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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01058-6. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA.
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2
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Maeda T, Furusawa C. Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies. Antibiotics (Basel) 2024; 13:94. [PMID: 38247653 PMCID: PMC10812413 DOI: 10.3390/antibiotics13010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Laboratory evolution studies, particularly with Escherichia coli, have yielded invaluable insights into the mechanisms of antimicrobial resistance (AMR). Recent investigations have illuminated that, with repetitive antibiotic exposures, bacterial populations will adapt and eventually become tolerant and resistant to the drugs. Through intensive analyses, these inquiries have unveiled instances of convergent evolution across diverse antibiotics, the pleiotropic effects of resistance mutations, and the role played by loss-of-function mutations in the evolutionary landscape. Moreover, a quantitative analysis of multidrug combinations has shed light on collateral sensitivity, revealing specific drug combinations capable of suppressing the acquisition of resistance. This review article introduces the methodologies employed in the laboratory evolution of AMR in bacteria and presents recent discoveries concerning AMR mechanisms derived from laboratory evolution. Additionally, the review outlines the application of laboratory evolution in endeavors to formulate rational treatment strategies.
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Affiliation(s)
- Tomoya Maeda
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita 565-0874, Japan;
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita 565-0874, Japan;
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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3
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Windels EM, Cool L, Persy E, Swinnen J, Matthay P, Van den Bergh B, Wenseleers T, Michiels J. Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence. THE ISME JOURNAL 2024; 18:wrae070. [PMID: 38691440 PMCID: PMC11102087 DOI: 10.1093/ismejo/wrae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known about the impact of the environmental conditions on resistance and persistence evolution and the potential interplay between both phenotypes. Based on the distinct growth and survival characteristics of resistance and persistence mutants, we hypothesized that the antibiotic dose and availability of nutrients during treatment might play a key role in the evolutionary adaptation to antibiotic stress. To test this hypothesis, we combined high-throughput experimental evolution with a mathematical model of bacterial evolution under intermittent antibiotic exposure. We show that high nutrient levels during antibiotic treatment promote selection of high-level resistance, but that resistance mainly emerges independently of persistence when the antibiotic concentration is sufficiently low. At higher doses, resistance evolution is facilitated by the preceding or concurrent selection of persistence mutants, which ensures survival of populations in harsh conditions. Collectively, our experimental data and mathematical model elucidate the evolutionary routes toward increased bacterial survival under different antibiotic treatment schedules, which is key to designing effective antibiotic therapies.
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Affiliation(s)
- Etthel M Windels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- Department of Biosystems Science and Engineering, ETH Zürich, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lloyd Cool
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, 3000 Leuven, Belgium
| | - Eline Persy
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Janne Swinnen
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Paul Matthay
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, KU Leuven, 3000 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
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4
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Pont CL, Bernay B, Gérard M, Dhalluin A, Gravey F, Giard JC. Proteomic characterization of persisters in Enterococcus faecium. BMC Microbiol 2024; 24:9. [PMID: 38172710 PMCID: PMC10765921 DOI: 10.1186/s12866-023-03162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Enterococcus faecium is a Gram-positive bacterium, naturally present in the human intestinal microbiota, but is also an opportunistic pathogen responsible for healthcare-associated infections. Persisters are individuals of a subpopulation able to survive by arrest of growth coping with conditions that are lethal for the rest of the population. These persistent cells can grow again when the stress disappears from their environment and can cause relapses. RESULTS In this study, we highlighted that ciprofloxacin (10-fold the MIC) led to the formation of persister cells of E. faecium. The kill curve was typically biphasic with an initial drop of survival (more than 2 orders of magnitude reduction) followed by a constant bacterial count. Growth curves and antimicrobial susceptibility tests of these persisters were similar to those of the original cells. In addition, by genomic analyses, we confirmed that the persisters were genotypically identical to the wild type. Comparative proteomic analysis revealed that 56 proteins have significantly different abundances in persisters compared to cells harvested before the addition of stressing agent. Most of them were related to energetic metabolisms, some polypeptides were involved in transcription regulation, and seven were stress proteins like CspA, PrsA, ClpX and particularly enzymes linked to the oxidative stress response. CONCLUSIONS This work provided evidences that the pathogen E. faecium was able to enter a state of persister that may have an impact in chronic infections and relapses. Moreover, putative key effectors of this phenotypical behavior were identified by proteomic approach.
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Affiliation(s)
- Charlotte Le Pont
- UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - Benoît Bernay
- Plateforme Proteogen SFR ICORE 4206, Université de Caen Normandie, Caen, 14000, France
| | - Mattéo Gérard
- UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - Anne Dhalluin
- UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - François Gravey
- Department of infectious agents, UNICAEN, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, CHU Caen, Caen, F-14000, France
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5
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Lin T, Pan J, Gregory C, Wang Y, Tincher C, Rivera C, Lynch M, Long H, Zhang Y. Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in E. coli. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:538-550. [PMID: 38045542 PMCID: PMC10689325 DOI: 10.1007/s42995-023-00185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/27/2023] [Indexed: 12/05/2023]
Abstract
Antibiotic-resistant bacteria severely threaten human health. Besides spontaneous mutations generated by endogenous factors, the resistance might also originate from mutations induced by certain antibiotics, such as the fluoroquinolones. Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems. However, the relative contributions of these molecular mechanisms remain unclear, hindering understanding of the generation of resistant pathogens. Here, using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains, as well as those of the strains deficient for the mismatch repair (MMR) and the oxidative damage repair pathways, we find that the SOS response is the major mutagenesis contributor in mutation elevation, responsible for ~ 30-50% of the total base-pair substitution (BPS) mutation-rate elevation upon treatment with sublethal levels of norfloxacin (0 ~ 50 ng/mL). We further estimate the significance of the effects on other mutational features of these mechanisms (i.e., transversions, structural variations, and mutation spectrum) in E. coli using linear models. The SOS response plays a positive role in all three mutational features (mutation rates of BPSs, transversions, structural variations) and affects the mutational spectrum. The repair systems significantly reduce the BPS mutation rate and the transversion rate, regardless of whether antibiotics are present, while significantly increasing the structural variation rate in E. coli. Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00185-y.
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Affiliation(s)
- Tongtong Lin
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, 47405 USA
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, 47405 USA
| | - Caitlyn Rivera
- Department of Biology, Indiana University, Bloomington, 47405 USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, 85281 USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, 266237 China
| | - Yu Zhang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003 China
- School of Mathematics Science, Ocean University of China, Qingdao, 266000 China
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6
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Jara M, Arevalo J, Llanos-Cuentas A, den Broeck FV, Domagalska MA, Dujardin JC. Unveiling drug-tolerant and persister-like cells in Leishmania braziliensis lines derived from patients with cutaneous leishmaniasis. Front Cell Infect Microbiol 2023; 13:1253033. [PMID: 37790908 PMCID: PMC10543814 DOI: 10.3389/fcimb.2023.1253033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction Resistance against anti-Leishmania drugs (DR) has been studied for years, giving important insights into long-term adaptations of these parasites to drugs, through genetic modifications. However, microorganisms can also survive lethal drug exposure by entering into temporary quiescence, a phenomenon called drug tolerance (DT), which is rather unexplored in Leishmania. Methods We studied a panel of nine Leishmania braziliensis strains highly susceptible to potassium antimonyl tartrate (PAT), exposed promastigotes to lethal PAT pressure, and compared several cellular and molecular parameters distinguishing DT from DR. Results and discussion We demonstrated in vitro that a variable proportion of cells remained viable, showing all the criteria of DT and not of DR: i) signatures of quiescence, under drug pressure: reduced proliferation and significant decrease of rDNA transcription; ii) reversibility of the phenotype: return to low IC50 after removal of drug pressure; and iii) absence of significant genetic differences between exposed and unexposed lineages of each strain and absence of reported markers of DR. We found different levels of quiescence and DT among the different L. braziliensis strains. We provide here a new in-vitro model of drug-induced quiescence and DT in Leishmania. Research should be extended in vivo, but the current model could be further exploited to support R&D, for instance, to guide the screening of compounds to overcome the quiescence resilience of the parasite, thereby improving the therapy of leishmaniasis.
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Affiliation(s)
- Marlene Jara
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Jorge Arevalo
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Frederik Van den Broeck
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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7
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Bollen C, Louwagie E, Verstraeten N, Michiels J, Ruelens P. Environmental, mechanistic and evolutionary landscape of antibiotic persistence. EMBO Rep 2023; 24:e57309. [PMID: 37395716 PMCID: PMC10398667 DOI: 10.15252/embr.202357309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Recalcitrant infections pose a serious challenge by prolonging antibiotic therapies and contributing to the spread of antibiotic resistance, thereby threatening the successful treatment of bacterial infections. One potential contributing factor in persistent infections is antibiotic persistence, which involves the survival of transiently tolerant subpopulations of bacteria. This review summarizes the current understanding of antibiotic persistence, including its clinical significance and the environmental and evolutionary factors at play. Additionally, we discuss the emerging concept of persister regrowth and potential strategies to combat persister cells. Recent advances highlight the multifaceted nature of persistence, which is controlled by deterministic and stochastic elements and shaped by genetic and environmental factors. To translate in vitro findings to in vivo settings, it is crucial to include the heterogeneity and complexity of bacterial populations in natural environments. As researchers continue to gain a more holistic understanding of this phenomenon and develop effective treatments for persistent bacterial infections, the study of antibiotic persistence is likely to become increasingly complex.
