI, Hughes D. Evolution of antibiotic resistance at non-lethal drug concentrations. Drug Resist Updat 2012; 15:162-72. [PMID: 22516308 DOI: 10.1016/j.drup.2012.03.005] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 03/22/2012] [Accepted: 03/26/2012] [Indexed: 11/30/2022]
Abstract
Human use of antimicrobials in the clinic, community and agricultural systems has driven selection for resistance in bacteria. Resistance can be selected at antibiotic concentrations that are either lethal or non-lethal, and here we argue that selection and enrichment for antibiotic resistant bacteria is often a consequence of weak, non-lethal selective pressures - caused by low levels of antibiotics - that operates on small differences in relative bacterial fitness. Such conditions may occur during antibiotic therapy or in anthropogenically drug-polluted natural environments. Non-lethal selection increases rates of mutant appearance and promotes enrichment of highly fit mutants and stable mutators.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Box 582, SE-75123 Uppsala, Sweden.
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19
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Zechiedrich L. Editorial Comment to Genome-wide transcriptome analysis of fluoroquinolone resistance in clinical isolates of Escherichia coli. Int J Urol 2012; 19:368-9. [DOI: 10.1111/j.1442-2042.2012.02996.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Abstract
Hypermutability is a phenotype characterized by a moderate to high elevation of spontaneous mutation rates and could result from DNA replication errors, defects in error correction mechanisms and many other causes. The elevated mutation rates are helpful to organisms to adapt to sudden and unforeseen threats to survival. At the same time hypermutability also leads to the generation of many deleterious mutations which offset its adaptive value and therefore disadvantageous. Nevertheless, it is very common in nature, especially among clinical isolates of pathogens. Hypermutability is inherited by indirect (second order) selection along with the beneficial mutations generated. At large population sizes and high mutation rates many cells in the population could concurrently acquire beneficial mutations of varying adaptive (fitness) values. These lineages compete with the ancestral cells and also among themselves for fixation. The one with the 'fittest' mutation gets fixed ultimately while the others are lost. This has been called 'clonal interference' which puts a speed limit on adaptation. The original clonal interference hypothesis has been modified recently. Nonheritable (transient) hypermtability conferring significant adaptive benefits also occur during stress response although its molecular basis remains controversial. The adaptive benefits of heritable hypermutability are discussed with emphasis on host-pathogen interactions.
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21
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Andersson DI, Hughes D. Persistence of antibiotic resistance in bacterial populations. FEMS Microbiol Rev 2011; 35:901-11. [DOI: 10.1111/j.1574-6976.2011.00289.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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22
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Nazir H, Cao S, Hasan F, Hughes D. Can phylogenetic type predict resistance development? J Antimicrob Chemother 2011; 66:778-87. [DOI: 10.1093/jac/dkq505] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Dörr T, Lewis K, Vulić M. SOS response induces persistence to fluoroquinolones in Escherichia coli. PLoS Genet 2009; 5:e1000760. [PMID: 20011100 PMCID: PMC2780357 DOI: 10.1371/journal.pgen.1000760] [Citation(s) in RCA: 347] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 11/09/2009] [Indexed: 01/12/2023] Open
Abstract
Bacteria can survive antibiotic treatment without acquiring heritable antibiotic resistance. We investigated persistence to the fluoroquinolone ciprofloxacin in Escherichia coli. Our data show that a majority of persisters to ciprofloxacin were formed upon exposure to the antibiotic, in a manner dependent on the SOS gene network. These findings reveal an active and inducible mechanism of persister formation mediated by the SOS response, challenging the prevailing view that persisters are pre-existing and formed purely by stochastic means. SOS-induced persistence is a novel mechanism by which cells can counteract DNA damage and promote survival to fluoroquinolones. This unique survival mechanism may be an important factor influencing the outcome of antibiotic therapy in vivo.
