401
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Moreno-Gamez S, Hill AL, Rosenbloom DIS, Petrov DA, Nowak MA, Pennings PS. Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance. Proc Natl Acad Sci U S A 2015; 112:E2874-83. [PMID: 26038564 PMCID: PMC4460514 DOI: 10.1073/pnas.1424184112] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infections with rapidly evolving pathogens are often treated using combinations of drugs with different mechanisms of action. One of the major goal of combination therapy is to reduce the risk of drug resistance emerging during a patient's treatment. Although this strategy generally has significant benefits over monotherapy, it may also select for multidrug-resistant strains, particularly during long-term treatment for chronic infections. Infections with these strains present an important clinical and public health problem. Complicating this issue, for many antimicrobial treatment regimes, individual drugs have imperfect penetration throughout the body, so there may be regions where only one drug reaches an effective concentration. Here we propose that mismatched drug coverage can greatly speed up the evolution of multidrug resistance by allowing mutations to accumulate in a stepwise fashion. We develop a mathematical model of within-host pathogen evolution under spatially heterogeneous drug coverage and demonstrate that even very small single-drug compartments lead to dramatically higher resistance risk. We find that it is often better to use drug combinations with matched penetration profiles, although there may be a trade-off between preventing eventual treatment failure due to resistance in this way and temporarily reducing pathogen levels systemically. Our results show that drugs with the most extensive distribution are likely to be the most vulnerable to resistance. We conclude that optimal combination treatments should be designed to prevent this spatial effective monotherapy. These results are widely applicable to diverse microbial infections including viruses, bacteria, and parasites.
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Affiliation(s)
- Stefany Moreno-Gamez
- Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; Theoretical Biology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Alison L Hill
- Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Daniel I S Rosenbloom
- Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Pleuni S Pennings
- Department of Biology, Stanford University, Stanford, CA 94305; Department of Biology, San Francisco State University, San Francisco, CA 94132; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
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402
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Zhang G, Wang C, Sui Z, Feng J. Insights into the evolutionary trajectories of fluoroquinolone resistance in Streptococcus pneumoniae. J Antimicrob Chemother 2015; 70:2499-506. [PMID: 26031465 DOI: 10.1093/jac/dkv134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/24/2015] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Fluoroquinolone resistance in Streptococcus pneumoniae typically arises through specific site mutations, but dynamic variation of mutations in the resistance evolution and interaction among these mutations have not been clearly demonstrated. The objectives of this study were to investigate the dynamics of allele frequency in populations evolved under fluoroquinolone pressure and pervasive interactions among mutations present in the evolutionary trajectories. METHODS Thirty-three evolved populations were obtained by serial passages in the presence of antibiotic pressure and these populations were sequenced by using the Paired-End Illumina method. Mutants that occurred in the evolutionary trajectories were constructed by transforming the parental strain with PCR fragments containing corresponding mutations. RESULTS The number of target mutations increased progressively, consistent with phenotypic adaptation to moxifloxacin and levofloxacin. However, more mutations are required for high-level resistance to moxifloxacin than levofloxacin. Pervasive interactions, including positive epistasis between mutations, play a role in the evolutionary trajectories of resistance to the two drugs. Two mutations (R447C and P454S) in gyrB were identified to confer 2-fold increases in resistance to moxifloxacin and levofloxacin based on the background of the double mutant S81F/S79F in parC. Moreover, the dynamics of allele frequency in evolved populations was revealed and found to be directly correlated with the resistance levels of evolved populations. Clonal interference among alleles of mutations contributed to the molecular dynamics of resistance evolution. CONCLUSIONS Our results provide novel insights into the evolutionary trajectories of resistance to fluoroquinolones and may serve as a theoretical basis for predicting resistance development and provide references for the clinical use of these drugs.
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Affiliation(s)
- Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihai Sui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing 100101, China
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403
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Downing T. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics. Microorganisms 2015; 3:236-67. [PMID: 27682088 PMCID: PMC5023239 DOI: 10.3390/microorganisms3020236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 11/16/2022] Open
Abstract
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)-a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.
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Affiliation(s)
- Tim Downing
- School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin 9, Ireland.
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404
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Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E. Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. Cell Rep 2015; 11:645-56. [PMID: 25892240 DOI: 10.1016/j.celrep.2015.03.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 02/20/2015] [Accepted: 03/23/2015] [Indexed: 11/18/2022] Open
Abstract
Linking the molecular effects of mutations to fitness is central to understanding evolutionary dynamics. Here, we establish a quantitative relation between the global effect of mutations on the E. coli proteome and bacterial fitness. We created E. coli strains with specific destabilizing mutations in the chromosomal folA gene encoding dihydrofolate reductase (DHFR) and quantified the ensuing changes in the abundances of 2,000+ E. coli proteins in mutant strains using tandem mass tags with subsequent LC-MS/MS. mRNA abundances in the same E. coli strains were also quantified. The proteomic effects of mutations in DHFR are quantitatively linked to phenotype: the SDs of the distributions of logarithms of relative (to WT) protein abundances anticorrelate with bacterial growth rates. Proteomes hierarchically cluster first by media conditions, and within each condition, by the severity of the perturbation to DHFR function. These results highlight the importance of a systems-level layer in the genotype-phenotype relationship.
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Affiliation(s)
- Shimon Bershtein
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Jeong-Mo Choi
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Sanchari Bhattacharyya
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- MSPRL, Center of Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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405
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406
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Pál C, Papp B, Lázár V. Collateral sensitivity of antibiotic-resistant microbes. Trends Microbiol 2015; 23:401-7. [PMID: 25818802 DOI: 10.1016/j.tim.2015.02.009] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/09/2015] [Accepted: 02/23/2015] [Indexed: 11/15/2022]
Abstract
Understanding how evolution of microbial resistance towards a given antibiotic influences susceptibility to other drugs is a challenge of profound importance. By combining laboratory evolution, genome sequencing, and functional analyses, recent works have charted the map of evolutionary trade-offs between antibiotics and have explored the underlying molecular mechanisms. Strikingly, mutations that caused multidrug resistance in bacteria simultaneously enhanced sensitivity to many other unrelated drugs (collateral sensitivity). Here, we explore how this emerging research sheds new light on resistance mechanisms and the way it could be exploited for the development of alternative antimicrobial strategies.