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Affiliation(s)
- Celien Bollen
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Elen Louwagie
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Jan Michiels
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
| | - Philip Ruelens
- Centre of Microbial and Plant GeneticsKU LeuvenLeuvenBelgium
- Center for Microbiology, VIBLeuvenBelgium
- Laboratory of Socioecology and Social EvolutionKU LeuvenLeuvenBelgium
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8
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Usui M, Yoshii Y, Thiriet-Rupert S, Ghigo JM, Beloin C. Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance. Commun Biol 2023; 6:275. [PMID: 36928386 PMCID: PMC10020551 DOI: 10.1038/s42003-023-04601-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial antibiotic resistance is a global health concern of increasing importance and intensive study. Although biofilms are a common source of infections in clinical settings, little is known about the development of antibiotic resistance within biofilms. Here, we use experimental evolution to compare selection of resistance mutations in planktonic and biofilm Escherichia coli populations exposed to clinically relevant cycles of lethal treatment with the aminoglycoside amikacin. Consistently, mutations in sbmA, encoding an inner membrane peptide transporter, and fusA, encoding the essential elongation factor G, are rapidly selected in biofilms, but not in planktonic cells. This is due to a combination of enhanced mutation rate, increased adhesion capacity and protective biofilm-associated tolerance. These results show that the biofilm environment favors rapid evolution of resistance and provide new insights into the dynamic evolution of antibiotic resistance in biofilms.
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Affiliation(s)
- Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan.
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Stanislas Thiriet-Rupert
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
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9
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Singh G, Orman MA, Conrad JC, Nikolaou M. Systematic design of pulse dosing to eradicate persister bacteria. PLoS Comput Biol 2023; 19:e1010243. [PMID: 36649322 PMCID: PMC9882918 DOI: 10.1371/journal.pcbi.1010243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 01/27/2023] [Accepted: 11/29/2022] [Indexed: 01/18/2023] Open
Abstract
A small fraction of infectious bacteria use persistence as a strategy to survive exposure to antibiotics. Periodic pulse dosing of antibiotics has long been considered a potentially effective strategy towards eradication of persisters. Recent studies have demonstrated through in vitro experiments that it is indeed feasible to achieve such effectiveness. However, systematic design of periodic pulse dosing regimens to treat persisters is currently lacking. Here we rigorously develop a methodology for the systematic design of optimal periodic pulse dosing strategies for rapid eradication of persisters. A key outcome of the theoretical analysis, on which the proposed methodology is based, is that bactericidal effectiveness of periodic pulse dosing depends mainly on the ratio of durations of the corresponding on and off parts of the pulse. Simple formulas for critical and optimal values of this ratio are derived. The proposed methodology is supported by computer simulations and in vitro experiments.
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Affiliation(s)
- Garima Singh
- Chemical and Biomolecular Engineering Department, University of Houston, Houston, Texas, United States of America
| | - Mehmet A. Orman
- Chemical and Biomolecular Engineering Department, University of Houston, Houston, Texas, United States of America
| | - Jacinta C. Conrad
- Chemical and Biomolecular Engineering Department, University of Houston, Houston, Texas, United States of America
| | - Michael Nikolaou
- Chemical and Biomolecular Engineering Department, University of Houston, Houston, Texas, United States of America
- * E-mail:
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10
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Geerts N, De Vooght L, Passaris I, Delputte P, Van den Bergh B, Cos P. Antibiotic Tolerance Indicative of Persistence Is Pervasive among Clinical Streptococcus pneumoniae Isolates and Shows Strong Condition Dependence. Microbiol Spectr 2022; 10:e0270122. [PMID: 36374111 PMCID: PMC9769776 DOI: 10.1128/spectrum.02701-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Streptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem, as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet for S. pneumoniae, little is known about antibiotic-tolerant persisters and robust experimental means are lacking. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. In this study, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as a confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. Under optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which assumes that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof of concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections, which will set the stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research. IMPORTANCE S. pneumoniae is considered a serious threat by the Centers for Disease Control and Prevention because of rising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance, more specifically, antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure, and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting that persistence is a general trait in S. pneumoniae cultures. Our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.
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Affiliation(s)
- Nele Geerts
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | - Linda De Vooght
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
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11
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Aljghami ME, Barghash MM, Majaesic E, Bhandari V, Houry WA. Cellular functions of the ClpP protease impacting bacterial virulence. Front Mol Biosci 2022; 9:1054408. [PMID: 36533084 PMCID: PMC9753991 DOI: 10.3389/fmolb.2022.1054408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/15/2022] [Indexed: 09/28/2023] Open
Abstract
Proteostasis mechanisms significantly contribute to the sculpting of the proteomes of all living organisms. ClpXP is a central AAA+ chaperone-protease complex present in both prokaryotes and eukaryotes that facilitates the unfolding and subsequent degradation of target substrates. ClpX is a hexameric unfoldase ATPase, while ClpP is a tetradecameric serine protease. Substrates of ClpXP belong to many cellular pathways such as DNA damage response, metabolism, and transcriptional regulation. Crucially, disruption of this proteolytic complex in microbes has been shown to impact the virulence and infectivity of various human pathogenic bacteria. Loss of ClpXP impacts stress responses, biofilm formation, and virulence effector protein production, leading to decreased pathogenicity in cell and animal infection models. Here, we provide an overview of the multiple critical functions of ClpXP and its substrates that modulate bacterial virulence with examples from several important human pathogens.
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Affiliation(s)
- Mazen E. Aljghami
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Emily Majaesic
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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12
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Biofilm antimicrobial susceptibility through an experimental evolutionary lens. NPJ Biofilms Microbiomes 2022; 8:82. [PMID: 36257971 PMCID: PMC9579162 DOI: 10.1038/s41522-022-00346-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
Experimental evolution experiments in which bacterial populations are repeatedly exposed to an antimicrobial treatment, and examination of the genotype and phenotype of the resulting evolved bacteria, can help shed light on mechanisms behind reduced susceptibility. In this review we present an overview of why it is important to include biofilms in experimental evolution, which approaches are available to study experimental evolution in biofilms and what experimental evolution has taught us about tolerance and resistance in biofilms. Finally, we present an emerging consensus view on biofilm antimicrobial susceptibility supported by data obtained during experimental evolution studies.
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13
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Design and Evaluation of Short Bovine Lactoferrin-Derived Antimicrobial Peptides against Multidrug-Resistant Enterococcus faecium. Antibiotics (Basel) 2022; 11:antibiotics11081085. [PMID: 36009954 PMCID: PMC9404989 DOI: 10.3390/antibiotics11081085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022] Open
Abstract
Enterococcus faecium has become an important drug-resistant nosocomial pathogen because of widespread antibiotic abuse. We developed short and chemically simple antimicrobial peptides (AMPs) with a selective amino acid composition, fixed charge, and hydrophobicity ratio based on the core antimicrobial motif of bovine lactoferrin (LfcinB6). Among these peptides, 5L and 6L (both 12 residues long) demonstrated a narrow spectrum and high antibacterial activity against drug-resistant E. faecium isolates with a minimal inhibitory concentration (MIC) that ranged from 4–16 µg/mL. At 32 µg/mL, peptides 5L and 6L inhibited E. faecium strain C68 biofilm formation by 90% and disrupted established biofilms by 75%. At 40 µg/mL, 5L reduced 1 × 107E. faecium persister cells by 3 logs within 120 min of exposure, whereas 6L eliminated all persister cells within 60 min. At 0.5× MIC, 5L and 6L significantly downregulated the expression of a crucial biofilm gene ace by 8 folds (p = 0.02) and 4 folds (p = 0.01), respectively. At 32 µg/mL, peptides 5L and 6L both depolarized the E. faecium membrane, increased fluidity, and eventually ruptured the membrane. Physiologically, 5L (at 8 µg/mL) altered the tricarboxylic acid cycle, glutathione, and purine metabolism. Interestingly, in an ex vivo model of porcine skin infection, compared to no treatment, 5L (at 10× MIC) effectively eliminated all 1 × 106 exponential (p = 0.0045) and persister E. faecium cells (p = 0.0002). In conclusion, the study outlines a roadmap for developing narrow-spectrum selective AMPs and presents peptide 5L as a potential therapeutic candidate to be explored against E. faecium.
