301
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Abstract
There is much controversy about the metabolic state of cells that are tolerant to antibiotics, known as persister cells. In this opinion piece, we offer an explanation for the discrepancy seen: some laboratories are studying metabolically active and growing cell populations (e.g., as a result of nutrient shifts) and attributing the phenotypes that they discern to persister cells while other labs are studying dormant cells. We argue here that the metabolically active cell population should more accurately be considered tolerant cells, while the dormant cells are the true persister population.
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302
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Turnbull KJ, Gerdes K. HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin. Mol Microbiol 2017; 104:781-792. [PMID: 28266056 DOI: 10.1111/mmi.13662] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Abstract
Antitoxins encoded by type II toxin - antitoxin (TA) modules neutralize cognate toxins by direct protein - protein contact and in addition, regulate TA operon transcription by binding to operators in the promoter regions. On top of the simple negative feed-back regulation, canonical type II TA operons are regulated by a mechanism called 'Conditional Cooperativity'(CC). In CC, the cellular toxin:antitoxin (T:A) ratio controls the transcription-rate such that low T:A ratios favour repression and high T:A ratios favour de-repression of TA operon transcription. Here a new molecular mechanism that secures selective synthesis of antitoxin in the presence of excess toxin was unravelled. The hicAB locus of E. coli K-12 encodes HicA mRNase and HicB antitoxin. It was shown that hicAB is transcribed by two promoters, an upstream one that is activated by CRP-cAMP and competence factor Sxy and a downstream one that is autorepressed solely by HicB. Excess HicA destabilizes the HicB•operator complex in vitro and consistently, activates hicAB transcription in vivo. Remarkably, the hicAB transcript synthesized from the HicB-controlled promoter produces HicB but not HicA. Thus, the HicA-mediated derepression of hicAB transcription provides a mechanism that conditionally and selectively stimulates synthesis of HicB antitoxin under conditions of excess HicA toxin.
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Affiliation(s)
- Kathryn J Turnbull
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK-2200, Denmark
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK-2200, Denmark
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303
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Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R. Spatiotemporal microbial evolution on antibiotic landscapes. Science 2017; 353:1147-51. [PMID: 27609891 DOI: 10.1126/science.aag0822] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/28/2016] [Indexed: 01/03/2023]
Abstract
A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front. While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front, we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behind more sensitive lineages. The MEGA-plate provides a versatile platform for studying microbial adaption and directly visualizing evolutionary dynamics.
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Affiliation(s)
- Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Tami D Lieberman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Eric D Kelsic
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Remy Chait
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Rotem Gross
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Idan Yelin
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA. Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel. Faculty of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
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304
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Lukačišinová M, Bollenbach T. Toward a quantitative understanding of antibiotic resistance evolution. Curr Opin Biotechnol 2017; 46:90-97. [PMID: 28292709 DOI: 10.1016/j.copbio.2017.02.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/27/2023]
Abstract
The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance.
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Affiliation(s)
| | - Tobias Bollenbach
- IST Austria, Am Campus 1, A-3400 Klosterneuburg, Austria; University of Cologne, Zülpicher Str. 47a, D-50674 Cologne, Germany.
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305
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Andriukonis E, Gorokhova E. Kinetic 15N-isotope effects on algal growth. Sci Rep 2017; 7:44181. [PMID: 28281640 PMCID: PMC5345060 DOI: 10.1038/srep44181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 12/25/2022] Open
Abstract
Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.
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Affiliation(s)
- Eivydas Andriukonis
- Faculty of Chemistry and Geosciences, Department of Physical Chemistry, Vilnius University, Vilnius, Lithuania
- Laboratory of Bio-Nanotechnology, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
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306
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Van den Bergh B, Fauvart M, Michiels J. Formation, physiology, ecology, evolution and clinical importance of bacterial persisters. FEMS Microbiol Rev 2017; 41:219-251. [DOI: 10.1093/femsre/fux001] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
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307
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Eco-evolutionary feedbacks can rescue cooperation in microbial populations. Sci Rep 2017; 7:42561. [PMID: 28211914 PMCID: PMC5304172 DOI: 10.1038/srep42561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/12/2017] [Indexed: 11/08/2022] Open
Abstract
Bacterial populations whose growth depends on the cooperative production of public goods are usually threatened by the rise of cheaters that do not contribute but just consume the common resource. Minimizing cheater invasions appears then as a necessary mechanism to maintain these populations. However, that invasions result instead in the persistence of cooperation is a prospect that has yet remained largely unexplored. Here, we show that the demographic collapse induced by cheaters in the population can actually contribute to the rescue of cooperation, in a clear illustration of how ecology and evolution can influence each other. The effect is made possible by the interplay between spatial constraints and the essentiality of the shared resource. We validate this result by carefully combining theory and experiments, with the engineering of a synthetic bacterial community in which the public compound allows survival to a lethal stress. The characterization of the experimental system identifies additional factors that can matter, like the impact of the lag phase on the tolerance to stress, or the appearance of spontaneous mutants. Our work explains the unanticipated dynamics that eco-evolutionary feedbacks can generate in microbial communities, feedbacks that reveal fundamental for the adaptive change of ecosystems at all scales.
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308
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Levin-Reisman I, Ronin I, Gefen O, Braniss I, Shoresh N, Balaban NQ. Antibiotic tolerance facilitates the
evolution of resistance. Science 2017; 355:826-830. [DOI: 10.1126/science.aaj2191] [Citation(s) in RCA: 634] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/16/2017] [Indexed: 12/24/2022]
Abstract
Controlled experimental evolution during
antibiotic treatment can help to explain the
processes leading to antibiotic resistance in
bacteria. Recently, intermittent antibiotic
exposures have been shown to lead rapidly to the
evolution of tolerance—that is, the ability to
survive under treatment without developing
resistance. However, whether tolerance delays or
promotes the eventual emergence of resistance is
unclear. Here we used in vitro evolution
experiments to explore this question. We found
that in all cases, tolerance preceded resistance.
A mathematical population-genetics model showed
how tolerance boosts the chances for resistance
mutations to spread in the population. Thus,
tolerance mutations pave the way for the rapid
subsequent evolution of resistance. Preventing the
evolution of tolerance may offer a new strategy
for delaying the emergence of resistance.
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Affiliation(s)
- Irit Levin-Reisman
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Irine Ronin
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Orit Gefen
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ilan Braniss
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Noam Shoresh
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nathalie Q. Balaban
- Racah Institute of Physics and the Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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309
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Gefen O, Chekol B, Strahilevitz J, Balaban NQ. TDtest: easy detection of bacterial tolerance and persistence in clinical isolates by a modified disk-diffusion assay. Sci Rep 2017; 7:41284. [PMID: 28145464 PMCID: PMC5286521 DOI: 10.1038/srep41284] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/16/2016] [Indexed: 01/08/2023] Open
Abstract
Antibiotic tolerance - the ability for prolonged survival under bactericidal treatments - is a potentially clinically significant phenomenon that is commonly overlooked in the clinical microbiology laboratory. Recent in vitro experiments show that high tolerance can evolve under intermittent antibiotic treatments in as little as eight exposures to high doses of antibiotics, suggesting that tolerance may evolve also in patients. However, tests for antibiotic susceptibilities, such as the disk-diffusion assay, evaluate only the concentration at which a bacterial strain stops growing, namely resistance level. High tolerance strains will not be detected using these tests. We present a simple modification of the standard disk-diffusion assay that allows the semi-quantitative evaluation of tolerance levels. This novel method, the “TDtest”, enabled the detection of tolerant and persistent bacteria by promoting the growth of the surviving bacteria in the inhibition zone, once the antibiotic has diffused away. Using the TDtest, we were able to detect different levels of antibiotic tolerance in clinical isolates of E. coli. The TDtest also identified antibiotics that effectively eliminate tolerant bacteria. The additional information on drug susceptibility provided by the TDtest should enable tailoring better treatment regimens for pathogenic bacteria.