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Affiliation(s)
- Tobias Dörr
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Marin Vulić
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail:
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24
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Mandsberg LF, Ciofu O, Kirkby N, Christiansen LE, Poulsen HE, Høiby N. Antibiotic resistance in Pseudomonas aeruginosa strains with increased mutation frequency due to inactivation of the DNA oxidative repair system. Antimicrob Agents Chemother 2009; 53:2483-91. [PMID: 19332676 PMCID: PMC2687204 DOI: 10.1128/aac.00428-08] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 06/06/2008] [Accepted: 02/19/2009] [Indexed: 12/29/2022] Open
Abstract
The chronic Pseudomonas aeruginosa infection of the lungs of cystic fibrosis (CF) patients is characterized by the biofilm mode of growth and chronic inflammation dominated by polymorphonuclear leukocytes (PMNs). A high percentage of P. aeruginosa strains show high frequencies of mutations (hypermutators [HP]). P. aeruginosa is exposed to oxygen radicals, both those generated by its own metabolism and especially those released by a large number of PMNs in response to the chronic CF lung infection. Our work therefore focused on the role of the DNA oxidative repair system in the development of HP and antibiotic resistance. We have constructed and characterized mutT, mutY, and mutM mutants in P. aeruginosa strain PAO1. The mutT and mutY mutants showed 28- and 7.5-fold increases in mutation frequencies, respectively, over that for PAO1. These mutators had more oxidative DNA damage (higher levels of 7,8-dihydro-8-oxodeoxyguanosine) than PAO1 after exposure to PMNs, and they developed resistance to antibiotics more frequently. The mechanisms of resistance were increased beta-lactamase production and overexpression of the MexCD-OprJ efflux-pump. Mutations in either the mutT or the mutY gene were found in resistant HP clinical isolates from patients with CF, and complementation with wild-type genes reverted the phenotype. In conclusion, oxidative stress might be involved in the development of resistance to antibiotics. We therefore suggest the possible use of antioxidants for CF patients to prevent the development of antibiotic resistance.
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Affiliation(s)
- L F Mandsberg
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, Denmark
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25
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Abstract
In recent years, there has been accumulating evidence that antibiotics, besides their antimicrobial action, potentially have a number of undesired side effects that can, at least in some cases, promote genetic variability of bacteria. In addition to resistant variants, antibiotics have also been shown to select mutator clones, thus stimulating evolution towards further resistance. Furthermore, mutations, recombination and horizontal gene transfer have been reported to be somehow affected when bacteria are exposed to subinhibitory concentrations of certain antibiotics. These findings may have implications for the use of antibiotics, because they may have undesired side effects, such as enhancing antibiotic resistance evolution. Here we present data supporting (or not) this fearsome possibility and discuss whether this potential threat should be taken into consideration.
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Affiliation(s)
- Alejandro Couce
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
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26
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Gould CV, Sniegowski PD, Shchepetov M, Metlay JP, Weiser JN. Identifying mutator phenotypes among fluoroquinolone-resistant strains of Streptococcus pneumoniae using fluctuation analysis. Antimicrob Agents Chemother 2007; 51:3225-9. [PMID: 17664329 PMCID: PMC2043225 DOI: 10.1128/aac.00336-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 04/06/2007] [Accepted: 07/03/2007] [Indexed: 11/20/2022] Open
Abstract
The occurrence of mutator phenotypes among laboratory-generated and clinical levofloxacin-resistant strains of Streptococcus pneumoniae was determined using fluctuation analysis. The in vitro selection for levofloxacin-resistant mutants of strain D39, each with point mutations in both gyrA and parC or parE, was not associated with a significant change in the mutation rate. Two of eight clinical isolates resistant to levofloxacin (MIC, >8 microg/ml) had estimated mutation rates of 1.2 x 10(-7) and 9.4 x 10(-8) mutations per cell division, indicating potential mutator phenotypes, compared to strain D39, which had an estimated mutation rate of 1.4 x 10(-8) mutations per cell division. The levofloxacin-resistant isolates with the highest mutation rates showed evidence of dysfunctional mismatch repair and contained missense mutations in mut genes at otherwise highly conserved sites. The association of hypermutability in levofloxacin-resistant S. pneumoniae clinical isolates with mutations in DNA mismatch repair genes provides further evidence that mismatch repair mutants may have a selective advantage in the setting of antibiotic pressure, facilitating the development of further antibiotic resistance.
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Affiliation(s)
- Carolyn V Gould
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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