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14
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Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck. Microbiol Spectr 2022; 10:e0168722. [PMID: 35913149 PMCID: PMC9431245 DOI: 10.1128/spectrum.01687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a useful tool to study the evolution of antibiotic tolerance in bacterial populations under diverse environmental conditions. The role of population bottlenecks in the evolution of tolerance has been investigated in Escherichia coli, but not in a more clinically relevant pathogen, methicillin-resistant Staphylococcus aureus (MRSA). In this study, we used ALE to evolve MRSA under repetitive daptomycin treatment and incorporated population bottlenecks following antibiotic exposure. We observed that the populations finally attained a tolerance mutation in the yycH gene after 2 weeks of evolution with population bottlenecks, and additional mutations in yycI and several other genes further increased the tolerance level. The tolerant populations also became resistant to another glycopeptide antibiotic, vancomycin. Through proteomics, we showed that yycH and yycI mutations led to the loss of function of the proteins and downregulated the WalKR two-component system and the downstream players, including the autolysin Atl and amidase Sle1, which are important for cell wall metabolism. Overall, our study offers new insights into the evolution of daptomycin tolerance under population bottlenecking conditions, which are commonly faced by pathogens during infection; the study also identified new mutations conferring daptomycin tolerance and revealed the proteome alterations in the evolved tolerant populations. IMPORTANCE Although population bottlenecks are known to influence the evolutionary dynamics of microbial populations, how such bottlenecks affect the evolution of tolerance to antibiotics in a clinically relevant methicillin-resistant S. aureus (MRSA) pathogen are still unclear. Here, we performed in vitro evolution of MRSA under cyclic daptomycin treatment and applied population bottlenecks following the treatment. We showed that under these experimental conditions, MRSA populations finally attained mutations in yycH, yycI, and several other genes that led to daptomycin tolerance. The discovered yycH and yycI mutations caused early termination of the genes and loss of function of the proteins, and they subsequently downregulated the expression of proteins controlled by the WalKR two-component system, such as Atl and Sle1. In addition, we compared our proteomics data with multiple studies on distinct daptomycin-tolerant MRSA mutants to identify proteins with a consistent expression pattern that could serve as biological markers for daptomycin tolerance in MRSA.
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15
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Trubenová B, Roizman D, Rolff J, Regoes RR. Modeling Polygenic Antibiotic Resistance Evolution in Biofilms. Front Microbiol 2022; 13:916035. [PMID: 35875522 PMCID: PMC9301000 DOI: 10.3389/fmicb.2022.916035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
The recalcitrance of biofilms to antimicrobials is a multi-factorial phenomenon, including genetic, physical, and physiological changes. Individually, they often cannot account for biofilm recalcitrance. However, their combination can increase the minimal inhibitory concentration of antibiotics needed to kill bacterial cells by three orders of magnitude, explaining bacterial survival under otherwise lethal drug treatment. The relative contributions of these factors depend on the specific antibiotics, bacterial strain, as well as environmental and growth conditions. An emerging population genetic property—increased biofilm genetic diversity—further enhances biofilm recalcitrance. Here, we develop a polygenic model of biofilm recalcitrance accounting for multiple phenotypic mechanisms proposed to explain biofilm recalcitrance. The model can be used to generate predictions about the emergence of resistance—its timing and population genetic consequences. We use the model to simulate various treatments and experimental setups. Our simulations predict that the evolution of resistance is impaired in biofilms at low antimicrobial concentrations while it is facilitated at higher concentrations. In scenarios that allow bacteria exchange between planktonic and biofilm compartments, the evolution of resistance is further facilitated compared to scenarios without exchange. We compare these predictions to published experimental observations.
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Affiliation(s)
- Barbora Trubenová
- Institute of Integrative Biology, ETH Zürich, Zurich, Switzerland
- *Correspondence: Barbora Trubenová
| | - Dan Roizman
- Institute of Biology – Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Jens Rolff
- Institute of Biology – Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zürich, Zurich, Switzerland
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16
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Cui S, Qiao J, Xiong MP. Antibacterial and Biofilm-Eradicating Activities of pH-Responsive Vesicles against Pseudomonas aeruginosa. Mol Pharm 2022; 19:2406-2417. [PMID: 35507414 DOI: 10.1021/acs.molpharmaceut.2c00165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The formation of biofilms by a microcolony of bacteria is a significant burden on the healthcare industry due to difficulty eradicating it. In this study, pH-responsive vesicles capable of releasing apramycin (APR), a model aminoglycoside antibiotic, in response to the low pH typical of establishedPseudomonas aeruginosa biofilms resulted in improved eradication of existing biofilms in comparison to the free drug. The amphiphilic polymeric vesicle (PV) comprised of block polymer poly (ethylene glycol)-block-poly 2-(dimethylamino) ethyl methacrylate (mPEG-b-pDEAEMA) averaged 128 nm. The drug encapsulation content of APR in PV/APR was confirmed to be 28.2%, and the drug encapsulation efficiency was confirmed to be 51.2%. At pH 5.5, PV/APR released >90% APR after 24 h compared to <20% at pH 7.4. At pH 5.5, protonation of the pDEAEMA block results in a zeta potential of +23 mV compared to a neutral zeta potential of +2.2 mV at pH 7.4. Confocal microscopy, flow cytometry, and scanning electron microscopy reveal that the positively charged vesicles can compromise the integrity of the planktonic bacterial membrane in a pH-dependent manner. In addition, PV/APR is able to diffuse into mature biofilms to release APR in the acidic milieu of biofilm bacteria, and PV/APR was more efficient at eliminating preexisting biofilms compared to free APR at 128 and 256 μg/mL. This study reveals that dynamic charge density in response to pH can lead to differential levels of interactions with the biofilm and bacterial membrane. This effectively results in enhanced antibacterial and antibiofilm properties against both planktonic and difficult-to-treat biofilm bacteria at concentrations significantly lower than those of the free drug. Overall, this pH-responsive vesicle could be especially promising for treating biofilm-associated infectious diseases.
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Affiliation(s)
- Shuolin Cui
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602-2352, United States
| | - Jing Qiao
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602-2352, United States.,Institute of Advanced Materials, School of Chemistry and Chemical Engineering, and, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 211189, China
| | - May P Xiong
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602-2352, United States
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17
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Van den Bergh B, Schramke H, Michiels JE, Kimkes TEP, Radzikowski JL, Schimpf J, Vedelaar SR, Burschel S, Dewachter L, Lončar N, Schmidt A, Meijer T, Fauvart M, Friedrich T, Michiels J, Heinemann M. Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis. Nat Commun 2022; 13:546. [PMID: 35087069 PMCID: PMC8795404 DOI: 10.1038/s41467-022-28141-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
Abstract
Antibiotic persistence describes the presence of phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Perturbations of metabolic homeostasis can promote antibiotic persistence, but the precise mechanisms are not well understood. Here, we use laboratory evolution, population-wide sequencing and biochemical characterizations to identify mutations in respiratory complex I and discover how they promote persistence in Escherichia coli. We show that persistence-inducing perturbations of metabolic homeostasis are associated with cytoplasmic acidification. Such cytoplasmic acidification is further strengthened by compromised proton pumping in the complex I mutants. While RpoS regulon activation induces persistence in the wild type, the aggravated cytoplasmic acidification in the complex I mutants leads to increased persistence via global shutdown of protein synthesis. Thus, we propose that cytoplasmic acidification, amplified by a compromised complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.
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Affiliation(s)
- Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Hannah Schramke
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Joran Elie Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Jakub Leszek Radzikowski
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Johannes Schimpf
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Silke R Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Sabrina Burschel
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Nikola Lončar
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Meijer
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Thorsten Friedrich
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium.
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands.
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18
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Bugs on Drugs: A Drosophila melanogaster Gut Model to Study In Vivo Antibiotic Tolerance of E. coli. Microorganisms 2022; 10:microorganisms10010119. [PMID: 35056568 PMCID: PMC8780219 DOI: 10.3390/microorganisms10010119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
With an antibiotic crisis upon us, we need to boost antibiotic development and improve antibiotics’ efficacy. Crucial is knowing how to efficiently kill bacteria, especially in more complex in vivo conditions. Indeed, many bacteria harbor antibiotic-tolerant persisters, variants that survive exposure to our most potent antibiotics and catalyze resistance development. However, persistence is often only studied in vitro as we lack flexible in vivo models. Here, I explored the potential of using Drosophila melanogaster as a model for antimicrobial research, combining methods in Drosophila with microbiology techniques: assessing fly development and feeding, generating germ-free or bacteria-associated Drosophila and in situ microscopy. Adult flies tolerate antibiotics at high doses, although germ-free larvae show impaired development. Orally presented E. coli associates with Drosophila and mostly resides in the crop. E. coli shows an overall high antibiotic tolerance in vivo potentially resulting from heterogeneity in growth rates. The hipA7 high-persistence mutant displays an increased antibiotic survival while the expected low persistence of ΔrelAΔspoT and ΔrpoS mutants cannot be confirmed in vivo. In conclusion, a Drosophila model for in vivo antibiotic tolerance research shows high potential and offers a flexible system to test findings from in vitro assays in a broader, more complex condition.
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19
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Korzekwa K, Kędziora A, Stańczykiewicz B, Bugla-Płoskońska G, Wojnicz D. Benefits of Usage of Immobilized Silver Nanoparticles as Pseudomonas aeruginosa Antibiofilm Factors. Int J Mol Sci 2021; 23:284. [PMID: 35008720 PMCID: PMC8745484 DOI: 10.3390/ijms23010284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to assess the beneficial inhibitory effect of silver nanoparticles immobilized on SiO2 or TiO2 on biofilm formation by Pseudomonas aeruginosa-one of the most dangerous pathogens isolated from urine and bronchoalveolar lavage fluid of patients hospitalized in intensive care units. Pure and silver doped nanoparticles of SiO2 and TiO2 were prepared using a novel modified sol-gel method. Ten clinical strains of P. aeruginosa and the reference PAO1 strain were used. The minimal inhibitory concentration (MIC) was determined by the broth microdilution method. The minimal biofilm inhibitory concentration (MBIC) and biofilm formation were assessed by colorimetric assay. Bacterial enumeration was used to assess the viability of bacteria in the biofilm. Silver nanoparticles immobilized on the SiO2 and TiO2 indicated high antibacterial efficacy against P. aeruginosa planktonic and biofilm cultures. TiO2/Ag0 showed a better bactericidal effect than SiO2/Ag0. Our results indicate that the inorganic compounds (SiO2, TiO2) after nanotechnological modification may be successfully used as antibacterial agents against multidrug-resistant P. aeruginosa strains.