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Affiliation(s)
- Orit Gefen
- Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Betty Chekol
- Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jacob Strahilevitz
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - Nathalie Q Balaban
- Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Harvey M. Kruger Family Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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310
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In Vitro Tolerance of Drug-Naive Staphylococcus aureus Strain FDA209P to Vancomycin. Antimicrob Agents Chemother 2017; 61:AAC.01154-16. [PMID: 27855063 PMCID: PMC5278750 DOI: 10.1128/aac.01154-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/03/2016] [Indexed: 12/26/2022] Open
Abstract
The mechanisms underlying bacterial tolerance to antibiotics are unclear. A possible adaptation strategy was explored by exposure of drug-naive methicillin-susceptible Staphylococcus aureus strain FDA209P to vancomycin in vitro. Strains surviving vancomycin treatment (vancomycin survivor strains), which appeared after 96 h of exposure, were slow-growing derivatives of the parent strain. Although the vancomycin MICs for the survivor strains were within the susceptible range, the cytokilling effects of vancomycin at 20-fold the MIC were significantly lower for the survivor strains than for the parent strain. Whole-genome sequencing demonstrated that ileS, encoding isoleucyl-tRNA synthetase (IleRS), was mutated in two of the three vancomycin survivor strains. The IleRS Y723H mutation is located close to the isoleucyl-tRNA contact site and potentially affects the affinity of IleRS binding to isoleucyl-tRNA, thereby inhibiting protein synthesis and leading to vancomycin tolerance. Introduction of the mutation encoding IleRS Y723H into FDA209P by allelic replacement successfully transferred the vancomycin tolerance phenotype. We have identified mutation of ileS to be one of the bona fide genetic events leading to the acquisition of vancomycin tolerance in S. aureus, potentially acting via inhibition of the function of IleRS.
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311
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Otoupal PB, Erickson KE, Escalas-Bordoy A, Chatterjee A. CRISPR Perturbation of Gene Expression Alters Bacterial Fitness under Stress and Reveals Underlying Epistatic Constraints. ACS Synth Biol 2017; 6:94-107. [PMID: 27529436 DOI: 10.1021/acssynbio.6b00050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The evolution of antibiotic resistance has engendered an impending global health crisis that necessitates a greater understanding of how resistance emerges. The impact of nongenetic factors and how they influence the evolution of resistance is a largely unexplored area of research. Here we present a novel application of CRISPR-Cas9 technology for investigating how gene expression governs the adaptive pathways available to bacteria during the evolution of resistance. We examine the impact of gene expression changes on bacterial adaptation by constructing a library of deactivated CRISPR-Cas9 synthetic devices to tune the expression of a set of stress-response genes in Escherichia coli. We show that artificially inducing perturbations in gene expression imparts significant synthetic control over fitness and growth during stress exposure. We present evidence that these impacts are reversible; strains with synthetically perturbed gene expression regained wild-type growth phenotypes upon stress removal, while maintaining divergent growth characteristics under stress. Furthermore, we demonstrate a prevailing trend toward negative epistatic interactions when multiple gene perturbations are combined simultaneously, thereby posing an intrinsic constraint on gene expression underlying adaptive trajectories. Together, these results emphasize how CRISPR-Cas9 can be employed to engineer gene expression changes that shape bacterial adaptation, and present a novel approach to synthetically control the evolution of antimicrobial resistance.
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Affiliation(s)
- Peter B. Otoupal
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Keesha E. Erickson
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Antoni Escalas-Bordoy
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Anushree Chatterjee
- Department
of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, United States
- BioFrontiers
Institute, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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312
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Cruz Olivo EA, Santos D, de Lima ME, Dos Santos VL, Sinisterra RD, Cortés ME. Antibacterial Effect of Synthetic Peptide LyeTxI and LyeTxI/β-Cyclodextrin Association Compound Against Planktonic and Multispecies Biofilms of Periodontal Pathogens. J Periodontol 2016; 88:e88-e96. [PMID: 27989223 DOI: 10.1902/jop.2016.160438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Antimicrobial peptides (AMPs) have shown rapid and potent effect against planktonic bacteria. However, control of periodontopathic biofilms is a challenge even for AMPs. Thus, the present study evaluates in vitro antimicrobial activity of synthetic peptide LyeTxI and association compound LyeTxI/β-cyclodextrin (βCD) against multispecies biofilms. METHODS Sensibility to LyeTxI and LyeTxI/βCD was determined for planktonic Gram-negative periodontopathogens. Time-kill kinetic assay was performed at minimum inhibitory concentrations (MICs) in all planktonic strains. Multispecies biofilms were grown on pegs using a biofilm device and studied by scanning electron microscopy at 2, 5, and 10 days. Minimal biofilm eradication concentration (MBEC) was determined for 2- and 4-day multispecies biofilms. Metabolic activity of biofilms was determined by fluorometry study. RESULTS Biofilms showed reproducible cell density on pegs of the biofilm device. LyeTxI and LyeTxI/βCD were active against all strains tested at concentrations ≤62.5 μg/mL. Kinetic assays showed rapid bactericidal effect of LyeTxI against all periodontopathogens. MBECs of LyeTxI and LyeTxI/βCD against multispecies 2-day biofilms were two-fold higher than MICs of cells shed from biofilms. LyeTxI was able to reduce multispecies 2-day metabolic activity by 90%. Multispecies 4-day biofilms were tolerant to all agents tested. CONCLUSIONS LyeTxI and LyeTxI/βCD are active against periodontopathic bacteria, showing rapid bactericidal effect and may be used to prevent biofilm development. In the future, AMPs could be therapeutic tools for treatment of periodontitis.
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Affiliation(s)
- Edison Andrés Cruz Olivo
- Department of Periodontology, Faculty of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Daniel Santos
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais
| | - Maria Elena de Lima
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais
| | - Vera Lúcia Dos Santos
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais
| | - Rubén Dario Sinisterra
- Department of Inorganic Chemistry, Exacts Science Institute, Federal University of Minas Gerais
| | - María Esperanza Cortés
- Department of Restorative Dentistry, Faculty of Dentistry, Federal University of Minas Gerais
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313
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Prince A, Sandhu P, Ror P, Dash E, Sharma S, Arakha M, Jha S, Akhter Y, Saleem M. Lipid-II Independent Antimicrobial Mechanism of Nisin Depends On Its Crowding And Degree Of Oligomerization. Sci Rep 2016; 6:37908. [PMID: 27897200 PMCID: PMC5126574 DOI: 10.1038/srep37908] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/02/2016] [Indexed: 02/07/2023] Open
Abstract
Nisin inhibits bacterial growth by generating pores in cell membrane and interrupting cell-wall biosynthesis through specific lipid II interaction. However, the role of the hinge region and C-terminus residues of the peptide in antibacterial action of nisin is largely unknown. Here, using molecular dynamics simulations and experimental approach, we report that at high concentration regimes of nisin, interaction with phospholipids may equally deform the bacterial cell membranes even under significantly varying amounts of lipid-II. Membrane thinning, destabilization and decrease in lipid density depend on the degree of oligomerization of nisin. Growth kinetics of Bacillus subtilis and Escherichia coli interestingly show recovery by extended lag phase under low concentrations of nisin treatment while high concentrations of nisin caused decrease in cell viability as recorded by striking reduction in membrane potential and surface area. The significant changes in the dipole potential and fluorescence anisotropy were observed in negatively charged membranes in the absence of lipid-II with increasing concentration of nisin. The identical correlation of cell viability, membrane potential dissipation and morphology with the concentration regime of nisin, in both Bacillus subtilis (lipid II rich) and Escherichia coli (lipid II impoverished), hints at a non-specific physical mechanism where degree of membrane deformation depends on degree of crowding and oligomerization of nisin.