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Affiliation(s)
- Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
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407
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Motta SS, Cluzel P, Aldana M. Adaptive resistance in bacteria requires epigenetic inheritance, genetic noise, and cost of efflux pumps. PLoS One 2015; 10:e0118464. [PMID: 25781931 PMCID: PMC4363326 DOI: 10.1371/journal.pone.0118464] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Adaptive resistance emerges when populations of bacteria are subjected to gradual increases of antibiotics. It is characterized by a rapid emergence of resistance and fast reversibility to the non-resistant phenotype when the antibiotic is removed from the medium. Recent work shows that adaptive resistance requires epigenetic inheritance and heterogeneity of gene expression patterns that are, in particular, associated with the production of porins and efflux pumps. However, the precise mechanisms by which inheritance and variability govern adaptive resistance, and what processes cause its reversibility remain unclear. Here, using an efflux pump regulatory network (EPRN) model, we show that the following three mechanisms are essential to obtain adaptive resistance in a bacterial population: 1) intrinsic variability in the expression of the EPRN transcription factors; 2) epigenetic inheritance of the transcription rate of EPRN associated genes; and 3) energetic cost of the efflux pumps activity that slows down cell growth. While the first two mechanisms acting together are responsible for the emergence and gradual increase of the resistance, the third one accounts for its reversibility. In contrast with the standard assumption, our model predicts that adaptive resistance cannot be explained by increased mutation rates. Our results identify the molecular mechanism of epigenetic inheritance as the main target for therapeutic treatments against the emergence of adaptive resistance. Finally, our theoretical framework unifies known and newly identified determinants such as the burden of efflux pumps that underlie bacterial adaptive resistance to antibiotics.
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Affiliation(s)
| | - Philippe Cluzel
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Maximino Aldana
- Instituto de Ciencias Físicas, UNAM, Cuernavaca, Morelos, Mexico
- * E-mail:
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408
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Suzuki S, Horinouchi T, Furusawa C. Suppression of antibiotic resistance acquisition by combined use of antibiotics. J Biosci Bioeng 2015; 120:467-9. [PMID: 25746894 DOI: 10.1016/j.jbiosc.2015.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 01/29/2015] [Accepted: 02/05/2015] [Indexed: 11/19/2022]
Abstract
We analyzed the effect of combinatorial use of antibiotics with a trade-off relationship of resistance, i.e., resistance acquisition to one drug causes susceptibility to the other drug, and vice versa, on the evolution of antibiotic resistance. We demonstrated that this combinatorial use of antibiotics significantly suppressed the acquisition of resistance.
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Affiliation(s)
- Shingo Suzuki
- Laboratory for Multiscale Biosystem Dynamics, Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Takaaki Horinouchi
- Laboratory for Multiscale Biosystem Dynamics, Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Chikara Furusawa
- Laboratory for Multiscale Biosystem Dynamics, Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
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409
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Rodriguez de Evgrafov M, Gumpert H, Munck C, Thomsen TT, Sommer MOA. Collateral Resistance and Sensitivity Modulate Evolution of High-Level Resistance to Drug Combination Treatment in Staphylococcus aureus. Mol Biol Evol 2015; 32:1175-85. [PMID: 25618457 DOI: 10.1093/molbev/msv006] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
As drug-resistant pathogens continue to emerge, combination therapy will increasingly be relied upon to treat infections and to help combat further development of multidrug resistance. At present a dichotomy exists between clinical practice, which favors therapeutically synergistic combinations, and the scientific model emerging from in vitro experimental work, which maintains that this interaction provides greater selective pressure toward resistance development than other interaction types. We sought to extend the current paradigm, based on work below or near minimum inhibitory concentration levels, to reflect drug concentrations more likely to be encountered during treatment. We performed a series of adaptive evolution experiments using Staphylococcus aureus. Interestingly, no relationship between drug interaction type and resistance evolution was found as resistance increased significantly beyond wild-type levels. All drug combinations, irrespective of interaction types, effectively limited resistance evolution compared with monotreatment. Cross-resistance and collateral sensitivity were found to be important factors in the extent of resistance evolution toward a combination. Comparative genomic analyses revealed that resistance to drug combinations was mediated largely by mutations in the same genes as single-drug-evolved lineages highlighting the importance of the component drugs in determining the rate of resistance evolution. Results of this work suggest that the mechanisms of resistance to constituent drugs should be the focus of future resistance evolution work.
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Affiliation(s)
| | - Heidi Gumpert
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Munck
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Thomas T Thomsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten O A Sommer
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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410
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Takahashi CN, Miller AW, Ekness F, Dunham MJ, Klavins E. A low cost, customizable turbidostat for use in synthetic circuit characterization. ACS Synth Biol 2015; 4:32-8. [PMID: 25036317 PMCID: PMC4304434 DOI: 10.1021/sb500165g] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Engineered biological circuits are
often disturbed by a variety
of environmental factors. In batch culture, where the majority of
synthetic circuit characterization occurs, environmental conditions
vary as the culture matures. Turbidostats are powerful characterization
tools that provide static culture environments; however, they are
often expensive, especially when purchased in custom configurations,
and are difficult to design and construct in a lab. Here, we present
a low cost, open source multiplexed turbidostat that can be manufactured
and used with minimal experience in electrical or software engineering.
We demonstrate the utility of this system to profile synthetic circuit
behavior in S. cerevisiae. We also demonstrate the
flexibility of the design by showing that a fluorometer can be easily
integrated.
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Affiliation(s)
| | | | - Felix Ekness
- Department
of Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
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411
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Prediction of antibiotic resistance by gene expression profiles. Nat Commun 2014; 5:5792. [PMID: 25517437 PMCID: PMC4351646 DOI: 10.1038/ncomms6792] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 11/07/2014] [Indexed: 12/22/2022] Open
Abstract
Although many mutations contributing to antibiotic resistance have been identified, the relationship between the mutations and the related phenotypic changes responsible for the resistance has yet to be fully elucidated. To better characterize phenotype–genotype mapping for drug resistance, here we analyse phenotypic and genotypic changes of antibiotic-resistant Escherichia coli strains obtained by laboratory evolution. We demonstrate that the resistances can be quantitatively predicted by the expression changes of a small number of genes. Several candidate mutations contributing to the resistances are identified, while phenotype–genotype mapping is suggested to be complex and includes various mutations that cause similar phenotypic changes. The integration of transcriptome and genome data enables us to extract essential phenotypic changes for drug resistances. The relationship between mutations and phenotypic changes associated with drug resistance in bacteria remains unclear. Here, the authors use antibiotic-resistant E. coli strains, obtained by laboratory evolution, to show that resistance profiles can be predicted by changes in expression of a few genes.