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Affiliation(s)
- Kamila Korzekwa
- Department of Microbiology, Faculty of Biological Sciences, University of Wroclaw, 50-137 Wroclaw, Poland; (A.K.); (G.B.-P.)
| | - Anna Kędziora
- Department of Microbiology, Faculty of Biological Sciences, University of Wroclaw, 50-137 Wroclaw, Poland; (A.K.); (G.B.-P.)
| | | | - Gabriela Bugla-Płoskońska
- Department of Microbiology, Faculty of Biological Sciences, University of Wroclaw, 50-137 Wroclaw, Poland; (A.K.); (G.B.-P.)
| | - Dorota Wojnicz
- Department of Biology and Medical Parasitology, Wroclaw Medical University, 50-345 Wroclaw, Poland
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20
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Hill PWS, Moldoveanu AL, Sargen M, Ronneau S, Glegola-Madejska I, Beetham C, Fisher RA, Helaine S. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 2021; 29:1757-1773.e10. [PMID: 34731646 DOI: 10.1016/j.chom.2021.10.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/23/2021] [Accepted: 10/08/2021] [Indexed: 11/30/2022]
Abstract
Tolerance and persistence are superficially similar phenomena by which bacteria survive bactericidal antibiotics. It is assumed that the same physiology underlies survival of individual tolerant and persistent bacteria. However, by comparing tolerance and persistence during Salmonella Typhimurium infection, we reveal that these two phenomena are underpinned by different bacterial physiologies. Multidrug-tolerant mutant Salmonella enter a near-dormant state protected from immune-mediated genotoxic damages. However, the numerous tolerant cells, optimized for survival, lack the capabilities necessary to initiate infection relapse following antibiotic withdrawal. In contrast, persisters retain an active state. This leaves them vulnerable to accumulation of macrophage-induced dsDNA breaks but concurrently confers the versatility to initiate infection relapse if protected by RecA-mediated DNA repair. Accordingly, recurrent, invasive, non-typhoidal Salmonella clinical isolates display hallmarks of persistence rather than tolerance during antibiotic treatment. Our study highlights the complex trade-off that antibiotic-recalcitrant Salmonella balance to act as a reservoir for infection relapse.
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Affiliation(s)
- Peter W S Hill
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
| | - Ana Laura Moldoveanu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Molly Sargen
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Séverin Ronneau
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Izabela Glegola-Madejska
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Catrin Beetham
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Robert A Fisher
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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21
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Verstraete L, Van den Bergh B, Verstraeten N, Michiels J. Ecology and evolution of antibiotic persistence. Trends Microbiol 2021; 30:466-479. [PMID: 34753652 DOI: 10.1016/j.tim.2021.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
Bacteria have at their disposal a battery of strategies to withstand antibiotic stress. Among these, resistance is a well-known mechanism, yet bacteria can also survive antibiotic attack by adopting a tolerant phenotype. In the case of persistence, only a small fraction within an isogenic population switches to this antibiotic-tolerant state. Persistence depends on the ecological niche and the genetic background of the strains involved. Furthermore, it has been shown to be under direct and indirect evolutionary pressure. Persister cells play a role in chronic infections and the development of resistance, and therefore a better understanding of this phenotype could contribute to the development of effective antibacterial therapies. In the current review, we discuss how ecological and evolutionary forces shape persistence.
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Affiliation(s)
- L Verstraete
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium; Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - B Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium; Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - N Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium; Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - J Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium; Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.
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22
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Detecting Persister Awakening Determinants. Methods Mol Biol 2021. [PMID: 34590260 DOI: 10.1007/978-1-0716-1621-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
For long, persistence research has focused primarily on disentangling mechanisms of persister state entry. Due to the rapid advances in the field of single-cell techniques and newly obtained insights in the persister phenotype, studying persister awakening has been unlocked and it has gained much interest in the scientific community. However, a framework on how this research should be conducted is currently lacking. Therefore, we here present a method to detect and validate genes important for persister awakening.
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23
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The Use of Experimental Evolution to Study the Response of Pseudomonas aeruginosa to Single or Double Antibiotic Treatment. Methods Mol Biol 2021. [PMID: 34590259 DOI: 10.1007/978-1-0716-1621-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The widespread use of antibiotics promotes the evolution and dissemination of drug resistance and tolerance. Both mechanisms promote survival during antibiotic exposure and their role and development can be studied in vitro with different assays to document the gradual adaptation through the selective enrichment of resistant or tolerant mutant variants. Here, we describe the use of experimental evolution in combination with time-resolved genome analysis as a powerful tool to study the interaction of antibiotic tolerance and resistance in the human pathogen Pseudomonas aeruginosa . This method guides the identification of components involved in alleviating antibiotic stress and helps to unravel specific molecular pathways leading to drug tolerance or resistance. We discuss the influence of single or double drug treatment regimens and environmental aspects on the evolution of antibiotic resilience mechanisms.
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24
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Windels EM, Fox R, Yerramsetty K, Krouse K, Wenseleers T, Swinnen J, Matthay P, Verstraete L, Wilmaerts D, Van den Bergh B, Michiels J. Population Bottlenecks Strongly Affect the Evolutionary Dynamics of Antibiotic Persistence. Mol Biol Evol 2021; 38:3345-3357. [PMID: 33871643 PMCID: PMC8321523 DOI: 10.1093/molbev/msab107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacterial persistence is a potential cause of antibiotic therapy failure. Antibiotic-tolerant persisters originate from phenotypic differentiation within a susceptible population, occurring with a frequency that can be altered by mutations. Recent studies have proven that persistence is a highly evolvable trait and, consequently, an important evolutionary strategy of bacterial populations to adapt to high-dose antibiotic therapy. Yet, the factors that govern the evolutionary dynamics of persistence are currently poorly understood. Theoretical studies predict far-reaching effects of bottlenecking on the evolutionary adaption of bacterial populations, but these effects have never been investigated in the context of persistence. Bottlenecking events are frequently encountered by infecting pathogens during host-to-host transmission and antibiotic treatment. In this study, we used a combination of experimental evolution and barcoded knockout libraries to examine how population bottlenecking affects the evolutionary dynamics of persistence. In accordance with existing hypotheses, small bottlenecks were found to restrict the adaptive potential of populations and result in more heterogeneous evolutionary outcomes. Evolutionary trajectories followed in small-bottlenecking regimes additionally suggest that the fitness landscape associated with persistence has a rugged topography, with distinct trajectories toward increased persistence that are accessible to evolving populations. Furthermore, sequencing data of evolved populations and knockout libraries after selection reveal various genes that are potentially involved in persistence, including previously known as well as novel targets. Together, our results do not only provide experimental evidence for evolutionary theories, but also contribute to a better understanding of the environmental and genetic factors that guide bacterial adaptation to antibiotic treatment.
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Affiliation(s)
- Etthel M Windels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | | | | | | | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Janne Swinnen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Paul Matthay
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Laure Verstraete
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Dorien Wilmaerts
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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25
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Neubauer D, Jaśkiewicz M, Bauer M, Olejniczak-Kęder A, Sikorska E, Sikora K, Kamysz W. Biological and Physico-Chemical Characteristics of Arginine-Rich Peptide Gemini Surfactants with Lysine and Cystine Spacers. Int J Mol Sci 2021; 22:3299. [PMID: 33804887 PMCID: PMC8036666 DOI: 10.3390/ijms22073299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/11/2022] Open
Abstract
Ultrashort cationic lipopeptides (USCLs) and gemini cationic surfactants are classes of potent antimicrobials. Our recent study has shown that the branching and shortening of the fatty acids chains with the simultaneous addition of a hydrophobic N-terminal amino acid in USCLs result in compounds with enhanced selectivity. Here, this approach was introduced into arginine-rich gemini cationic surfactants. l-cystine diamide and l-lysine amide linkers were used as spacers. Antimicrobial activity against planktonic and biofilm cultures of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) strains and Candida sp. as well as hemolytic and cytotoxic activities were examined. Moreover, antimicrobial activity in the presence of human serum and the ability to form micelles were evaluated. Membrane permeabilization study, serum stability assay, and molecular dynamics were performed. Generally, critical aggregation concentration was linearly correlated with hydrophobicity. Gemini surfactants were more active than the parent USCLs, and they turned out to be selective antimicrobial agents with relatively low hemolytic and cytotoxic activities. Geminis with the l-cystine diamide spacer seem to be less cytotoxic than their l-lysine amide counterparts, but they exhibited lower antibiofilm and antimicrobial activities in serum. In some cases, geminis with branched fatty acid chains and N-terminal hydrophobic amino acid resides exhibited enhanced selectivity to pathogens over human cells.
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Affiliation(s)
- Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Maciej Jaśkiewicz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Marta Bauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Agata Olejniczak-Kęder
- Department of Histology, Faculty of Medicine, Medical University of Gdańsk, 80-211 Gdańsk, Poland;
| | - Emilia Sikorska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;
| | - Karol Sikora
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (M.B.); (K.S.); (W.K.)