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Affiliation(s)
- Ashutosh Prince
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Padmani Sandhu
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, India
| | - Pankaj Ror
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Eva Dash
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Shingarika Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, India
| | - Manoranjan Arakha
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Suman Jha
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Yusuf Akhter
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, India
| | - Mohammed Saleem
- Department of Life Sciences, National Institute of Technology, Rourkela, India
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314
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Stress-Induced Evolution of Heat Resistance and Resuscitation Speed in Escherichia coli O157:H7 ATCC 43888. Appl Environ Microbiol 2016; 82:6656-6663. [PMID: 27590820 DOI: 10.1128/aem.02027-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/27/2016] [Indexed: 11/20/2022] Open
Abstract
The development of resistance in foodborne pathogens to food preservation techniques is an issue of increasing concern, especially in minimally processed foods where safety relies on hurdle technology. In this context, mild heat can be used in combination with so-called nonthermal processes, such as high hydrostatic pressure (HHP), at lower individual intensities to better retain the quality of the food. However, mild stresses may increase the risk of (cross-)resistance development in the surviving population, which in turn might compromise food safety. In this investigation, we examined the evolution of Escherichia coli O157:H7 strain ATCC 43888 after recurrent exposure to progressively intensifying mild heat shocks (from 54.0°C to 60.0°C in 0.5°C increments) with intermittent resuscitation and growth of survivors. As such, mutant strains were obtained after 10 cycles of selection with ca. 106-fold higher heat resistance than that for the parental strain at 58.0°C, although this resistance did not extend to temperatures exceeding 60.0°C. Moreover, these mutant strains typically displayed cross-resistance against HHP shock and displayed signs of enhanced RpoS and RpoH activity. Interestingly, additional cycles of selection maintaining the intensity of the heat shock constant (58.5°C) selected for mutant strains in which resuscitation speed, rather than resistance, appeared to be increased. Therefore, it seems that resistance and resuscitation speed are rapidly evolvable traits in E. coli ATCC 43888 that can compromise food safety. IMPORTANCE In this investigation, we demonstrated that Escherichia coli O157:H7 ATCC 43888 rapidly acquires resistance to mild heat exposure, with this resistance yielding cross-protection to high hydrostatic pressure treatment. In addition, mutants of E. coli ATCC 43888 in which resuscitation speed, rather than resistance, appeared to be improved were selected. As such, both resistance and resuscitation speed seem to be rapidly evolvable traits that can compromise the control of foodborne pathogens in minimal processing strategies, which rely on the efficacy of combined mild preservation stresses for food safety.
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315
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Gillings MR, Paulsen IT, Tetu SG. Genomics and the evolution of antibiotic resistance. Ann N Y Acad Sci 2016; 1388:92-107. [DOI: 10.1111/nyas.13268] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
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316
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Michiels JE, Van den Bergh B, Verstraeten N, Michiels J. Molecular mechanisms and clinical implications of bacterial persistence. Drug Resist Updat 2016; 29:76-89. [PMID: 27912845 DOI: 10.1016/j.drup.2016.10.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Any bacterial population harbors a small number of phenotypic variants that survive exposure to high concentrations of antibiotic. Importantly, these so-called 'persister cells' compromise successful antibiotic therapy of bacterial infections and are thought to contribute to the development of antibiotic resistance. Intriguingly, drug-tolerant persisters have also been identified as a factor underlying failure of chemotherapy in tumor cell populations. Recent studies have begun to unravel the complex molecular mechanisms underlying persister formation and revolve around stress responses and toxin-antitoxin modules. Additionally, in vitro evolution experiments are revealing insights into the evolutionary and adaptive aspects of this phenotype. Furthermore, ever-improving experimental techniques are stimulating efforts to investigate persisters in their natural, infection-associated, in vivo environment. This review summarizes recent insights into the molecular mechanisms of persister formation, explains how persisters complicate antibiotic treatment of infections, and outlines emerging strategies to combat these tolerant cells.
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Affiliation(s)
| | | | | | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
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317
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A cell-based approach to characterize antimicrobial compounds through kinetic dose response. Bioorg Med Chem 2016; 24:6315-6319. [PMID: 27713016 DOI: 10.1016/j.bmc.2016.09.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 12/18/2022]
Abstract
The rapid spread of antibiotic resistance has created a pressing need for the development of novel drug screening platforms. Herein, we report on the use of cell-based kinetic dose response curves for small molecule characterization in antibiotic discovery efforts. Kinetically monitoring bacterial growth at sub-inhibitory concentrations of antimicrobial small molecules generates unique dose response profiles. We show that clustering of profiles by growth characteristics can classify antibiotics by mechanism of action. Furthermore, changes in growth kinetics have the potential to offer insight into the mechanistic action of novel molecules and can be used to predict off-target effects generated through structure-activity relationship studies. Kinetic dose response also allows for detection of unstable compounds early in the lead development process. We propose that this kinetic approach is a rapid and cost-effective means to gather critical information on antimicrobial small molecules during the hit selection and lead development pipeline.
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318
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High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays. Nat Biotechnol 2016; 34:1052-1059. [PMID: 27598230 PMCID: PMC5064867 DOI: 10.1038/nbt.3666] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 08/10/2016] [Indexed: 12/21/2022]
Abstract
Methods to rapidly assess cell growth would be useful for many applications, including drug susceptibility testing, but current technologies have limited sensitivity or throughput. Here we present an approach to precisely and rapidly measure growth rates of many individual cells simultaneously. We flow cells in suspension through a microfluidic channel with 10–12 resonant mass sensors distributed along its length, weighing each cell repeatedly over the 4–20 min it spends in the channel. Because multiple cells traverse the channel at the same time, we obtain growth rates for >60 cells/h with a resolution of 0.2 pg/h for mammalian cells and 0.02 pg/h for bacteria. We measure the growth of single lymphocytic cells, mouse and human T cells, primary human leukemia cells, yeast, Escherichia coli and Enterococcus faecalis. Our system reveals subpopulations of cells with divergent growth kinetics and enables assessment of cellular responses to antibiotics and antimicrobial peptides within minutes.
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319
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Baumgartner M, Neu TR, Blom JF, Pernthaler J. Protistan predation interferes with bacterial long-term adaptation to substrate restriction by selecting for defence morphotypes. J Evol Biol 2016; 29:2297-2310. [PMID: 27488245 DOI: 10.1111/jeb.12957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/11/2016] [Accepted: 07/26/2016] [Indexed: 11/26/2022]
Abstract
Bacteria that are introduced into aquatic habitats face a low substrate environment interspersed with rare productive 'hotspots', as well as high protistan grazing. Whereas the former condition should select for growth performance, the latter should favour traits that reduce predation mortality, such as the formation of large cell aggregates. However, protected morphotypes often convey a growth disadvantage, and bacteria thus face a trade-off between investing in growth or defence traits. We set up an evolutionary experiment with the freshwater isolate Sphingobium sp. strain Z007 that conditionally increases aggregate formation in supernatants from a predator-prey coculture. We hypothesized that low substrate levels would favour growth performance and reduce the aggregated subpopulation, but that the concomitant presence of a flagellate predator might conserve the defence trait. After 26 (1-week) growth cycles either with (P+) or without (P-) predators, bacteria had evolved into strikingly different phenotypes. Strains from P- had low numbers of aggregates and increased growth yield, both at the original rich growth conditions and on various single carbon sources. By contrast, isolates from the P+ treatment formed elevated proportions of defence morphotypes, but exhibited lower growth yield and metabolic versatility. Moreover, the evolved strains from both treatments had lost phenotypic plasticity of aggregate formation. In summary, the (transient) residence of bacteria at oligotrophic conditions may promote a facultative oligotrophic life style, which is advantageous for survival in aquatic habitats. However, the investment in defence against predation mortality may constrain microbial adaptation to the abiotic environment.
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Affiliation(s)
- M Baumgartner
- Limnological Station, Department of Plant and Microbial Biology, University of Zürich, Kilchberg, Switzerland
| | - T R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - J F Blom
- Limnological Station, Department of Plant and Microbial Biology, University of Zürich, Kilchberg, Switzerland
| | - J Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zürich, Kilchberg, Switzerland.
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320
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The essential mycobacterial amidotransferase GatCAB is a modulator of specific translational fidelity. Nat Microbiol 2016; 1:16147. [PMID: 27564922 DOI: 10.1038/nmicrobiol.2016.147] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/19/2016] [Indexed: 01/14/2023]
Abstract
Although regulation of translation fidelity is an essential process1-7, diverse organisms and organelles have differing requirements of translational accuracy8-15, and errors in gene translation serve an adaptive function under certain conditions16-20. Therefore, optimal levels of fidelity may vary according to context. Most bacteria utilize a two-step pathway for the specific synthesis of aminoacylated glutamine and/or asparagine tRNAs, involving the glutamine amidotransferase GatCAB21-25, but it had not been appreciated that GatCAB may play a role in modulating mistranslation rates. Here, by using a forward genetic screen, we show that the mycobacterial GatCAB enzyme complex mediates the translational fidelity of glutamine and asparagine codons. We identify mutations in gatA that cause partial loss of function in the holoenzyme, with a consequent increase in rates of mistranslation. By monitoring single-cell transcription dynamics, we demonstrate that reduced gatCAB expression leads to increased mistranslation rates, which result in enhanced rifampicin-specific phenotypic resistance. Consistent with this, strains with mutations in gatA from clinical isolates of Mycobacterium tuberculosis show increased mistranslation, with associated antibiotic tolerance, suggesting a role for mistranslation as an adaptive strategy in tuberculosis. Together, our findings demonstrate a potential role for the indirect tRNA aminoacylation pathway in regulating translational fidelity and adaptive mistranslation.