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412
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Wozniak M, Tiuryn J, Wong L. GWAMAR: genome-wide assessment of mutations associated with drug resistance in bacteria. BMC Genomics 2014; 15 Suppl 10:S10. [PMID: 25559874 PMCID: PMC4304204 DOI: 10.1186/1471-2164-15-s10-s10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Development of drug resistance in bacteria causes antibiotic therapies to be less effective and more costly. Moreover, our understanding of the process remains incomplete. One promising approach to improve our understanding of how resistance is being acquired is to use whole-genome comparative approaches for detection of drug resistance-associated mutations. Results We present GWAMAR, a tool we have developed for detecting of drug resistance-associated mutations in bacteria through comparative analysis of whole-genome sequences. The pipeline of GWAMAR comprises several steps. First, for a set of closely related bacterial genomes, it employs eCAMBer to identify homologous gene families. Second, based on multiple alignments of the gene families, it identifies mutations among the strains of interest. Third, it calculates several statistics to identify which mutations are the most associated with drug resistance. Conclusions Based on our analysis of two large datasets retrieved from publicly available data for M. tuberculosis, we identified a set of novel putative drug resistance-associated mutations. As a part of this work, we present also an application of our tool to detect putative compensatory mutations.
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413
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Baquero F, Lanza VF, Cantón R, Coque TM. Public health evolutionary biology of antimicrobial resistance: priorities for intervention. Evol Appl 2014; 8:223-39. [PMID: 25861381 PMCID: PMC4380917 DOI: 10.1111/eva.12235] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/12/2014] [Indexed: 12/19/2022] Open
Abstract
The three main processes shaping the evolutionary ecology of antibiotic resistance (AbR) involve the emergence, invasion and occupation by antibiotic-resistant genes of significant environments for human health. The process of emergence in complex bacterial populations is a high-frequency, continuous swarming of ephemeral combinatory genetic and epigenetic explorations inside cells and among cells, populations and communities, expanding in different environments (migration), creating the stochastic variation required for evolutionary progress. Invasion refers to the process by which AbR significantly increases in frequency in a given (invaded) environment, led by external invaders local multiplication and spread, or by endogenous conversion. Conversion occurs because of the spread of AbR genes from an exogenous resistant clone into an established (endogenous) bacterial clone(s) colonizing the environment; and/or because of dissemination of particular resistant genetic variants that emerged within an endogenous clonal population. Occupation of a given environment by a resistant variant means a permanent establishment of this organism in this environment, even in the absence of antibiotic selection. Specific interventions on emergence influence invasion, those acting on invasion also influence occupation and interventions on occupation determine emergence. Such interventions should be simultaneously applied, as they are not simple solutions to the complex problem of AbR.
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Affiliation(s)
- Fernando Baquero
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| | - Val F Lanza
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| | - Rafael Cantón
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III Madrid, Spain
| | - Teresa M Coque
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
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414
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Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y. Mutations in global regulators lead to metabolic selection during adaptation to complex environments. PLoS Genet 2014; 10:e1004872. [PMID: 25501822 PMCID: PMC4263409 DOI: 10.1371/journal.pgen.1004872] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 11/04/2014] [Indexed: 01/12/2023] Open
Abstract
Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes if many mutations are required to achieve even modest gains in fitness. Since changing complex environments are quite common in nature, we investigated how such an epistatic bottleneck can be avoided to allow rapid adaptation. We show that adaptive mutations arise repeatedly in independently evolved populations in the context of greatly increased genetic and phenotypic diversity. We go on to show that weak selection requiring substantial metabolic reprogramming can be readily achieved by mutations in the global response regulator arcA and the stress response regulator rpoS. We identified 46 unique single-nucleotide variants of arcA and 18 mutations in rpoS, nine of which resulted in stop codons or large deletions, suggesting that subtle modulations of ArcA function and knockouts of rpoS are largely responsible for the metabolic shifts leading to adaptation. These mutations allow a higher order metabolic selection that eliminates epistatic bottlenecks, which could occur when many changes would be required. Proteomic and carbohydrate analysis of adapting E. coli populations revealed an up-regulation of enzymes associated with the TCA cycle and amino acid metabolism, and an increase in the secretion of putrescine. The overall effect of adaptation across populations is to redirect and efficiently utilize uptake and catabolism of abundant amino acids. Concomitantly, there is a pronounced spread of more ecologically limited strains that results from specialization through metabolic erosion. Remarkably, the global regulators arcA and rpoS can provide a “one-step” mechanism of adaptation to a novel environment, which highlights the importance of global resource management as a powerful strategy to adaptation. Changing environmental conditions are the norm in biology. However, understanding adaptation to complex environments presents many challenges. For example, adaptation to resource-rich environments can potentially have many successful evolutionary trajectories to increased fitness. Even in conditions of plenty, the utilization of numerous but novel resources can require multiple mutations before a benefit is accrued. We evolved two bacterial species isolated from the gut of healthy humans in two different, resource-rich media commonly used in the laboratory. We anticipated that under weak selection the population would evolve tremendous genetic diversity. Despite such a complex genetic background we were able to identify a strong degree of parallel evolution and using a combination of population proteomic and population genomic approaches we show that two global regulators, arcA and rpoS, are the principle targets of selection. Up-regulation of the different metabolic pathways that are controlled by these global regulators in combination with up-regulation of transporters that transport nutrients into the cell revealed increased use of the novel resources. Thus global regulators can provide a one-step model to shift metabolism efficiently and provide rapid a one-step reprogramming of the cell metabolic profile.
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Affiliation(s)
- Gerda Saxer
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail: (GS); (YS)
| | - Michael D. Krepps
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America
- EXCET, Inc, Springfield, Virginia, United States of America
| | - Eric D. Merkley
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Charles Ansong
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | | | | | - Nikola Ristic
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Ping T. Yeh
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Vittal P. Prakash
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Owen P. Leiser
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Henry S. Gibbons
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America
| | - Helen W. Kreuzer
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail: (GS); (YS)
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415
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Mitosch K, Bollenbach T. Bacterial responses to antibiotics and their combinations. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:545-557. [PMID: 25756107 DOI: 10.1111/1758-2229.12190] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome-wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria.