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26
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Sulaiman JE, Lam H. Evolution of Bacterial Tolerance Under Antibiotic Treatment and Its Implications on the Development of Resistance. Front Microbiol 2021; 12:617412. [PMID: 33717007 PMCID: PMC7952611 DOI: 10.3389/fmicb.2021.617412] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/12/2021] [Indexed: 01/08/2023] Open
Abstract
Recent laboratory evolution studies have shown that upon repetitive antibiotic treatments, bacterial populations will adapt and eventually became tolerant and resistant to the drug. Drug tolerance rapidly evolves upon frequent, intermittent antibiotic treatments, and such emerging drug tolerance seems to be specific to the treatment conditions, complicating clinical practice. Moreover, it has been shown that tolerance often promotes the development of resistance, which further reinforces the need of clinical diagnostics for antibiotic tolerance to reduce the occurrence of acquired resistance. Here, we discuss the laboratory evolution studies that were performed to track the development of tolerance in bacterial populations, and highlight the urgency of developing a comprehensive knowledge base of various tolerance phenotypes and their detection in clinics. Finally, we propose future directions for basic research in this growing field.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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27
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Chung ES, Ko KS. Eradication of persister cells of Acinetobacter baumannii through combination of colistin and amikacin antibiotics. J Antimicrob Chemother 2021; 74:1277-1283. [PMID: 30759206 DOI: 10.1093/jac/dkz034] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Persister cells following antibiotic exposure may cause failure of antibiotic treatment. The synergistic effects of antibiotic combinations with respect to eliminating persister cells were investigated based on their characteristics. METHODS For Acinetobacter baumannii clinical isolates, persister assays were performed using colistin, amikacin, imipenem and ciprofloxacin in various ways, including exposure to antibiotics in combination and sequentially. Persister phenotypes were observed through analysis of ATP concentration, membrane potential and transmission electron microscopy. RESULTS Each A. baumannii isolate showed a specific survival rate of persister cells against each antibiotic. The persister cells were eradicated effectively by exposure to the combination of colistin and amikacin, especially in the sequential order of colistin then amikacin. While the persister cells were not identified after 6 h when exposed to the antibiotics in the order colistin then amikacin, they remained at 0.016% when antibiotic exposure was done in the order amikacin then colistin. Although membrane potential was low in both colistin and amikacin persisters, depletion of the intracellular ATP concentration was only observed in colistin persisters. In addition, transmission electron microscopy analysis showed that colistin persisters have a unique morphology with a rough and rippled membrane and many outer membrane vesicles. Empty pore-like structures surrounded by cracks were also observed. CONCLUSIONS In A. baumannii, the combination of colistin and amikacin was most effective for eradication of persister cells, probably due to different mechanisms of persister cell formation between antibiotics. It was also identified that the sequential order of colistin followed by amikacin was important to eradicate the persister cells.
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Affiliation(s)
- Eun Seon Chung
- Department of Molecular Cell Biology and Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology and Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, South Korea
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28
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Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. Antimicrob Agents Chemother 2020; 65:AAC.01273-20. [PMID: 33106260 PMCID: PMC7927859 DOI: 10.1128/aac.01273-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022] Open
Abstract
As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will be increasingly relied upon to treat infections and to lower the rate of multidrug resistance. The majority of work in this area has investigated how resistance evolution toward a single antibiotic effects a specific organism’s collateral response to a wide variety of antibiotics. The results of these studies have been used to identify networks of drugs which can be used to drive resistance in a particular direction. As drug resistance continues to grow, treatment strategies that turn resistance into a disadvantage for the organism will be increasingly relied upon to treat infections and to lower the rate of multidrug resistance. The majority of work in this area has investigated how resistance evolution toward a single antibiotic effects a specific organism’s collateral response to a wide variety of antibiotics. The results of these studies have been used to identify networks of drugs which can be used to drive resistance in a particular direction. However, little is known about the extent of evolutionary conservation of these responses across species. We sought to address this knowledge gap by performing a systematic resistance evolution study of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) under uniform growth conditions using five clinically relevant antibiotics with diverse modes of action. Evolved lineages were analyzed for collateral effects and the molecular mechanisms behind the observed phenotypes. Fourteen universal cross-resistance and two global collateral sensitivity relationships were found among the lineages. Genomic analyses revealed drug-dependent divergent and conserved evolutionary trajectories among the pathogens. Our findings suggest that collateral responses may be preserved across species. These findings may help extend the contribution of previous collateral network studies in the development of treatment strategies to address the problem of antibiotic resistance.
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29
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Soares A, Alexandre K, Etienne M. Tolerance and Persistence of Pseudomonas aeruginosa in Biofilms Exposed to Antibiotics: Molecular Mechanisms, Antibiotic Strategies and Therapeutic Perspectives. Front Microbiol 2020; 11:2057. [PMID: 32973737 PMCID: PMC7481396 DOI: 10.3389/fmicb.2020.02057] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/05/2020] [Indexed: 01/19/2023] Open
Abstract
Pseudomonas aeruginosa biofilm-related infections are difficult to treat with antibiotics. Along the different layers of the biofilm, the P. aeruginosa population is heterogeneous, exhibiting an extreme ability to adapt his metabolic activity to the local microenvironment. At the deepest layers of the biofilm is a subset of dormant cells, called persister cells. Though antimicrobial failure might be multifactorial, it is now demonstrated that these persister cells, genetically identical to a fully susceptible strain, but phenotypically divergent, are highly tolerant to antibiotics, and contribute to antimicrobial failure. By eradicating susceptible, metabolically active cells, antibiotics bring out pre-existing persister cells. The biofilm mode of growth creates microenvironment conditions that activate stringent response mechanisms, SOS response and toxin-antitoxin systems that render the bacterial population highly tolerant to antibiotics. Using diverse, not standardized, models of biofilm infection, a large panel of antibiotic regimen has been evaluated. They demonstrated that biofilm growth had an unequal impact of antibiotic activity, colistin and meropenem being the less impacted antibiotics. Different combination and sequential antimicrobial therapies were also evaluated, and could be partially efficient, but none succeeded in eradicating persister cells, so that non-antibiotic alternative strategies are currently under development. This article reviews the molecular mechanisms involved in antibiotic tolerance and persistence in P. aeruginosa biofilm infections. A review of the antimicrobial regimen evaluated for the treatment of P. aeruginosa biofilm infection is also presented. While tremendous progress has been made in the understanding of biofilm-related infections, alternative non-antibiotic strategies are now urgently needed.
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Affiliation(s)
- Anaïs Soares
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France
| | - Kévin Alexandre
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France.,Infectious Diseases Department, Rouen University Hospital, Rouen, France
| | - Manuel Etienne
- GRAM 2.0, EA 2656, Normandie University, UNIROUEN, Rouen, France.,Infectious Diseases Department, Rouen University Hospital, Rouen, France
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30
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Rocha-Granados MC, Zenick B, Englander HE, Mok WWK. The social network: Impact of host and microbial interactions on bacterial antibiotic tolerance and persistence. Cell Signal 2020; 75:109750. [PMID: 32846197 DOI: 10.1016/j.cellsig.2020.109750] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/07/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022]
Abstract
Antibiotics have vastly improved our quality of life since their discovery and introduction into modern medicine. Yet, widespread use and misuse have compromised the efficacy of these compounds and put our ability to cure infectious diseases in jeopardy. To defend themselves against antibiotics, bacteria have evolved an arsenal of survival strategies. In addition to acquiring mutations and genetic determinants that confer antibiotic resistance, bacteria can respond to environmental cues and adopt reversible phenotypic changes that transiently enhance their ability to survive adverse conditions, including those brought on by antibiotics. These antibiotic tolerant and persistent bacteria, which are prevalent in biofilms and can survive antimicrobial therapy without inheriting resistance, are thought to underlie treatment failure and infection relapse. At infection sites, bacteria encounter a range of signals originating from host immunity and the local microbiota that can induce transcriptomic and metabolic reprogramming. In this review, we will focus on the impact of host factors and microbial interactions on antibiotic tolerance and persistence. We will also outline current efforts in leveraging the knowledge of host-microbe and microbe-microbe interactions in designing therapies that potentiate antibiotic activity and reduce the burden caused by recurrent infections.
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Affiliation(s)
| | - Blesing Zenick
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, CT, 06032, USA
| | - Hanna E Englander
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, CT, 06032, USA; Department of Physiology & Neurobiology, University of Connecticut, Storrs, CT 06269-3156, United States of America
| | - Wendy W K Mok
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, CT, 06032, USA.