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321
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Abstract
The problem of antibiotic resistance poses challenges across many disciplines. One such challenge is to understand the fundamental science of how antibiotics work, and how resistance to them can emerge. This is an area where physicists can make important contributions. Here, we highlight cases where this is already happening, and suggest directions for further physics involvement in antimicrobial research.
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Affiliation(s)
- Rosalind Allen
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK. Centre for Synthetic and Systems Biology, The University of Edinburgh, UK
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322
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Govers SK, Gayan E, Aertsen A. Intracellular movement of protein aggregates reveals heterogeneous inactivation and resuscitation dynamics in stressed populations ofEscherichia coli. Environ Microbiol 2016; 19:511-523. [DOI: 10.1111/1462-2920.13460] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sander K. Govers
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M S), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
| | - Elisa Gayan
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M S), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M S), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
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323
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Michiels JE, Van den Bergh B, Verstraeten N, Fauvart M, Michiels J. In Vitro Emergence of High Persistence upon Periodic Aminoglycoside Challenge in the ESKAPE Pathogens. Antimicrob Agents Chemother 2016; 60:4630-7. [PMID: 27185802 PMCID: PMC4958152 DOI: 10.1128/aac.00757-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/10/2016] [Indexed: 12/31/2022] Open
Abstract
Health care-associated infections present a major threat to modern medical care. Six worrisome nosocomial pathogens-Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.-are collectively referred to as the "ESKAPE bugs." They are notorious for extensive multidrug resistance, yet persistence, or the phenotypic tolerance displayed by a variant subpopulation, remains underappreciated in these pathogens. Importantly, persistence can prevent eradication of antibiotic-sensitive bacterial populations and is thought to act as a catalyst for the development of genetic resistance. Concentration- and time-dependent aminoglycoside killing experiments were used to investigate persistence in the ESKAPE pathogens. Additionally, a recently developed method for the experimental evolution of persistence was employed to investigate adaptation to high-dose, extended-interval aminoglycoside therapy in vitro We show that ESKAPE pathogens exhibit biphasic killing kinetics, indicative of persister formation. In vitro cycling between aminoglycoside killing and persister cell regrowth, evocative of clinical high-dose extended-interval therapy, caused a 37- to 213-fold increase in persistence without the emergence of resistance. Increased persistence also manifested in biofilms and provided cross-tolerance to different clinically important antibiotics. Together, our results highlight a possible drawback of intermittent, high-dose antibiotic therapy and suggest that clinical diagnostics might benefit from taking into account persistence.
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Affiliation(s)
| | | | | | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium Smart Systems and Emerging Technologies Unit, Department of Life Science Technologies, imec, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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324
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Verstraeten N, Knapen W, Fauvart M, Michiels J. A Historical Perspective on Bacterial Persistence. Methods Mol Biol 2016; 1333:3-13. [PMID: 26468095 DOI: 10.1007/978-1-4939-2854-5_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Bactericidal antibiotics quickly kill the majority of a bacterial population. However, a small fraction of cells typically survive through entering the so-called persister state. Persister cells are increasingly being viewed as a major cause of the recurrence of chronic infectious disease and could be an important factor in the emergence of antibiotic resistance. The phenomenon of persistence was first described in the 1940s, but remained poorly understood for decades afterwards. Only recently, a series of breakthrough discoveries has started to shed light on persister physiology and the molecular and genetic underpinnings of persister formation. We here provide an overview of the key studies that have paved the way for the current boom in persistence research, with a special focus on the technological and methodological advances that have enabled this progress.
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Affiliation(s)
- Natalie Verstraeten
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium
| | - Wouter Knapen
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, box 2460, 3001, Heverlee, Belgium.
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325
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Experimental Evolution of Escherichia coli Persister Levels Using Cyclic Antibiotic Treatments. Methods Mol Biol 2016; 1333:131-43. [PMID: 26468106 DOI: 10.1007/978-1-4939-2854-5_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Persister cells are difficult to study owing to their transient nature and their usually small number in bacterial populations. In the past, numerous attempts have been made to elucidate persistence mechanisms. However, because of the challenges involved in studying persisters and the clear redundancy in mechanisms underlying their generation, our knowledge of molecular pathways to persistence remains incomplete. Here, we describe how to use experimental evolution with cyclic antibiotic treatments to generate mutants with an increased persister level in stationary phase, ranging from the initial ancestral level up to 100 %. This method will help to unravel molecular pathways to persistence, and opens up a myriad of new possibilities in persister research, such as the convenient study of nearly pure persister cultures and the possibility to investigate the role of time and environmental aspects in the evolution of persistence.
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326
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Curtis TD, Gram L, Knudsen GM. The Small Colony Variant of Listeria monocytogenes Is More Tolerant to Antibiotics and Has Altered Survival in RAW 264.7 Murine Macrophages. Front Microbiol 2016; 7:1056. [PMID: 27458449 PMCID: PMC4932272 DOI: 10.3389/fmicb.2016.01056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/23/2016] [Indexed: 12/11/2022] Open
Abstract
Small Colony Variant (SCV) cells of bacteria are a slow-growing phenotype that result from specific defects in the electron transport chain. They form pinpoint colonies on agar plates and have a variety of phenotypic characteristics, such as altered carbon metabolism, decreased toxin and lytic enzyme production, aminoglycoside resistance, and increased intracellular persistence. They are clinically relevant in Staphylococcus aureus and Pseudomonas aeruginosa, serving as a reservoir for recurrent or prolonged infections. Here, we found that a SCV mutant in the foodborne pathogen Listeria monocytogenes (strain SCV E18), similar to the high persister mutant phenotype, survived significantly better than the wild type when exposed over a 48-h period to concentrations above Minimal Inhibitory Concentration for most tested antibiotics. SCV E18 survived more poorly than the wildtype in unactivated RAW264.7 macrophage cells, presumably because of its reduced listeriolysin O expression, however, it survived better in reactive oxygen species producing, phorbol 12-myristate 13-acetate-activated macrophages. Although SCV E18 was sensitive to oxygen as it entered the stationary phase, it was significantly more tolerant to H2O2 than the wild type, which may result from a shift in metabolism, however, further investigation is needed to resolve this. SCV E18 is a spontaneous mutant with a point mutation in the hemA gene. A wild type copy of hemA was complemented on plasmid pSOG30222, which restored the wild type phenotype. The results reported here suggest that the SCV of L. monocytogenes could be of clinical importance and highlight a need for adequate clinical screening for this phenotype, as it could affect antibiotic treatment outcomes.
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Affiliation(s)
- Thomas D Curtis
- Gram Lab, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Lone Gram
- Gram Lab, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Gitte M Knudsen
- Gram Lab, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
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327
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Abstract
Mycobacteria grow and divide asymmetrically, creating variability in growth pole age, growth properties, and antibiotic susceptibilities. Here, we investigate the importance of growth pole age and other growth properties in determining the spectrum of responses of Mycobacterium smegmatis to challenge with rifampicin. We used a combination of live-cell microscopy and modeling to prospectively identify subpopulations with altered rifampicin susceptibility. We found two subpopulations that had increased susceptibility. At the initiation of treatment, susceptible cells were either small and at early stages of the cell cycle, or large and in later stages of their cell cycle. In contrast to this temporal window of susceptibility, tolerance was associated with factors inherited at division: long birth length and mature growth poles. Thus, rifampicin response is complex and due to a combination of differences established from both asymmetric division and the timing of treatment relative to cell birth.