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416
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Winkler JD, Kao KC. Recent advances in the evolutionary engineering of industrial biocatalysts. Genomics 2014; 104:406-11. [DOI: 10.1016/j.ygeno.2014.09.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 11/15/2022]
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417
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Brooks BD, Brooks AE. Therapeutic strategies to combat antibiotic resistance. Adv Drug Deliv Rev 2014; 78:14-27. [PMID: 25450262 DOI: 10.1016/j.addr.2014.10.027] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 10/20/2014] [Accepted: 10/22/2014] [Indexed: 12/16/2022]
Abstract
With multidrug resistant bacteria on the rise, new antibiotic approaches are required. Although a number of new small molecule antibiotics are currently in the development pipeline with many more in preclinical development, the clinical options and practices for infection control must be expanded. Biologics and non-antibiotic adjuvants offer this opportunity for expansion. Nevertheless, to avoid known mechanisms of resistance, intelligent combination approaches for multiple simultaneous and complimentary therapies must be designed. Combination approaches should extend beyond biologically active molecules to include smart controlled delivery strategies. Infection control must integrate antimicrobial stewardship, new antibiotic molecules, biologics, and delivery strategies into effective combination therapies designed to 1) fight the infection, 2) avoid resistance, and 3) protect the natural microbiome. This review explores these developing strategies in the context of circumventing current mechanisms of resistance.
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Affiliation(s)
| | - Amanda E Brooks
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA; Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND58108, USA.
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418
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Badran AH, Liu DR. In vivo continuous directed evolution. Curr Opin Chem Biol 2014; 24:1-10. [PMID: 25461718 DOI: 10.1016/j.cbpa.2014.09.040] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/12/2014] [Indexed: 01/22/2023]
Abstract
The development and application of methods for the laboratory evolution of biomolecules has rapidly progressed over the last few decades. Advancements in continuous microbe culturing and selection design have facilitated the development of new technologies that enable the continuous directed evolution of proteins and nucleic acids. These technologies have the potential to support the extremely rapid evolution of biomolecules with tailor-made functional properties. Continuous evolution methods must support all of the key steps of laboratory evolution - translation of genes into gene products, selection or screening, replication of genes encoding the most fit gene products, and mutation of surviving genes - in a self-sustaining manner that requires little or no researcher intervention. Continuous laboratory evolution has been historically used to study problems including antibiotic resistance, organismal adaptation, phylogenetic reconstruction, and host-pathogen interactions, with more recent applications focusing on the rapid generation of proteins and nucleic acids with useful, tailor-made properties. The advent of increasingly general methods for continuous directed evolution should enable researchers to address increasingly complex questions and to access biomolecules with more novel or even unprecedented properties.
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Affiliation(s)
- Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, United States
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, United States.
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419
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Alexander HK, Martin G, Martin OY, Bonhoeffer S. Evolutionary rescue: linking theory for conservation and medicine. Evol Appl 2014; 7:1161-79. [PMID: 25558278 PMCID: PMC4275089 DOI: 10.1111/eva.12221] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/16/2014] [Indexed: 02/01/2023] Open
Abstract
Evolutionary responses that rescue populations from extinction when drastic environmental changes occur can be friend or foe. The field of conservation biology is concerned with the survival of species in deteriorating global habitats. In medicine, in contrast, infected patients are treated with chemotherapeutic interventions, but drug resistance can compromise eradication of pathogens. These contrasting biological systems and goals have created two quite separate research communities, despite addressing the same central question of whether populations will decline to extinction or be rescued through evolution. We argue that closer integration of the two fields, especially of theoretical understanding, would yield new insights and accelerate progress on these applied problems. Here, we overview and link mathematical modelling approaches in these fields, suggest specific areas with potential for fruitful exchange, and discuss common ideas and issues for empirical testing and prediction.
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Affiliation(s)
- Helen K Alexander
- Institute for Integrative Biology, D-USYS, ETH Zürich Zürich, Switzerland
| | - Guillaume Martin
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier 2 - CNRS - IRD Montpellier Cedex, France
| | - Oliver Y Martin
- Institute for Integrative Biology, D-USYS, ETH Zürich Zürich, Switzerland
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420
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Mogre A, Sengupta T, Veetil RT, Ravi P, Seshasayee ASN. Genomic analysis reveals distinct concentration-dependent evolutionary trajectories for antibiotic resistance in Escherichia coli. DNA Res 2014; 21:711-26. [PMID: 25281544 PMCID: PMC4263303 DOI: 10.1093/dnares/dsu032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Evolution of bacteria under sublethal concentrations of antibiotics represents a trade-off between growth and resistance to the antibiotic. To understand this trade-off, we performed in vitro evolution of laboratory Escherichia coli under sublethal concentrations of the aminoglycoside kanamycin over short time durations. We report that fixation of less costly kanamycin-resistant mutants occurred earlier in populations growing at lower sublethal concentration of the antibiotic, compared with those growing at higher sublethal concentrations; in the latter, resistant mutants with a significant growth defect persisted longer. Using deep sequencing, we identified kanamycin resistance-conferring mutations, which were costly or not in terms of growth in the absence of the antibiotic. Multiple mutations in the C-terminal end of domain IV of the translation elongation factor EF-G provided low-cost resistance to kanamycin. Despite targeting the same or adjacent residues of the protein, these mutants differed from each other in the levels of resistance they provided. Analysis of one of these mutations showed that it has little defect in growth or in synthesis of green fluorescent protein (GFP) from an inducible plasmid in the absence of the antibiotic. A second class of mutations, recovered only during evolution in higher sublethal concentrations of the antibiotic, deleted the C-terminal end of the ATP synthase shaft. This mutation confers basal-level resistance to kanamycin while showing a strong growth defect in the absence of the antibiotic. In conclusion, the early dynamics of the development of resistance to an aminoglycoside antibiotic is dependent on the levels of stress (concentration) imposed by the antibiotic, with the evolution of less costly variants only a matter of time.