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31
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Salcedo-Sora JE, Kell DB. A Quantitative Survey of Bacterial Persistence in the Presence of Antibiotics: Towards Antipersister Antimicrobial Discovery. Antibiotics (Basel) 2020; 9:E508. [PMID: 32823501 PMCID: PMC7460088 DOI: 10.3390/antibiotics9080508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Bacterial persistence to antibiotics relates to the phenotypic ability to survive lethal concentrations of otherwise bactericidal antibiotics. The quantitative nature of the time-kill assay, which is the sector's standard for the study of antibiotic bacterial persistence, is an invaluable asset for global, unbiased, and cross-species analyses. Methods: We compiled the results of antibiotic persistence from antibiotic-sensitive bacteria during planktonic growth. The data were extracted from a sample of 187 publications over the last 50 years. The antibiotics used in this compilation were also compared in terms of structural similarity to fluorescent molecules known to accumulate in Escherichia coli. Results: We reviewed in detail data from 54 antibiotics and 36 bacterial species. Persistence varies widely as a function of the type of antibiotic (membrane-active antibiotics admit the fewest), the nature of the growth phase and medium (persistence is less common in exponential phase and rich media), and the Gram staining of the target organism (persistence is more common in Gram positives). Some antibiotics bear strong structural similarity to fluorophores known to be taken up by E. coli, potentially allowing competitive assays. Some antibiotics also, paradoxically, seem to allow more persisters at higher antibiotic concentrations. Conclusions: We consolidated an actionable knowledge base to support a rational development of antipersister antimicrobials. Persistence is seen as a step on the pathway to antimicrobial resistance, and we found no organisms that failed to exhibit it. Novel antibiotics need to have antipersister activity. Discovery strategies should include persister-specific approaches that could find antibiotics that preferably target the membrane structure and permeability of slow-growing cells.
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Affiliation(s)
- Jesus Enrique Salcedo-Sora
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
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32
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Juhas M, Widlake E, Teo J, Huseby DL, Tyrrell JM, Polikanov YS, Ercan O, Petersson A, Cao S, Aboklaish AF, Rominski A, Crich D, Böttger EC, Walsh TR, Hughes D, Hobbie SN. In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii. J Antimicrob Chemother 2020; 74:944-952. [PMID: 30629184 PMCID: PMC6419615 DOI: 10.1093/jac/dky546] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/17/2018] [Accepted: 11/29/2018] [Indexed: 02/01/2023] Open
Abstract
Objectives Widespread antimicrobial resistance often limits the availability of therapeutic options to only a few last-resort drugs that are themselves challenged by emerging resistance and adverse side effects. Apramycin, an aminoglycoside antibiotic, has a unique chemical structure that evades almost all resistance mechanisms including the RNA methyltransferases frequently encountered in carbapenemase-producing clinical isolates. This study evaluates the in vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii, and provides a rationale for its superior antibacterial activity in the presence of aminoglycoside resistance determinants. Methods A thorough antibacterial assessment of apramycin with 1232 clinical isolates from Europe, Asia, Africa and South America was performed by standard CLSI broth microdilution testing. WGS and susceptibility testing with an engineered panel of aminoglycoside resistance-conferring determinants were used to provide a mechanistic rationale for the breadth of apramycin activity. Results MIC distributions and MIC90 values demonstrated broad antibacterial activity of apramycin against Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Morganella morganii, Citrobacter freundii, Providencia spp., Proteus mirabilis, Serratia marcescens and A. baumannii. Genotypic analysis revealed the variety of aminoglycoside-modifying enzymes and rRNA methyltransferases that rendered a remarkable proportion of clinical isolates resistant to standard-of-care aminoglycosides, but not to apramycin. Screening a panel of engineered strains each with a single well-defined resistance mechanism further demonstrated a lack of cross-resistance to gentamicin, amikacin, tobramycin and plazomicin. Conclusions Its superior breadth of activity renders apramycin a promising drug candidate for the treatment of systemic Gram-negative infections that are resistant to treatment with other aminoglycoside antibiotics.
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Affiliation(s)
- Mario Juhas
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
| | - Emma Widlake
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeanette Teo
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, Singapore, Singapore
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Jonathan M Tyrrell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Yury S Polikanov
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, 900 South Ashland Avenue, MBRB 4170, Chicago, IL, USA
| | - Onur Ercan
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Anna Petersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Ali F Aboklaish
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Anna Rominski
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, USA
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
| | - Timothy R Walsh
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, Uppsala, Sweden
| | - Sven N Hobbie
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, Zürich, Switzerland
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33
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Fino C, Vestergaard M, Ingmer H, Pierrel F, Gerdes K, Harms A. PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10. Microbiologyopen 2020; 9:e1064. [PMID: 32558363 PMCID: PMC7424257 DOI: 10.1002/mbo3.1064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Antibiotic‐tolerant persisters are often implicated in treatment failure of chronic and relapsing bacterial infections, but the underlying molecular mechanisms have remained elusive. Controversies revolve around the relative contribution of specific genetic switches called toxin–antitoxin (TA) modules and global modulation of cellular core functions such as slow growth. Previous studies on uropathogenic Escherichia coli observed impaired persister formation for mutants lacking the pasTI locus that had been proposed to encode a TA module. Here, we show that pasTI is not a TA module and that the supposed toxin PasT is instead the bacterial homolog of mitochondrial protein Coq10 that enables the functionality of the respiratory electron carrier ubiquinone as a “lipid chaperone.” Consistently, pasTI mutants show pleiotropic phenotypes linked to defective electron transport such as decreased membrane potential and increased sensitivity to oxidative stress. We link impaired persister formation of pasTI mutants to a global distortion of cellular stress responses due to defective respiration. Remarkably, the ectopic expression of human coq10 largely complements the respiratory defects and decreased persister levels of pasTI mutants. Our work suggests that PasT/Coq10 has a central role in respiratory electron transport that is conserved from bacteria to humans and sustains bacterial tolerance to antibiotics.
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Affiliation(s)
- Cinzia Fino
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hanne Ingmer
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabien Pierrel
- CNRS, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Kenn Gerdes
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Harms
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark.,Focal Area of Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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34
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Ferreira MA, Pereira ML, Dos Santos KV. Drug-induced tolerance: the effects of antibiotic pre-exposure in Stenotrophomonas maltophilia. Future Microbiol 2020; 15:497-508. [PMID: 32478618 DOI: 10.2217/fmb-2019-0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Aim: To investigate if the prior use of nontargeted antibiotics induces cross-tolerance in Stenotrophomonas maltophilia. Methods: Antibiotic induction was performed to evaluate daptomycin and vancomycin as possible tolerance-inducing drugs measured by minimum bactericidal concentration/minimum inhibitory concentration (MIC) ratio, adapted disk-diffusion tests and time-kill curves. Results: After antibiotic exposure, three potentially tolerant strains were isolated, maintaining the same MIC value of levofloxacin, with minimum bactericidal concentration/MIC ratio slightly higher than the parental. In the adapted disk-diffusion test, one strain (D25) showed high tolerance level for levofloxacin, ceftazidime and ticarcillin-clavulanate. In time-kill activity of levofloxacin, D25 presented a subpopulation of persisters with survival rate higher (1.6-fold) than the parental. Conclusion: Previous exposure of S. maltophilia to daptomycin can induce cross-tolerance to ceftazidime and ticarcillin-clavulanate and cross-persistence to levofloxacin.
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Affiliation(s)
- Mariana Am Ferreira
- Department of Pathology, Health Sciences Center, Universidade Federal do Espírito Santo (UFES), Av. Marechal Campos, 1468, 29040-090 Vitória, Espírito Santo, Brazil
| | - Maria Ls Pereira
- Department of Pathology, Health Sciences Center, Universidade Federal do Espírito Santo (UFES), Av. Marechal Campos, 1468, 29040-090 Vitória, Espírito Santo, Brazil
| | - Kênia V Dos Santos
- Department of Pathology, Health Sciences Center, Universidade Federal do Espírito Santo (UFES), Av. Marechal Campos, 1468, 29040-090 Vitória, Espírito Santo, Brazil
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35
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Evolutionary causes and consequences of bacterial antibiotic persistence. Nat Rev Microbiol 2020; 18:479-490. [PMID: 32461608 DOI: 10.1038/s41579-020-0378-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 12/12/2022]
Abstract
Antibiotic treatment failure is of growing concern. Genetically encoded resistance is key in driving this process. However, there is increasing evidence that bacterial antibiotic persistence, a non-genetically encoded and reversible loss of antibiotic susceptibility, contributes to treatment failure and emergence of resistant strains as well. In this Review, we discuss the evolutionary forces that may drive the selection for antibiotic persistence. We review how some aspects of antibiotic persistence have been directly selected for whereas others result from indirect selection in disparate ecological contexts. We then discuss the consequences of antibiotic persistence on pathogen evolution. Persisters can facilitate the evolution of antibiotic resistance and virulence. Finally, we propose practical means to prevent persister formation and how this may help to slow down the evolution of virulence and resistance in pathogens.
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36
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Windels EM, Van den Bergh B, Michiels J. Bacteria under antibiotic attack: Different strategies for evolutionary adaptation. PLoS Pathog 2020; 16:e1008431. [PMID: 32379814 PMCID: PMC7205213 DOI: 10.1371/journal.ppat.1008431] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Bacteria are well known for their extremely high adaptability in stressful environments. The clinical relevance of this property is clearly illustrated by the ever-decreasing efficacy of antibiotic therapies. Frequent exposures to antibiotics favor bacterial strains that have acquired mechanisms to overcome drug inhibition and lethality. Many strains, including life-threatening pathogens, exhibit increased antibiotic resistance or tolerance, which considerably complicates clinical practice. Alarmingly, recent studies show that in addition to resistance, tolerance levels of bacterial populations are extremely flexible in an evolutionary context. Here, we summarize laboratory studies providing insight in the evolution of resistance and tolerance and shed light on how the treatment conditions could affect the direction of bacterial evolution under antibiotic stress.