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328
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Colistin and Polymyxin B Dosage Regimens against Acinetobacter baumannii: Differences in Activity and the Emergence of Resistance. Antimicrob Agents Chemother 2016; 60:3921-33. [PMID: 27067324 DOI: 10.1128/aac.02927-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/05/2016] [Indexed: 12/24/2022] Open
Abstract
Infections caused by multidrug-resistant Acinetobacter baumannii are a major public health problem, and polymyxins are often the last line of therapy for recalcitrant infections by such isolates. The pharmacokinetics of the two clinically used polymyxins, polymyxin B and colistin, differ considerably, since colistin is administered as an inactive prodrug that undergoes slow conversion to colistin. However, the impact of these substantial pharmacokinetic differences on bacterial killing and resistance emergence is poorly understood. We assessed clinically relevant polymyxin B and colistin dosage regimens against one reference and three clinical A. baumannii strains in a dynamic one-compartment in vitro model. A new mechanism-based pharmacodynamic model was developed to describe and predict the drug concentrations and viable counts of the total and resistant populations. Rapid attainment of target concentrations was shown to be critical for polymyxin-induced bacterial killing. All polymyxin B regimens achieved peak concentrations of at least 1 mg/liter within 1 h and caused ≥4 log10 killing at 1 h. In contrast, the slow rise of colistin concentrations to 3 mg/liter over 48 h resulted in markedly reduced bacterial killing. A significant (4 to 6 log10 CFU/ml) amplification of resistant bacterial populations was common to all dosage regimens. The developed mechanism-based model explained the observed bacterial killing, regrowth, and resistance. The model also implicated adaptive polymyxin resistance as a key driver of bacterial regrowth and predicted the amplification of preexisting, highly polymyxin-resistant bacterial populations following polymyxin treatment. Antibiotic combination therapies seem the most promising option for minimizing the emergence of polymyxin resistance.
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329
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Van den Bergh B, Michiels JE, Fauvart M, Michiels J. Should we develop screens for multi-drug antibiotic tolerance? Expert Rev Anti Infect Ther 2016; 14:613-6. [DOI: 10.1080/14787210.2016.1194754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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330
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Bernier SP, Workentine ML, Li X, Magarvey NA, O'Toole GA, Surette MG. Cyanide Toxicity to Burkholderia cenocepacia Is Modulated by Polymicrobial Communities and Environmental Factors. Front Microbiol 2016; 7:725. [PMID: 27242743 PMCID: PMC4870242 DOI: 10.3389/fmicb.2016.00725] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 05/02/2016] [Indexed: 12/31/2022] Open
Abstract
Microbes within polymicrobial communities can establish positive and negative interactions that have the potential to influence the overall behavior of the community. Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc) can co-exist in the lower airways, however several studies have shown that P. aeruginosa can effectively kill the Bcc in vitro, for which hydrogen cyanide (HCN) was recently proposed to play a critical role. Here we show that modification of the environment (i.e., culture medium), long-term genetic adaptation of P. aeruginosa to the cystic fibrosis (CF) lung, or the addition of another bacterial species to the community can alter the sensitivity of Burkholderia cenocepacia to P. aeruginosa toxins. We specifically demonstrate that undefined rich media leads to higher susceptibility of B. cenocepacia to P. aeruginosa toxins like cyanide as compared to a synthetic medium (SCFM), that mimics the CF lung nutritional content. Overall, our study shows that the polymicrobial environment can have profound effects on negative interactions mediated by P. aeruginosa against B. cenocepacia. In fact, evolved P. aeruginosa or the presence of other species such as Staphylococcus aureus can directly abolish the direct competition mediated by cyanide and consequently maintaining a higher level of species diversity within the community.
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Affiliation(s)
- Steve P Bernier
- Department of Medicine, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University Hamilton, ON, Canada
| | - Matthew L Workentine
- Department of Medicine, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University Hamilton, ON, Canada
| | - Xiang Li
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University Hamilton, ON, Canada
| | - Nathan A Magarvey
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University Hamilton, ON, Canada
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth Hanover, NH, USA
| | - Michael G Surette
- Department of Medicine, Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster UniversityHamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster UniversityHamilton, ON, Canada
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331
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332
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Sandoval-Motta S, Aldana M. Adaptive resistance to antibiotics in bacteria: a systems biology perspective. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:253-67. [DOI: 10.1002/wsbm.1335] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Santiago Sandoval-Motta
- Centro de Ciencias de la Complejidad; Universidad Nacional Autónoma de México; Ciudad de México Mexico
| | - Maximino Aldana
- Centro de Ciencias de la Complejidad; Universidad Nacional Autónoma de México; Ciudad de México Mexico
- Instituto de Ciencias Físicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos Mexico
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333
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Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat Rev Microbiol 2016; 14:320-30. [DOI: 10.1038/nrmicro.2016.34] [Citation(s) in RCA: 816] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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334
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Cerulus B, New AM, Pougach K, Verstrepen KJ. Noise and Epigenetic Inheritance of Single-Cell Division Times Influence Population Fitness. Curr Biol 2016; 26:1138-47. [PMID: 27068419 DOI: 10.1016/j.cub.2016.03.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 01/24/2023]
Abstract
The fitness effect of biological noise remains unclear. For example, even within clonal microbial populations, individual cells grow at different speeds. Although it is known that the individuals' mean growth speed can affect population-level fitness, it is unclear how or whether growth speed heterogeneity itself is subject to natural selection. Here, we show that noisy single-cell division times can significantly affect population-level growth rate. Using time-lapse microscopy to measure the division times of thousands of individual S. cerevisiae cells across different genetic and environmental backgrounds, we find that the length of individual cells' division times can vary substantially between clonal individuals and that sublineages often show epigenetic inheritance of division times. By combining these experimental measurements with mathematical modeling, we find that, for a given mean division time, increasing heterogeneity and epigenetic inheritance of division times increases the population growth rate. Furthermore, we demonstrate that the heterogeneity and epigenetic inheritance of single-cell division times can be linked with variation in the expression of catabolic genes. Taken together, our results reveal how a change in noisy single-cell behaviors can directly influence fitness through dynamics that operate independently of effects caused by changes to the mean. These results not only allow a better understanding of microbial fitness but also help to more accurately predict fitness in other clonal populations, such as tumors.
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Affiliation(s)
- Bram Cerulus
- KU Leuven Department Microbiële en Moleculaire Systemen, CMPG Laboratory of Genetics and Genomics, Gaston Geenslaan 1, 3001 Leuven, Belgium; VIB Laboratory of Systems Biology, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Aaron M New
- KU Leuven Department Microbiële en Moleculaire Systemen, CMPG Laboratory of Genetics and Genomics, Gaston Geenslaan 1, 3001 Leuven, Belgium; VIB Laboratory of Systems Biology, Gaston Geenslaan 1, 3001 Leuven, Belgium; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Ksenia Pougach
- KU Leuven Department Microbiële en Moleculaire Systemen, CMPG Laboratory of Genetics and Genomics, Gaston Geenslaan 1, 3001 Leuven, Belgium; VIB Laboratory of Systems Biology, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- KU Leuven Department Microbiële en Moleculaire Systemen, CMPG Laboratory of Genetics and Genomics, Gaston Geenslaan 1, 3001 Leuven, Belgium; VIB Laboratory of Systems Biology, Gaston Geenslaan 1, 3001 Leuven, Belgium.
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335
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Vogwill T, Comfort AC, Furió V, MacLean RC. Persistence and resistance as complementary bacterial adaptations to antibiotics. J Evol Biol 2016; 29:1223-33. [PMID: 26999656 PMCID: PMC5021160 DOI: 10.1111/jeb.12864] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/24/2016] [Accepted: 03/09/2016] [Indexed: 01/08/2023]
Abstract
Bacterial persistence represents a simple of phenotypic heterogeneity, whereby a proportion of cells in an isogenic bacterial population can survive exposure to lethal stresses such as antibiotics. In contrast, genetically based antibiotic resistance allows for continued growth in the presence of antibiotics. It is unclear, however, whether resistance and persistence are complementary or alternative evolutionary adaptations to antibiotics. Here, we investigate the co‐evolution of resistance and persistence across the genus Pseudomonas using comparative methods that correct for phylogenetic nonindependence. We find that strains of Pseudomonas vary extensively in both their intrinsic resistance to antibiotics (ciprofloxacin and rifampicin) and persistence following exposure to these antibiotics. Crucially, we find that persistence correlates positively to antibiotic resistance across strains. However, we find that different genes control resistance and persistence implying that they are independent traits. Specifically, we find that the number of type II toxin–antitoxin systems (TAs) in the genome of a strain is correlated to persistence, but not resistance. Our study shows that persistence and antibiotic resistance are complementary, but independent, evolutionary adaptations to stress and it highlights the key role played by TAs in the evolution of persistence.