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Affiliation(s)
- Aalap Mogre
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Titas Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Reshma T Veetil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Preethi Ravi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, Karnataka 560065, India
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421
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Gresham D, Dunham MJ. The enduring utility of continuous culturing in experimental evolution. Genomics 2014; 104:399-405. [PMID: 25281774 DOI: 10.1016/j.ygeno.2014.09.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/30/2022]
Abstract
Studying evolution in the laboratory provides a means of understanding the processes, dynamics and outcomes of adaptive evolution in precisely controlled and readily replicated conditions. The advantages of experimental evolution are maximized when the selection is well defined, which enables linking genotype, phenotype and fitness. One means of maintaining a defined selection is continuous culturing: chemostats enable the study of adaptive evolution in constant nutrient-limited environments, whereas cells in turbidostats evolve in constant nutrient abundance. Although the experimental effort required for continuous culturing is considerable relative to the experimental simplicity of serial batch culture, the opposite is true of the environments they produce: continuous culturing results in simplified and invariant conditions whereas serially diluted batch cultures are complex and dynamic. The comparative simplicity of the selective environment that is unique to continuous culturing provides an ideal experimental system for addressing key questions in adaptive evolution.
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Affiliation(s)
- David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York NY, USA.
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle WA, USA.
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422
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Abstract
Antibiotics have been a cornerstone of innovation in the fields of public health, agriculture, and medicine. However, recent studies have shed new light on the collateral damage they impart on the indigenous host-associated communities. These drugs have been found to alter the taxonomic, genomic, and functional capacity of the human gut microbiota, with effects that are rapid and sometimes persistent. Broad-spectrum antibiotics reduce bacterial diversity while expanding and collapsing membership of specific indigenous taxa. Furthermore, antibiotic treatment selects for resistant bacteria, increases opportunities for horizontal gene transfer, and enables intrusion of pathogenic organisms through depletion of occupied natural niches, with profound implications for the emergence of resistance. Because these pervasive alterations can be viewed as an uncoupling of mutualistic host-microbe relationships, it is valuable to reconsider antimicrobial therapies in the context of an ecological framework. Understanding the biology of competitive exclusion, interspecies protection, and gene flow of adaptive functions in the gut environment may inform the design of new strategies that treat infections while preserving the ecology of our beneficial constituents.
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423
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Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance. Proc Natl Acad Sci U S A 2014; 111:14494-9. [PMID: 25246554 DOI: 10.1073/pnas.1409800111] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alternating antibiotic therapy, in which pairs of drugs are cycled during treatment, has been suggested as a means to inhibit the evolution of de novo resistance while avoiding the toxicity associated with more traditional combination therapy. However, it remains unclear under which conditions and by what means such alternating treatments impede the evolution of resistance. Here, we tracked multistep evolution of resistance in replicate populations of Staphylococcus aureus during 22 d of continuously increasing single-, mixed-, and alternating-drug treatment. In all three tested drug pairs, the alternating treatment reduced the overall rate of resistance by slowing the acquisition of resistance to one of the two component drugs, sometimes as effectively as mixed treatment. This slower rate of evolution is reflected in the genome-wide mutational profiles; under alternating treatments, bacteria acquire mutations in different genes than under corresponding single-drug treatments. To test whether this observed constraint on adaptive paths reflects trade-offs in which resistance to one drug is accompanied by sensitivity to a second drug, we profiled many single-step mutants for cross-resistance. Indeed, the average cross-resistance of single-step mutants can help predict whether or not evolution was slower in alternating drugs. Together, these results show that despite the complex evolutionary landscape of multidrug resistance, alternating-drug therapy can slow evolution by constraining the mutational paths toward resistance.
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424
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Kim HJ, Jeong H, Hwang S, Lee MS, Lee YJ, Lee DW, Lee SJ. Short-term differential adaptation to anaerobic stress via genomic mutations by Escherichia coli strains K-12 and B lacking alcohol dehydrogenase. Front Microbiol 2014; 5:476. [PMID: 25250024 PMCID: PMC4158980 DOI: 10.3389/fmicb.2014.00476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/25/2014] [Indexed: 01/01/2023] Open
Abstract
Microbial adaptations often occur via genomic mutations under adverse environmental conditions. This study used Escherichia coli ΔadhE cells as a model system to investigate adaptation to anaerobic conditions, which we then compared with the adaptive mechanisms of two closely related E. coli strains, K-12 and B. In contrast to K-12 ΔadhE cells, the E. coli B ΔadhE cells exhibited significantly delayed adaptive growth under anaerobic conditions. Adaptation by the K-12 and B strains mainly employed anaerobic lactate fermentation to restore cellular growth. Several mutations were identified in the pta or pflB genes of adapted K-12 cells, but mostly in the pta gene of the B strains. However, the types of mutation in the adapted K-12 and B strains were similar. Cellular viability was affected directly by severe redox imbalance in B ΔadhE cells, which also impaired their ability to adapt to anaerobic conditions. This study demonstrates that closely related microorganisms may undergo different adaptations under the same set of adverse conditions, which might be associated with the specific metabolic characteristics of each strain. This study provides new insights into short-term microbial adaptation to stressful conditions, which may reflect dynamic microbial population changes in nature.
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Affiliation(s)
- Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and Technology (UST) Daejeon, South Korea ; Infection and Immunity Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Haeyoung Jeong
- Biosystems and Bioengineering Program, University of Science and Technology (UST) Daejeon, South Korea ; Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Moo-Seung Lee
- Infection and Immunity Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
| | - Yong-Jik Lee
- School of Applied Biosciences, Kyungpook National University Daegu, South Korea
| | - Dong-Woo Lee
- School of Applied Biosciences, Kyungpook National University Daegu, South Korea
| | - Sang Jun Lee
- Biosystems and Bioengineering Program, University of Science and Technology (UST) Daejeon, South Korea ; Infection and Immunity Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) Daejeon, South Korea
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425
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Junier I. Conserved patterns in bacterial genomes: a conundrum physically tailored by evolutionary tinkering. Comput Biol Chem 2014; 53 Pt A:125-33. [PMID: 25239779 DOI: 10.1016/j.compbiolchem.2014.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 11/17/2022]
Abstract
The proper functioning of bacteria is encoded in their genome at multiple levels or scales, each of which is constrained by specific physical forces. At the smallest spatial scales, interatomic forces dictate the folding and function of proteins and nucleic acids. On longer length scales, stochastic forces emerging from the thermal jiggling of proteins and RNAs impose strong constraints on the organization of genes along chromosomes, more particularly in the context of the building of nucleoprotein complexes and the operational mode of regulatory agents. At the cellular level, transcription, replication and cell division activities generate forces that act on both the internal structure and cellular location of chromosomes. The overall result is a complex multi-scale organization of genomes that reflects the evolutionary tinkering of bacteria. The goal of this review is to highlight avenues for deciphering this complexity by focusing on patterns that are conserved among evolutionarily distant bacteria. To this end, I discuss three different organizational scales: the protein structures, the chromosomal organization of genes and the global structure of chromosomes.