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Affiliation(s)
- Etthel M. Windels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- * E-mail:
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37
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Kuehl R, Morata L, Meylan S, Mensa J, Soriano A. When antibiotics fail: a clinical and microbiological perspective on antibiotic tolerance and persistence of Staphylococcus aureus. J Antimicrob Chemother 2020; 75:1071-1086. [PMID: 32016348 DOI: 10.1093/jac/dkz559] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen causing a vast array of infections with significant mortality. Its versatile physiology enables it to adapt to various environments. Specific physiological changes are thought to underlie the frequent failure of antimicrobial therapy despite susceptibility in standard microbiological assays. Bacteria capable of surviving high antibiotic concentrations despite having a genetically susceptible background are described as 'antibiotic tolerant'. In this review, we put current knowledge on environmental triggers and molecular mechanisms of increased antibiotic survival of S. aureus into its clinical context. We discuss animal and clinical evidence of its significance and outline strategies to overcome infections with antibiotic-tolerant S. aureus.
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Affiliation(s)
- Richard Kuehl
- Service of Infectious Diseases, Hospital Clinic of Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Laura Morata
- Service of Infectious Diseases, Hospital Clinic of Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Sylvain Meylan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Division de Maladies Infectieuses, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Josep Mensa
- Service of Infectious Diseases, Hospital Clinic of Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Alex Soriano
- Service of Infectious Diseases, Hospital Clinic of Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
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Liu C, Huang H, Zhou Q, Liu B, Wang Y, Li P, Liao K, Su W. Antibacterial and antibiotic synergistic activities of the extract from Pithecellobium clypearia against clinically important multidrug-resistant gram-negative bacteria. Eur J Integr Med 2019. [DOI: 10.1016/j.eujim.2019.100999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Levin-Reisman I, Brauner A, Ronin I, Balaban NQ. Epistasis between antibiotic tolerance, persistence, and resistance mutations. Proc Natl Acad Sci U S A 2019; 116:14734-14739. [PMID: 31262806 PMCID: PMC6642377 DOI: 10.1073/pnas.1906169116] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Understanding the evolution of microorganisms under antibiotic treatments is a burning issue. Typically, several resistance mutations can accumulate under antibiotic treatment, and the way in which resistance mutations interact, i.e., epistasis, has been extensively studied. We recently showed that the evolution of antibiotic resistance in Escherichia coli is facilitated by the early appearance of tolerance mutations. In contrast to resistance, which reduces the effectiveness of the drug concentration, tolerance increases resilience to antibiotic treatment duration in a nonspecific way, for example when bacteria transiently arrest their growth. Both result in increased survival under antibiotics, but the interaction between resistance and tolerance mutations has not been studied. Here, we extend our analysis to include the evolution of a different type of tolerance and a different antibiotic class and measure experimentally the epistasis between tolerance and resistance mutations. We derive the expected model for the effect of tolerance and resistance mutations on the dynamics of survival under antibiotic treatment. We find that the interaction between resistance and tolerance mutations is synergistic in strains evolved under intermittent antibiotic treatment. We extend our analysis to mutations that result in antibiotic persistence, i.e., to tolerance that is conferred only on a subpopulation of cells. We show that even when this population heterogeneity is included in our analysis, a synergistic interaction between antibiotic persistence and resistance mutations remains. We expect our general framework for the epistasis in killing conditions to be relevant for other systems as well, such as bacteria exposed to phages or cancer cells under treatment.
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Affiliation(s)
- Irit Levin-Reisman
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Asher Brauner
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Irine Ronin
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Nathalie Q Balaban
- Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel;
- The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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40
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Lee JS, Choi JY, Chung ES, Peck KR, Ko KS. Variation in the formation of persister cells against meropenem in Klebsiella pneumoniae bacteremia and analysis of its clinical features. Diagn Microbiol Infect Dis 2019; 95:114853. [PMID: 31353067 DOI: 10.1016/j.diagmicrobio.2019.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 12/22/2022]
Abstract
We investigated variations in the rate of persister cell formation against meropenem in 68 Klebsiella pneumoniae isolates from blood. The persister cell formation rates varied markedly but were not significantly different between the patient survival group and death group at 30 days. In addition, they were not associated with the patients' underlying diseases. However, the isolates of CC15 and CC23 showed higher survival rates against 10× MIC of meropenem than CC11. The survival rate of persister cells was less for amikacin and colistin than that for ciprofloxacin. When combinations of meropenem and other antibiotics were administered, persister formation rates decreased compared with those against only meropenem. However, no synergistic effect to remove persister cells was observed. Further investigation is needed to understand persister cell formation in K. pneumoniae with respect to the mechanism involved and clinical implications and that diverse strategies should be explored to remove persister cells.
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Affiliation(s)
- Jin Seo Lee
- Division of Infectious Diseases, Department of Medicine, Hallym University Kangdong Sacred Heart Hospital, Seoul, South Korea
| | - Ji-Young Choi
- Department of Molecular Cell Biolog\y, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Eun Seon Chung
- Department of Molecular Cell Biolog\y, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biolog\y, Sungkyunkwan University School of Medicine, Suwon, South Korea.
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41
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Fraiha RO, Pereira APR, Brito EDCA, Borges CL, Parente AFA, Perdomo RT, Macedo MLR, Weber SS. Stress conditions in the host induce persister cells and influence biofilm formation by Staphylococcus epidermidis RP62A. Rev Soc Bras Med Trop 2019; 52:e20180001. [PMID: 30785531 DOI: 10.1590/0037-8682-0001-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 07/24/2018] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Studies have demonstrated that pathogens react to the harsh conditions in human tissues by inducing mechanisms that promote survival. METHODS Persistence and biofilm-forming ability were evaluated during stress conditions that mimic those in the host. RESULTS Carbon-source availability had a positive effect on Staphylococcus epidermidis RP62A adhesion during hypoxia, accompanied by a decrease in pH. In contrast, iron limitation led to decreased surface-adherent biomass, accompanied by an increase medium acidification and lactate levels. Interestingly, iron starvation and hypoxia induced persister cells in planktonic culture. CONCLUSIONS These findings highlight the role of host stress in the virulence of S. epidermidis.
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Affiliation(s)
- Rafael Ovando Fraiha
- Laboratório de Biociência, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - Ana Paula Ramos Pereira
- Laboratório de Biociência, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - Eliana da Costa Alvarenga Brito
- Laboratório de Biociência, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | | | - Renata Trentin Perdomo
- Laboratório de Biociência, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - Maria Ligia Rodrigues Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil
| | - Simone Schneider Weber
- Laboratório de Biociência, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brasil.,Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Itacoatiara, AM, Brasil
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42
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Yadav K, Yavvari PS, Pal S, Kumar S, Mishra D, Gupta S, Mitra M, Soni V, Khare N, Sharma P, Srikanth CV, Kapil A, Singh A, Nandicoori VK, Bajaj A. Oral Delivery of Cholic Acid-Derived Amphiphile Helps in Combating Salmonella-Mediated Gut Infection and Inflammation. Bioconjug Chem 2019; 30:721-732. [DOI: 10.1021/acs.bioconjchem.8b00880] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kavita Yadav
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
- Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Prabhu Srinivas Yavvari
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal-462026, Madhya Pradesh, India
| | - Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
- Kalinga Institute of Industrial Technology, Bhubaneswar-751024, Odisha India,
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
- Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Deepakkumar Mishra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Vijay Soni
- National Institute of Immunology, Aruna Asaf Ali
Marg, New Delhi-110067, India
| | - Neha Khare
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | - Chittur V. Srikanth
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi-110029, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India
| | | | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon
Expressway, Faridabad-121001, Haryana, India
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Windels EM, Michiels JE, Fauvart M, Wenseleers T, Van den Bergh B, Michiels J. Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates. ISME JOURNAL 2019; 13:1239-1251. [PMID: 30647458 DOI: 10.1038/s41396-019-0344-9] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/09/2018] [Accepted: 12/23/2018] [Indexed: 02/08/2023]
Abstract
Persisters are transiently antibiotic-tolerant cells that complicate the treatment of bacterial infections. Both theory and experiments have suggested that persisters facilitate genetic resistance by constituting an evolutionary reservoir of viable cells. Here, we provide evidence for a strong positive correlation between persistence and the likelihood to become genetically resistant in natural and lab strains of E. coli. This correlation can be partly attributed to the increased availability of viable cells associated with persistence. However, our data additionally show that persistence is pleiotropically linked with mutation rates. Our theoretical model further demonstrates that increased survival and mutation rates jointly affect the likelihood of evolving clinical resistance. Overall, these results suggest that the battle against antibiotic resistance will benefit from incorporating anti-persister therapies.
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Affiliation(s)
- Etthel Martha Windels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Joran Elie Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,imec, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.,Douglas lab, Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.