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Affiliation(s)
- T Vogwill
- Department of Zoology, University of Oxford, Oxford, UK
| | - A C Comfort
- Department of Zoology, University of Oxford, Oxford, UK
| | - V Furió
- Department of Zoology, University of Oxford, Oxford, UK
| | - R C MacLean
- Department of Zoology, University of Oxford, Oxford, UK
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336
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Orman MA, Brynildsen MP. Persister formation in Escherichia coli can be inhibited by treatment with nitric oxide. Free Radic Biol Med 2016; 93:145-54. [PMID: 26849946 PMCID: PMC4898466 DOI: 10.1016/j.freeradbiomed.2016.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/15/2016] [Accepted: 02/01/2016] [Indexed: 12/01/2022]
Abstract
Bacterial persisters are phenotypic variants that survive extraordinary concentrations of antibiotics, and are thought to underlie the propensity of biofilm infections to relapse. Unfortunately many aspects of persister physiology remain ill-defined, which prevents progress toward eradicating the phenotype. Recently, we identified respiration within non-growing Escherichia coli populations as a potential target for the elimination type I persisters, which are those that arise from passage through stationary phase. Here we discovered that nitric oxide (NO) treatment at the onset of stationary phase significantly reduced type I persister formation through its ability to inhibit respiration. NO decreased protein and RNA degradation in stationary phase cells, and produced populations that were more fit for protein synthesis and growth resumption upon introduction into fresh media than untreated controls. Overall, this data shows that NO, which is a therapeutically-relevant compound, has the potential to decrease the incidence of recurrent infections from persisters.
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Affiliation(s)
- Mehmet A Orman
- Department of Chemical and Biological Engineering, Princeton University, 205 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, 205 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544, USA.
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337
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Barr DA, Kamdolozi M, Nishihara Y, Ndhlovu V, Khonga M, Davies GR, Sloan DJ. Serial image analysis of Mycobacterium tuberculosis colony growth reveals a persistent subpopulation in sputum during treatment of pulmonary TB. Tuberculosis (Edinb) 2016; 98:110-5. [PMID: 27156626 PMCID: PMC4869592 DOI: 10.1016/j.tube.2016.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/02/2016] [Accepted: 03/10/2016] [Indexed: 12/01/2022]
Abstract
Faster elimination of drug tolerant ‘persister’ bacteria may shorten treatment of tuberculosis (TB) but no method exists to quantify persisters in clinical samples. We used automated image analysis to assess whether studying growth characteristics of individual Mycobacterium tuberculosis colonies from sputum on solid media during early TB treatment facilitates ‘persister’ phenotyping. As Time to Detection (TTD) in liquid culture inversely correlates with total bacterial load we also evaluated the relationship between individual colony growth parameters and TTD. Sputum from TB patients in Malawi was prepared for solid and liquid culture after 0, 2 and 4 weeks of treatment. Serial photography of agar plates was used to measure time to appearance (lag time) and radial growth rate for each colony. Mixed-effects modelling was used to analyse changing growth characteristics from serial samples. 20 patients had colony measurements recorded at ≥1 time-point. Overall lag time increased by 6.5 days between baseline and two weeks (p = 0.0001). Total colony count/ml showed typical biphasic elimination, but long lag time colonies (>20days) had slower, monophasic decline. TTD was associated with minimum lag time (time to appearance of first colony1). Slower elimination of long lag time colonies suggests that these may represent a persister subpopulation of bacilli.
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Affiliation(s)
- David A Barr
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, University of Liverpool, 70 Pembroke Place, Liverpool, L69 3GF, UK; Brownlee Centre for Infectious Disease, Gartnavel General Hospital, 1053 Great Western Road, Glasgow, G12 0YN, UK.
| | - Mercy Kamdolozi
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Yo Nishihara
- Queen Elizabeth Central Hospital, P.O. Box 95, Blantyre 3, Malawi; Malawi Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Victor Ndhlovu
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Margaret Khonga
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Geraint R Davies
- Department of Microbiology, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi; Institute of Infection and Global Health, The Ronald Ross Building, University of Liverpool, 8 West Derby Street, Liverpool, L69 7BE, UK; Malawi Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Mahatma Gandhi Road, Blantyre 3, Malawi.
| | - Derek J Sloan
- Liverpool Heart and Chest Hospital, Thomas Drive, Liverpool, L14 3PE, UK; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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338
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Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence. Nat Microbiol 2016; 1:16020. [PMID: 27572640 DOI: 10.1038/nmicrobiol.2016.20] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/29/2016] [Indexed: 12/24/2022]
Abstract
The evolution of antibiotic resistance is a major threat to society and has been predicted to lead to 10 million casualties annually by 2050(1). Further aggravating the problem, multidrug tolerance in bacteria not only relies on the build-up of resistance mutations, but also on some cells epigenetically switching to a non-growing antibiotic-tolerant 'persister' state(2-6). Yet, despite its importance, we know little of how persistence evolves in the face of antibiotic treatment(7). Our evolution experiments in Escherichia coli demonstrate that extremely high levels of multidrug tolerance (20-100%) are achieved by single point mutations in one of several genes and readily emerge under conditions approximating clinical, once-daily dosing schemes. In contrast, reversion to low persistence in the absence of antibiotic treatment is relatively slow and only partially effective. Moreover, and in support of previous mathematical models(8-10), we show that bacterial persistence quickly adapts to drug treatment frequency and that the observed rates of switching to the persister state can be understood in the context of 'bet-hedging' theory. We conclude that persistence is a major component of the evolutionary response to antibiotics that urgently needs to be considered in both diagnostic testing and treatment design in the battle against multidrug tolerance.
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339
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Chueca B, Berdejo D, Gomes-Neto NJ, Pagán R, García-Gonzalo D. Emergence of Hyper-Resistant Escherichia coli MG1655 Derivative Strains after Applying Sub-Inhibitory Doses of Individual Constituents of Essential Oils. Front Microbiol 2016; 7:273. [PMID: 26973641 PMCID: PMC4777736 DOI: 10.3389/fmicb.2016.00273] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 12/04/2022] Open
Abstract
The improvement of food preservation by using essential oils (EOs) and their individual constituents (ICs) is attracting enormous interest worldwide. Until now, researchers considered that treatments with such antimicrobial compounds did not induce bacterial resistance via a phenotypic (i.e., transient) response. Nevertheless, the emergence of genotypic (i.e., stable) resistance after treatment with these compounds had not been previously tested. Our results confirm that growth of Escherichia coli MG1655 in presence of sub-inhibitory concentrations of the ICs carvacrol, citral, and (+)-limonene oxide do not increase resistance to further treatments with either the same IC (direct resistance) or with other preservation treatments (cross-resistance) such as heat or pulsed electric fields (PEF). Bacterial mutation frequency was likewise lower when those IC's were applied; however, after 10 days of re-culturing cells in presence of sub-inhibitory concentrations of the ICs, we were able to isolate several derivative strains (i.e., mutants) displaying an increased minimum inhibitory concentration to those ICs. Furthermore, when compared to the wild type (WT) strain, they also displayed direct resistance and cross-resistance. Derivative strains selected with carvacrol and citral also displayed morphological changes involving filamentation along with cell counts at late-stationary growth phase that were lower than the WT strain. In addition, co-cultures of each derivative strain with the WT strain resulted in a predominance of the original strain in absence of ICs, indicating that mutants would not out-compete WT cells under optimal growth conditions. Nevertheless, growth in the presence of ICs facilitated the selection of these resistant mutants. Thus, as a result, subsequent food preservation treatments of these bacterial cultures might be less effective than expected for WT cultures. In conclusion, this study recommends that treatment with ICs at sub-inhibitory concentrations should be generally avoided, since it could favor the emergence of hyper-resistant strains. To ascertain the true value of EOs and their ICs in the field of food preservation, further research thus needs to be conducted on the induction of increased transient and stable bacterial resistance via such antimicrobial compounds, as revealed in this study.