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Affiliation(s)
- Ivan Junier
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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426
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Köser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet 2014; 30:401-7. [PMID: 25096945 PMCID: PMC4156311 DOI: 10.1016/j.tig.2014.07.003] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022]
Abstract
Following recent improvements in sequencing technologies, whole-genome sequencing (WGS) is positioned to become an essential tool in the control of antibiotic resistance, a major threat in modern healthcare. WGS has already found numerous applications in this area, ranging from the development of novel antibiotics and diagnostic tests through to antibiotic stewardship of currently available drugs via surveillance and the elucidation of the factors that allow the emergence and persistence of resistance. Numerous proof-of-principle studies have also highlighted the value of WGS as a tool for day-to-day infection control and, for some pathogens, as a primary diagnostic tool to detect antibiotic resistance. However, appropriate data analysis platforms will need to be developed before routine WGS can be introduced on a large scale.
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Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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427
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Lázár V, Nagy I, Spohn R, Csörgő B, Györkei Á, Nyerges Á, Horváth B, Vörös A, Busa-Fekete R, Hrtyan M, Bogos B, Méhi O, Fekete G, Szappanos B, Kégl B, Papp B, Pál C. Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network. Nat Commun 2014; 5:4352. [PMID: 25000950 PMCID: PMC4102323 DOI: 10.1038/ncomms5352] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 06/09/2014] [Indexed: 12/29/2022] Open
Abstract
Understanding how evolution of antimicrobial resistance increases resistance to other drugs is a challenge of profound importance. By combining experimental evolution and genome sequencing of 63 laboratory-evolved lines, we charted a map of cross-resistance interactions between antibiotics in Escherichia coli, and explored the driving evolutionary principles. Here, we show that (1) convergent molecular evolution is prevalent across antibiotic treatments, (2) resistance conferring mutations simultaneously enhance sensitivity to many other drugs and (3) 27% of the accumulated mutations generate proteins with compromised activities, suggesting that antibiotic adaptation can partly be achieved without gain of novel function. By using knowledge on antibiotic properties, we examined the determinants of cross-resistance and identified chemogenomic profile similarity between antibiotics as the strongest predictor. In contrast, cross-resistance between two antibiotics is independent of whether they show synergistic effects in combination. These results have important implications on the development of novel antimicrobial strategies. Understanding how evolution of antimicrobial resistance increases resistance to other drugs is of key importance. Here, Lazar et al. build a map of cross-resistance interactions between antibiotics in Escherichia coli and show that chemical and genomic similarities are good predictors of bacterial cross-resistance.
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Affiliation(s)
- Viktória Lázár
- 1] Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary [2]
| | - István Nagy
- 1] Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary [2]
| | - Réka Spohn
- 1] Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary [2]
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Ádám Györkei
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Horváth
- Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Andrea Vörös
- Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Róbert Busa-Fekete
- MTA-SZTE Research Group on Artificial Intelligence, Tisza Lajos krt 103., H-6720 Szeged, Hungary
| | - Mónika Hrtyan
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Bogos
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Szappanos
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Balázs Kégl
- Linear Accelerator Laboratory, University of Paris-Sud, CNRS, Orsay 91898, France
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62, Szeged 6726, Hungary
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428
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Fridman O, Goldberg A, Ronin I, Shoresh N, Balaban NQ. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 2014; 513:418-21. [DOI: 10.1038/nature13469] [Citation(s) in RCA: 374] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 05/12/2014] [Indexed: 12/26/2022]
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429
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Oz T, Guvenek A, Yildiz S, Karaboga E, Tamer YT, Mumcuyan N, Ozan VB, Senturk GH, Cokol M, Yeh P, Toprak E. Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. Mol Biol Evol 2014; 31:2387-401. [PMID: 24962091 PMCID: PMC4137714 DOI: 10.1093/molbev/msu191] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Revealing the genetic changes responsible for antibiotic resistance can be critical for developing novel antibiotic therapies. However, systematic studies correlating genotype to phenotype in the context of antibiotic resistance have been missing. In order to fill in this gap, we evolved 88 isogenic Escherichia coli populations against 22 antibiotics for 3 weeks. For every drug, two populations were evolved under strong selection and two populations were evolved under mild selection. By quantifying evolved populations’ resistances against all 22 drugs, we constructed two separate cross-resistance networks for strongly and mildly selected populations. Subsequently, we sequenced representative colonies isolated from evolved populations for revealing the genetic basis for novel phenotypes. Bacterial populations that evolved resistance against antibiotics under strong selection acquired high levels of cross-resistance against several antibiotics, whereas other bacterial populations evolved under milder selection acquired relatively weaker cross-resistance. In addition, we found that strongly selected strains against aminoglycosides became more susceptible to five other drug classes compared with their wild-type ancestor as a result of a point mutation on TrkH, an ion transporter protein. Our findings suggest that selection strength is an important parameter contributing to the complexity of antibiotic resistance problem and use of high doses of antibiotics to clear infections has the potential to promote increase of cross-resistance in clinics.