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Anti-persister activity of squalamine against Acinetobacter baumannii. Int J Antimicrob Agents 2018; 53:337-342. [PMID: 30423343 DOI: 10.1016/j.ijantimicag.2018.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/31/2018] [Accepted: 11/04/2018] [Indexed: 01/21/2023]
Abstract
Squalamine is a natural polycationic aminosterol extracted from the shark Squalus acanthias. Squalamine displays remarkable efficacy against antimicrobial-resistant Gram-negative and Gram-positive bacteria. Its membranolytic activity and low cytotoxicity make squalamine one of the most promising agents to fight nosocomial pathogens such as Acinetobacter baumannii. In the context of chronic diseases and therapeutic failures associated with this pathogen, the presence of dormant cells, i.e. persisters and viable but non-culturable cells (VBNCs), highly tolerant to antimicrobial compounds is problematic. The aim of this study was to investigate the antibacterial activity of squalamine against this bacterial population of A. baumannii. Bacterial dormancy was induced by cold shock and nutrient starvation in the presence of high doses of either colistin, ciprofloxacin or squalamine. Persisters and VBNCs induced by these treatments were then challenged with 100 mg/L squalamine. The efficacy of each treatment was determined by evaluating culturability on agar medium, membrane integrity (LIVE/DEAD®BacLightTM staining) and respiratory activity (BacLightTM RedoxSensorTM CTC staining) of bacteria. A. baumannii ATCC 17978 generated persisters as well as VBNCs in the presence of high doses of ciprofloxacin but not colistin or squalamine. Squalamine at 100 mg/L (below its haemolytic concentration) was able to kill dormant cells. Squalamine did not induce persister cell or VBNC formation in A. baumannii ATCC 17978. Interestingly, squalamine was significantly active against this type of dormant population generated by ciprofloxacin, making it a very promising anti-persister agent.
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45
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Sulaiman JE, Hao C, Lam H. Specific Enrichment and Proteomics Analysis of Escherichia coli Persisters from Rifampin Pretreatment. J Proteome Res 2018; 17:3984-3996. [PMID: 30336045 DOI: 10.1021/acs.jproteome.8b00625] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacterial persisters, a dormant and multidrug tolerant subpopulation that are able to resuscitate after antibiotic treatment, have recently received considerable attention as a major cause of relapse of various infectious diseases in the clinic. However, because of their low abundance and inherent transience, it is extremely difficult to study them by proteomics. Here we developed a magnetic-beads-based separation approach to enrich Escherichia coli persisters and then subjected them to shotgun proteomics. Rifampin pretreatment was employed to increase persister formation, and the resulting cells were exposed to a high concentration of ampicillin (10× MIC) to remove nonpersisters. The survivors were analyzed by spectral counting-based quantitative proteomics. On average, 710 proteins were identified at a false discovery rate of 0.01 for enriched E. coli persisters. By spectral counting-based quantification, 105 proteins (70 down-regulated, 35 up-regulated) were shown to be differentially expressed compared with normal cells. A comparison of the differentially expressed proteins between the magnetic beads-enriched persisters and nonenriched persisters (a mixture of persisters and intact dead cells) shows only around half (∼58%) overlap and different protein-protein interaction networks. This suggest that persister enrichment is important to eliminate the cumulative effect of dead cells that will obscure the proteome of persisters. As expected, proteins involved in carbohydrate metabolism, fatty acid and amino acid biosynthesis, and bacterial chemotaxis were found to be down-regulated in the persisters. Interestingly, membrane proteins including some transport proteins were up-regulated, indicating that they might be important for the drug tolerance of persisters. Knockout of the pal gene expressing peptidoglycan-associated lipoprotein, one of the most up-regulated proteins detected in persisters, led to 10-fold reduced persister formation under ampicillin treatment.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering , The Hong Kong University of Science & Technology , Clear Water Bay , Kowloon , Hong Kong
| | - Chunlin Hao
- Department of Chemical and Biological Engineering , The Hong Kong University of Science & Technology , Clear Water Bay , Kowloon , Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering , The Hong Kong University of Science & Technology , Clear Water Bay , Kowloon , Hong Kong
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46
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Chung ES, Wi YM, Ko KS. Variation in formation of persister cells against colistin in Acinetobacter baumannii isolates and its relationship with treatment failure. J Antimicrob Chemother 2018; 72:2133-2135. [PMID: 28379382 DOI: 10.1093/jac/dkx102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Eun Seon Chung
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Yu Mi Wi
- Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 51353, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
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47
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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48
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Timing of DNA damage responses impacts persistence to fluoroquinolones. Proc Natl Acad Sci U S A 2018; 115:E6301-E6309. [PMID: 29915065 DOI: 10.1073/pnas.1804218115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial persisters are subpopulations of phenotypic variants in isogenic cultures that can survive lethal doses of antibiotics. Their tolerances are often attributed to reduced activities of antibiotic targets, which limit corruption and damage in persisters compared with bacteria that die from treatment. However, that model does not hold for nongrowing populations treated with ofloxacin, a fluoroquinolone, where antibiotic-induced damage is comparable between cells that live and those that die. To understand how those persisters achieve this feat, we employed a genetic system that uses orthogonal control of MazF and MazE, a toxin and its cognate antitoxin, to generate model persisters that are uniformly tolerant to ofloxacin. Despite this complete tolerance, MazF model persisters required the same DNA repair machinery (RecA, RecB, and SOS induction) to survive ofloxacin treatment as their nongrowing, WT counterparts and exhibited similar indicators of DNA damage from treatment. Further investigation revealed that, following treatment, the timing of DNA repair was critical to MazF persister survival because, when repair was delayed until after growth and DNA synthesis resumed, survival was compromised. In addition, we found that, with nongrowing, WT planktonic and biofilm populations, stalling the resumption of growth and DNA synthesis after the conclusion of fluoroquinolone treatment with a prevalent type of stress at infection sites (nutrient limitation) led to near complete survival. These findings illustrate that the timing of events, such as DNA repair, following fluoroquinolone treatment is important to persister survival and provide further evidence that knowledge of the postantibiotic recovery period is critical to understanding persistence phenotypes.
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49
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Bahamondez-Canas TF, Zhang H, Tewes F, Leal J, Smyth HDC. PEGylation of Tobramycin Improves Mucus Penetration and Antimicrobial Activity against Pseudomonas aeruginosa Biofilms in Vitro. Mol Pharm 2018. [PMID: 29514003 DOI: 10.1021/acs.molpharmaceut.8b00011] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Pseudomonas aeruginosa is the predominant pathogen in the persistent lung infections of cystic fibrosis (CF) patients among other diseases. One of the mechanisms of resistance of P. aeruginosa infections is the formation and presence of biofilms. Previously, we demonstrated that PEGylated-tobramycin (Tob-PEG) had superior antimicrobial activity against P. aeruginosa biofilms compared to tobramycin (Tob). The goal of this study was to optimize the method of PEGylation of Tob and assess its activity in an in vitro CF-like mucus barrier biofilm model. Tob was PEGylated using three separate chemical conjugation methods and analyzed by 1H NMR. A comparison of the Tob-PEG products from the different conjugation methods showed significant differences in the reduction of biofilm proliferation after 24 h of treatment. In the CF-like mucus barrier model, Tob-PEG was significantly better than Tob in reducing P. aeruginosa proliferation after only 5 h of treatment ( p < 0.01). Finally, Tob-PEG caused a reduction in the number of surviving P. aeruginosa biofilm colonies higher than that of Tob ( p < 0.0001). We demonstrate the significantly improved antimicrobial activity of Tob-PEG against P. aeruginosa biofilms compared to Tob using two PEGylation methods. Tob-PEG had better in vitro activity compared to that of Tob against P. aeruginosa biofilms growing in a CF-like mucus barrier model.
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Affiliation(s)
- Tania F Bahamondez-Canas
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hairui Zhang
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Frederic Tewes
- INSERM, U1070, UFR de Médecine Pharmacie , Université de Poitiers , 86073 Poitiers Cedex 9 , France
| | - Jasmim Leal
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hugh D C Smyth
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States.,Center for Infectious Disease , The University of Texas at Austin , Austin , Texas 78712 , United States
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50
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Li Y, Zhang L, Zhou Y, Zhang Z, Zhang X. Survival of bactericidal antibiotic treatment by tolerant persister cells of Klebsiella pneumoniae. J Med Microbiol 2018; 67:273-281. [PMID: 29458540 DOI: 10.1099/jmm.0.000680] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Persister cells, a subpopulation of tolerant cells within the bacterial culture, are commonly thought to be responsible for antibiotic therapy failure and infection recurrence. Klebsiella pneumoniae is a notorious human pathogen for its increasing resistance to antibiotics and wide involvement in severe infections. In this study, we aimed to investigate the persister subpopulation of K. pneumoniae. METHODOLOGY The presence of persisters in K. pneumoniae was determined by treatment with high concentrations of antibiotics, used alone or in combination. The effect of low level of antibiotics on persister formation was investigated by pre-exposure of cells to antibiotics with low concentrations followed by higher doses. The dependence of persister levels on growth phase was determined by measuring the survival ability of cells along the growth stages upon exposure to a high concentration of antibiotic. Analysis on persister type was carried out by persister elimination assays.Results/Key findings. We show that K. pneumoniae produces high levels of tolerant persister cells to survive treatment by a variety of high concentrations of bactericidal antibiotics and persister formation is prevalent among K. pneumoniae clinical strains. Besides, we find that persister cells can be induced by low concentrations of antibiotics. Finally, we provide evidence that persister formation is growth phase-dependent and Type II persisters dominate the persister subpopulation during the entire exponential phase of K. pneumoniae. CONCLUSION Our study describes the formation of tolerant persister cells that allow survival of treatment by high concentrations of antibiotics in K. pneumoniae.
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Affiliation(s)
- Ying Li
- Department of Immunology, College of Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Luhua Zhang
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Yingshun Zhou
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Zhikun Zhang
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Xinzhuo Zhang
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, PR China
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