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Affiliation(s)
- Beatriz Chueca
- Tecnología de los Alimentos, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón, Universidad de Zaragoza-CITA Zaragoza, Spain
| | - Daniel Berdejo
- Tecnología de los Alimentos, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón, Universidad de Zaragoza-CITA Zaragoza, Spain
| | - Nelson J Gomes-Neto
- Laboratory of Food Microbiology, Department of Nutrition, Health Sciences Center, Federal University of Paraíba João Pessoa, Brazil
| | - Rafael Pagán
- Tecnología de los Alimentos, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón, Universidad de Zaragoza-CITA Zaragoza, Spain
| | - Diego García-Gonzalo
- Tecnología de los Alimentos, Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón, Universidad de Zaragoza-CITA Zaragoza, Spain
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340
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Abel Zur Wiesch P, Abel S, Gkotzis S, Ocampo P, Engelstädter J, Hinkley T, Magnus C, Waldor MK, Udekwu K, Cohen T. Classic reaction kinetics can explain complex patterns of antibiotic action. Sci Transl Med 2016; 7:287ra73. [PMID: 25972005 DOI: 10.1126/scitranslmed.aaa8760] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Finding optimal dosing strategies for treating bacterial infections is extremely difficult, and improving therapy requires costly and time-intensive experiments. To date, an incomplete mechanistic understanding of drug effects has limited our ability to make accurate quantitative predictions of drug-mediated bacterial killing and impeded the rational design of antibiotic treatment strategies. Three poorly understood phenomena complicate predictions of antibiotic activity: post-antibiotic growth suppression, density-dependent antibiotic effects, and persister cell formation. We show that chemical binding kinetics alone are sufficient to explain these three phenomena, using single-cell data and time-kill curves of Escherichia coli and Vibrio cholerae exposed to a variety of antibiotics in combination with a theoretical model that links chemical reaction kinetics to bacterial population biology. Our model reproduces existing observations, has a high predictive power across different experimental setups (R(2) = 0.86), and makes several testable predictions, which we verified in new experiments and by analyzing published data from a clinical trial on tuberculosis therapy. Although a variety of biological mechanisms have previously been invoked to explain post-antibiotic growth suppression, density-dependent antibiotic effects, and especially persister cell formation, our findings reveal that a simple model that considers only binding kinetics provides a parsimonious and unifying explanation for these three complex, phenotypically distinct behaviours. Current antibiotic and other chemotherapeutic regimens are often based on trial and error or expert opinion. Our "chemical reaction kinetics"-based approach may inform new strategies, which are based on rational design.
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Affiliation(s)
- Pia Abel Zur Wiesch
- Division of Global Health Equity, Brigham and Women's Hospital and Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA.
| | - Sören Abel
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA. Department of Pharmacy, UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Spyridon Gkotzis
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 17177 Stockholm, Sweden
| | - Paolo Ocampo
- Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland. Department of Environmental Microbiology, EAWAG, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Trevor Hinkley
- School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - Carsten Magnus
- Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA. Howard Hughes Medical Institute, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Klas Udekwu
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 17177 Stockholm, Sweden
| | - Ted Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT 06510, USA. Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
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341
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Baym M, Stone LK, Kishony R. Multidrug evolutionary strategies to reverse antibiotic resistance. Science 2016; 351:aad3292. [PMID: 26722002 DOI: 10.1126/science.aad3292] [Citation(s) in RCA: 405] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibiotic treatment has two conflicting effects: the desired, immediate effect of inhibiting bacterial growth and the undesired, long-term effect of promoting the evolution of resistance. Although these contrasting outcomes seem inextricably linked, recent work has revealed several ways by which antibiotics can be combined to inhibit bacterial growth while, counterintuitively, selecting against resistant mutants. Decoupling treatment efficacy from the risk of resistance can be achieved by exploiting specific interactions between drugs, and the ways in which resistance mutations to a given drug can modulate these interactions or increase the sensitivity of the bacteria to other compounds. Although their practical application requires much further development and validation, and relies on advances in genomic diagnostics, these discoveries suggest novel paradigms that may restrict or even reverse the evolution of resistance.
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Affiliation(s)
- Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Laura K Stone
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA. Department of Biology and Department of Computer Science, Technion - Israel Institute of Technology, Haifa, Israel.
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342
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El Meouche I, Siu Y, Dunlop MJ. Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells. Sci Rep 2016; 6:19538. [PMID: 26758525 PMCID: PMC4725842 DOI: 10.1038/srep19538] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/07/2015] [Indexed: 12/30/2022] Open
Abstract
Transient resistance can allow microorganisms to temporarily survive lethal concentrations of antibiotics. This can be accomplished through stochastic mechanisms, where individual cells within a population display diverse phenotypes to hedge against the appearance of an antibiotic. To date, research on transient stochastic resistance has focused primarily on mechanisms where a subpopulation of cells enters a dormant, drug-tolerant state. However, a fundamental question is whether stochastic gene expression can also generate variable resistance levels among growing cells in a population. We hypothesized that stochastic expression of antibiotic-inducible resistance mechanisms might play such a role. To investigate this, we focused on a prototypical example of such a system: the multiple antibiotic resistance activator MarA. Previous studies have shown that induction of MarA can lead to a multidrug resistant phenotype at the population level. We asked whether MarA expression also has a stochastic component, even when uninduced. Time lapse microscopy showed that isogenic cells express heterogeneous, dynamic levels of MarA, which were correlated with transient antibiotic survival. This finding has important clinical implications, as stochastic expression of resistance genes may be widespread, allowing populations to hedge against the sudden appearance of an antibiotic.
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Affiliation(s)
- Imane El Meouche
- School of Engineering, University of Vermont, Burlington, VT USA 05405
| | - Yik Siu
- School of Engineering, University of Vermont, Burlington, VT USA 05405
| | - Mary J Dunlop
- School of Engineering, University of Vermont, Burlington, VT USA 05405
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343
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Abstract
The present method quantifies the number of slow-growing bacteria leading to antibiotic persistence in a clonal population. First, it enables discriminating between slow growers that are generated by exposure to a stress signal (Type I persisters) and slow growers that are continuously generated during exponential growth (Type II persisters). Second, the method enables determining the amount of slow growers in a culture.
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344
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Erickson KE, Otoupal PB, Chatterjee A. Gene Expression Variability Underlies Adaptive Resistance in Phenotypically Heterogeneous Bacterial Populations. ACS Infect Dis 2015; 1:555-67. [PMID: 27623410 DOI: 10.1021/acsinfecdis.5b00095] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The root cause of the antibiotic resistance crisis is the ability of bacteria to evolve resistance to a multitude of antibiotics and other environmental toxins. The regulation of adaptation is difficult to pinpoint due to extensive phenotypic heterogeneity arising during evolution. Here, we investigate the mechanisms underlying general bacterial adaptation by evolving wild-type Escherichia coli populations to dissimilar chemical toxins. We demonstrate the presence of extensive inter- and intrapopulation phenotypic heterogeneity across adapted populations in multiple traits, including minimum inhibitory concentration, growth rate, and lag time. To search for a common response across the heterogeneous adapted populations, we measured gene expression in three stress-response networks: the mar regulon, the general stress response, and the SOS response. While few genes were differentially expressed, clustering revealed that interpopulation gene expression variability in adapted populations was distinct from that of unadapted populations. Notably, we observed both increases and decreases in gene expression variability upon adaptation. Sequencing select genes revealed that the observed gene expression trends are not necessarily attributable to genetic changes. To further explore the connection between gene expression variability and adaptation, we propagated single-gene knockout and CRISPR (clustered regularly interspaced short palindromic repeats) interference strains and quantified impact on adaptation to antibiotics. We identified significant correlations that suggest genes with low expression variability have greater impact on adaptation. This study provides evidence that gene expression variability can be used as an indicator of bacterial adaptive resistance, even in the face of the pervasive phenotypic heterogeneity underlying adaptation.