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Affiliation(s)
- Tugce Oz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Aysegul Guvenek
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Sadik Yildiz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Enes Karaboga
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Yusuf Talha Tamer
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Nirva Mumcuyan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Vedat Burak Ozan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Gizem Hazal Senturk
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Murat Cokol
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Pamela Yeh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Erdal Toprak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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430
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Laehnemann D, Peña-Miller R, Rosenstiel P, Beardmore R, Jansen G, Schulenburg H. Genomics of rapid adaptation to antibiotics: convergent evolution and scalable sequence amplification. Genome Biol Evol 2014; 6:1287-301. [PMID: 24850796 PMCID: PMC4079197 DOI: 10.1093/gbe/evu106] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Evolutionary adaptation can be extremely fast, especially in response to high selection intensities. A prime example is the surge of antibiotic resistance in bacteria. The genomic underpinnings of such rapid changes may provide information on the genetic processes that enhance fast responses and the particular trait functions under selection. Here, we use experimentally evolved Escherichia coli for a detailed dissection of the genomics of rapid antibiotic resistance evolution. Our new analyses demonstrate that amplification of a sequence region containing several known antibiotic resistance genes represents a fast genomic response mechanism under high antibiotic stress, here exerted by drug combination. In particular, higher dosage of such antibiotic combinations coincided with higher copy number of the sequence region. The amplification appears to be evolutionarily costly, because amplification levels rapidly dropped after removal of the drugs. Our results suggest that amplification is a scalable process, as copy number rapidly changes in response to the selective pressure encountered. Moreover, repeated patterns of convergent evolution were found across the experimentally evolved bacterial populations, including those with lower antibiotic selection intensities. Intriguingly, convergent evolution was identified on different organizational levels, ranging from the above sequence amplification, high variant frequencies in specific genes, prevalence of individual nonsynonymous mutations to the unusual repeated occurrence of a particular synonymous mutation in Glycine codons. We conclude that constrained evolutionary trajectories underlie rapid adaptation to antibiotics. Of the identified genomic changes, sequence amplification seems to represent the most potent, albeit costly genomic response mechanism to high antibiotic stress.
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Affiliation(s)
- David Laehnemann
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
| | - Rafael Peña-Miller
- Biosciences, Geoffrey Pope Building, University of Exeter, United KingdomDepartment of Zoology, University of Oxford, United Kingdom
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, Germany
| | - Robert Beardmore
- Biosciences, Geoffrey Pope Building, University of Exeter, United Kingdom
| | - Gunther Jansen
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Germany
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431
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Interaction between mutations and regulation of gene expression during development of de novo antibiotic resistance. Antimicrob Agents Chemother 2014; 58:4371-9. [PMID: 24841263 DOI: 10.1128/aac.02892-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria can become resistant not only by horizontal gene transfer or other forms of exchange of genetic information but also by de novo by adaptation at the gene expression level and through DNA mutations. The interrelationship between changes in gene expression and DNA mutations during acquisition of resistance is not well documented. In addition, it is not known whether the DNA mutations leading to resistance always occur in the same order and whether the final result is always identical. The expression of >4,000 genes in Escherichia coli was compared upon adaptation to amoxicillin, tetracycline, and enrofloxacin. During adaptation, known resistance genes were sequenced for mutations that cause resistance. The order of mutations varied within two sets of strains adapted in parallel to amoxicillin and enrofloxacin, respectively, whereas the buildup of resistance was very similar. No specific mutations were related to the rather modest increase in tetracycline resistance. Ribosome-sensed induction and efflux pump activation initially protected the cell through induction of expression and allowed it to survive low levels of antibiotics. Subsequently, mutations were promoted by the stress-induced SOS response that stimulated modulation of genetic instability, and these mutations resulted in resistance to even higher antibiotic concentrations. The initial adaptation at the expression level enabled a subsequent trial and error search for the optimal mutations. The quantitative adjustment of cellular processes at different levels accelerated the acquisition of antibiotic resistance.
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432
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Abstract
Antivirulence drugs are a new type of therapeutic drug that target virulence factors, potentially revitalising the drug-development pipeline with new targets. As antivirulence drugs disarm the pathogen, rather than kill or halt pathogen growth, it has been hypothesized that they will generate much weaker selection for resistance than traditional antibiotics. However, recent studies have shown that mechanisms of resistance to antivirulence drugs exist, seemingly damaging the 'evolution-proof' claim. In this Opinion article, we highlight a crucial distinction between whether resistance can emerge and whether it will spread to a high frequency under drug selection. We argue that selection for resistance can be reduced, or even reversed, using appropriate combinations of target and treatment environment, opening a path towards the development of evolutionarily robust novel therapeutics.
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433
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Kümpornsin K, Modchang C, Heinberg A, Ekland EH, Jirawatcharadech P, Chobson P, Suwanakitti N, Chaotheing S, Wilairat P, Deitsch KW, Kamchonwongpaisan S, Fidock DA, Kirkman LA, Yuthavong Y, Chookajorn T. Origin of robustness in generating drug-resistant malaria parasites. Mol Biol Evol 2014; 31:1649-60. [PMID: 24739308 DOI: 10.1093/molbev/msu140] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Biological robustness allows mutations to accumulate while maintaining functional phenotypes. Despite its crucial role in evolutionary processes, the mechanistic details of how robustness originates remain elusive. Using an evolutionary trajectory analysis approach, we demonstrate how robustness evolved in malaria parasites under selective pressure from an antimalarial drug inhibiting the folate synthesis pathway. A series of four nonsynonymous amino acid substitutions at the targeted enzyme, dihydrofolate reductase (DHFR), render the parasites highly resistant to the antifolate drug pyrimethamine. Nevertheless, the stepwise gain of these four dhfr mutations results in tradeoffs between pyrimethamine resistance and parasite fitness. Here, we report the epistatic interaction between dhfr mutations and amplification of the gene encoding the first upstream enzyme in the folate pathway, GTP cyclohydrolase I (GCH1). gch1 amplification confers low level pyrimethamine resistance and would thus be selected for by pyrimethamine treatment. Interestingly, the gch1 amplification can then be co-opted by the parasites because it reduces the cost of acquiring drug-resistant dhfr mutations downstream in the same metabolic pathway. The compensation of compromised fitness by extra GCH1 is an example of how robustness can evolve in a system and thus expand the accessibility of evolutionary trajectories leading toward highly resistant alleles. The evolution of robustness during the gain of drug-resistant mutations has broad implications for both the development of new drugs and molecular surveillance for resistance to existing drugs.