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Affiliation(s)
- Keesha E. Erickson
- Department of Chemical and Biological Engineering and ‡BioFrontiers
Institute, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Peter B. Otoupal
- Department of Chemical and Biological Engineering and ‡BioFrontiers
Institute, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering and ‡BioFrontiers
Institute, University of Colorado, 596 UCB, Boulder, Colorado 80303, United States
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345
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Delarze E, Sanglard D. Defining the frontiers between antifungal resistance, tolerance and the concept of persistence. Drug Resist Updat 2015; 23:12-19. [PMID: 26690338 DOI: 10.1016/j.drup.2015.10.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A restricted number of antifungal agents are available for the therapy of fungal diseases. With the introduction of epidemiological cut-off values for each agent in important fungal pathogens based on the distribution of minimal inhibitory concentration (MIC), the distinction between wild type and drug-resistant populations has been facilitated. Antifungal resistance has been described for all currently available antifungal agents in several pathogens and most of the associated resistance mechanisms have been deciphered at the molecular level. Clinical breakpoints for some agents have been proposed and can have predictive value for the success or failure of therapy. Tolerance to antifungals has been a much more ignored area. By definition, tolerance operates at antifungal concentrations above individual intrinsic inhibitory values. Important is that tolerance to antifungal agents favours the emergence of persister cells, which are able to survive antifungal therapy and can cause relapses. Here we will review the current knowledge on antifungal tolerance, its potential mechanisms and also evaluate the role of antifungal tolerance in the efficacy of drug treatments.
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Affiliation(s)
- Eric Delarze
- Institute of Microbiology, University Hospital Lausanne and University Hospital Center, Rue de Bugnon 48, CH-1011 Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University Hospital Lausanne and University Hospital Center, Rue de Bugnon 48, CH-1011 Lausanne, Switzerland.
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346
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Microscale insights into pneumococcal antibiotic mutant selection windows. Nat Commun 2015; 6:8773. [PMID: 26514094 PMCID: PMC4632196 DOI: 10.1038/ncomms9773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/30/2015] [Indexed: 11/26/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae shows alarming rates of antibiotic resistance emergence. The basic requirements for de novo resistance emergence are poorly understood in the pneumococcus. Here we systematically analyse the impact of antibiotics on S. pneumoniae at concentrations that inhibit wild type cells, that is, within the mutant selection window. We identify discrete growth-inhibition profiles for bacteriostatic and bactericidal compounds, providing a predictive framework for distinction between the two classifications. Cells treated with bacteriostatic agents show continued gene expression activity, and real-time mutation assays link this activity to the development of genotypic resistance. Time-lapse microscopy reveals that antibiotic-susceptible pneumococci display remarkable growth and death bistability patterns in response to many antibiotics. We furthermore capture the rise of subpopulations with decreased susceptibility towards cell wall synthesis inhibitors (heteroresisters). We show that this phenomenon is epigenetically inherited, and that heteroresistance potentiates the accumulation of genotypic resistance. The emergence of antibiotic resistance in bacteria is driven by inhibitory but non-lethal antibiotic concentrations. Here, Sorg and Veening study the effects of different antibiotics on the pneumococcus, with a focus on inhibition dynamics, metabolic activity and processes at the single-cell level.
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347
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Hypoionic shock treatment enables aminoglycosides antibiotics to eradicate bacterial persisters. Sci Rep 2015; 5:14247. [PMID: 26435063 PMCID: PMC4593029 DOI: 10.1038/srep14247] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/21/2015] [Indexed: 01/02/2023] Open
Abstract
Bacterial persisters, usually being considered as dormant cells that are tolerant to antibiotics, are an important source for recurrent infection and emergence of antibiotic resistant pathogens. Clinical eradication of pathogenic persisters is highly desired but greatly difficult mainly due to the substantial reduction in antibiotics uptake as well as the non-active state of the drug targets. Here we report that bacterial persisters (normal growing cells as well) can be effectively eradicated by aminoglycoside antibiotics upon hypoionic shock (e.g. pure water treatment) even for less than one minute. Such hypoionic shock potentiation effect on aminoglycosides is proton motive force-independent, and is apparently achieved by promoting the entrance of aminoglycosides, speculatively through the mechanosensitive ion channels. Our revelations may provide a simple and powerful strategy to eradicate pathogen persisters.
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348
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Huang KC. Applications of imaging for bacterial systems biology. Curr Opin Microbiol 2015; 27:114-20. [PMID: 26356259 DOI: 10.1016/j.mib.2015.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 01/27/2023]
Abstract
Imaging has fueled exciting advances in bacterial cell biology, which have led to exquisite understanding of mechanisms of protein localization and cell growth in select cases. Nonetheless, it remains a challenge to connect subcellular dynamics to cellular phenotypes. In this review, I explore synergies between imaging and systems approaches to bacterial physiology. I highlight how single-cell, time-lapse imaging under environmental or chemical perturbations yields insights that complement traditional observations based on population-level growth on long time-scales. Next, I discuss applications of high-throughput fluorescence imaging to dissect genetic pathways and drug targets. Finally, I describe how confocal imaging is illuminating the role of spatial organization in the structure and function of bacterial communities, from biofilms to the intestinal microbiota.
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Affiliation(s)
- Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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349
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Phenotypic Heterogeneity, a Phenomenon That May Explain Why Quorum Sensing Does Not Always Result in Truly Homogenous Cell Behavior. Appl Environ Microbiol 2015. [PMID: 26025903 DOI: 10.1128/aem.00900-15/format/epub] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Phenotypic heterogeneity describes the occurrence of "nonconformist" cells within an isogenic population. The nonconformists show an expression profile partially different from that of the remainder of the population. Phenotypic heterogeneity affects many aspects of the different bacterial lifestyles, and it is assumed that it increases bacterial fitness and the chances for survival of the whole population or smaller subpopulations in unfavorable environments. Well-known examples for phenotypic heterogeneity have been associated with antibiotic resistance and frequently occurring persister cells. Other examples include heterogeneous behavior within biofilms, DNA uptake and bacterial competence, motility (i.e., the synthesis of additional flagella), onset of spore formation, lysis of phages within a small subpopulation, and others. Interestingly, phenotypic heterogeneity was recently also observed with respect to quorum-sensing (QS)-dependent processes, and the expression of autoinducer (AI) synthase genes and other QS-dependent genes was found to be highly heterogeneous at a single-cell level. This phenomenon was observed in several Gram-negative bacteria affiliated with the genera Vibrio, Dinoroseobacter, Pseudomonas, Sinorhizobium, and Mesorhizobium. A similar observation was made for the Gram-positive bacterium Listeria monocytogenes. Since AI molecules have historically been thought to be the keys to homogeneous behavior within isogenic populations, the observation of heterogeneous expression is quite intriguing and adds a new level of complexity to the QS-dependent regulatory networks. All together, the many examples of phenotypic heterogeneity imply that we may have to partially revise the concept of homogeneous and coordinated gene expression in isogenic bacterial populations.
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350
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Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage. Nat Commun 2015; 6:7972. [PMID: 26268986 PMCID: PMC4557116 DOI: 10.1038/ncomms8972] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 07/01/2015] [Indexed: 12/12/2022] Open
Abstract
Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental stress. To characterize transcriptional differences associated with this variability, we have developed a method—FitFlow—that enables the sorting of subpopulations by growth rate. The slow-growing subpopulation shows a transcriptional stress response, but, more surprisingly, these cells have reduced RNA polymerase fidelity and exhibit a DNA damage response. As DNA damage is often caused by oxidative stress, we test the addition of an antioxidant, and find that it reduces the size of the slow-growing population. More generally, we find a significantly altered transcriptome in the slow-growing subpopulation that only partially resembles that of cells growing slowly due to environmental and culture conditions. Slow-growing cells upregulate transposons and express more chromosomal, viral and plasmid-borne transcripts, and thus explore a larger genotypic—and so phenotypic — space. Isogenic cells growing in the same environment show a large degree of variability. Here, by sorting yeast cells based on growth rate, the authors show that the slow-growing subpopulation exhibits stress responses, a high level of transcriptional diversity, and decreased RNA polymerase fidelity.
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