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Affiliation(s)
- Krittikorn Kümpornsin
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Charin Modchang
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, ThailandBiophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Adina Heinberg
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY
| | - Eric H Ekland
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY
| | | | - Pornpimol Chobson
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nattida Suwanakitti
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sastra Chaotheing
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapon Wilairat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NYDivision of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Laura A Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NYDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thanat Chookajorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, ThailandCenter of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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434
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Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. Appl Environ Microbiol 2014; 80:3729-40. [PMID: 24727267 DOI: 10.1128/aem.00499-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biocatalyst robustness toward stresses imposed during fermentation is important for efficient bio-based production. Osmotic stress, imposed by high osmolyte concentrations or dense populations, can significantly impact growth and productivity. In order to better understand the osmotic stress tolerance phenotype, we evolved sexual (capable of in situ DNA exchange) and asexual Escherichia coli strains under sodium chloride (NaCl) stress. All isolates had significantly improved growth under selection and could grow in up to 0.80 M (47 g/liter) NaCl, a concentration that completely inhibits the growth of the unevolved parental strains. Whole genome resequencing revealed frequent mutations in genes controlling N-acetylglucosamine catabolism (nagC, nagA), cell shape (mrdA, mreB), osmoprotectant uptake (proV), and motility (fimA). Possible epistatic interactions between nagC, nagA, fimA, and proV deletions were also detected when reconstructed as defined mutations. Biofilm formation under osmotic stress was found to be decreased in most mutant isolates, coupled with perturbations in indole secretion. Transcriptional analysis also revealed significant changes in ompACGL porin expression and increased transcription of sulfonate uptake systems in the evolved mutants. These findings expand our current knowledge of the osmotic stress phenotype and will be useful for the rational engineering of osmotic tolerance into industrial strains in the future.
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435
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Heath KD, Nuismer SL. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies. Front Genet 2014; 5:77. [PMID: 24782890 PMCID: PMC3990044 DOI: 10.3389/fgene.2014.00077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/24/2014] [Indexed: 12/22/2022] Open
Abstract
Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G) that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G). Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.
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Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois Urbana, IL, USA
| | - Scott L Nuismer
- Department of Biological Sciences, University of Idaho Moscow, ID, USA
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436
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Vyawahare S, Zhang Q, Lau A, Austin RH. In vitro microbial culture models and their application in drug development. Adv Drug Deliv Rev 2014; 69-70:217-24. [PMID: 24566269 DOI: 10.1016/j.addr.2014.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/23/2014] [Accepted: 02/14/2014] [Indexed: 01/09/2023]
Abstract
Drug development faces its nemesis in the form of drug resistance. The rate of bacterial resistance to antibiotics, or tumor resistance to chemotherapy decisively depends on the surrounding heterogeneous tissue. However, in vitro drug testing is almost exclusively done in well stirred, homogeneous environments. Recent advancements in microfluidics and microfabrication introduce opportunities to develop in vitro culture models that mimic the complex in vivo tissue environment. In this review, we will first discuss the design principles underlying such models. Then we will demonstrate two types of microfluidic devices that combine stressor gradients, cell motility, large population of competing/cooperative cells and time varying dosage of drugs. By incorporating ideas from how natural selection and evolution move drug resistance forward, we show that drug resistance can occur at much greater rates than in well-stirred environments. Finally, we will discuss the future direction of in vitro microbial culture models and how to extend the lessons learned from microbial systems to eukaryotic cells.
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437
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Dhar R, Bergmiller T, Wagner A. INCREASED GENE DOSAGE PLAYS A PREDOMINANT ROLE IN THE INITIAL STAGES OF EVOLUTION OF DUPLICATE TEM-1 BETA LACTAMASE GENES. Evolution 2014; 68:1775-91. [DOI: 10.1111/evo.12373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 01/22/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Riddhiman Dhar
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; CH-8057 Zurich Switzerland
- The Swiss Institute of Bioinformatics; CH-1015 Lausanne Switzerland
- Centre for Genomic Regulation (CRG); C/Dr. Aiguader 88 08003 Barcelona Spain
| | - Tobias Bergmiller
- ETH Zurich and Eawag; CH-8600 Dübendorf Switzerland
- Institute of Science and Technology; Am Campus 1 3400 Klosterneuburg Austria
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; CH-8057 Zurich Switzerland
- The Swiss Institute of Bioinformatics; CH-1015 Lausanne Switzerland
- The Santa Fe Institute; Santa Fe; New Mexico 87501
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438
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Experimental Simulation of the Effects of an Initial Antibiotic Treatment on a Subsequent Treatment after Initial Therapy Failure. Antibiotics (Basel) 2014; 3:49-63. [PMID: 27025733 PMCID: PMC4790345 DOI: 10.3390/antibiotics3010049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/23/2014] [Accepted: 01/29/2014] [Indexed: 11/17/2022] Open
Abstract
Therapy failure of empirical antibiotic treatments prescribed by primary care physicians occurs commonly. The effect of such a treatment on the susceptibility to second line antimicrobial drugs is unknown. Resistance to amoxicillin was rapidly induced or selected in E. coli at concentrations expected in the patient's body. Strains with reduced susceptibility outcompeted the wild-type whenever antibiotics were present, even in low concentrations that did not affect the growth rates of both strains. Exposure of E. coli to amoxicillin caused moderate resistance to cefotaxime. The combined evidence suggests that initial treatment by amoxicillin has a negative effect on subsequent therapy with beta-lactam antibiotics.
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439
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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440
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Schuurmans JM, van Hijum SAFT, Piet JR, Händel N, Smelt J, Brul S, ter Kuile BH. Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains. Plasmid 2014; 72:1-8. [PMID: 24525238 DOI: 10.1016/j.plasmid.2014.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
Abstract
Antibiotic resistance increases costs for health care and causes therapy failure. An important mechanism for spreading resistance is transfer of plasmids containing resistance genes and subsequent selection. Yet the factors that influence the rate of transfer are poorly known. Rates of plasmid transfer were measured in co-cultures in chemostats of a donor and a acceptor strain under various selective pressures. To document whether specific mutations in either plasmid or acceptor genome are associated with the plasmid transfer, whole genome sequencing was performed. The DM0133 TetR tetracycline resistance plasmid was transferred between Escherichia coli K-12 strains during co-culture at frequencies that seemed higher at increased growth rate. Modeling of the take-over of the culture by the transformed strain suggests that in reality more transfer events occurred at low growth rates. At moderate selection pressure due to an antibiotic concentration that still allowed growth, a maximum transfer frequency was determined of once per 10(11) cell divisions. In the absence of tetracycline or in the presence of high concentrations the frequency of transfer was sometimes zero, but otherwise reduced by at least a factor of 5. Whole genome sequencing showed that the plasmid was transferred without mutations, but two functional mutations in the genome of the recipient strain accompanied this transfer. Exposure to concentrations of antibiotics that fall within the mutant selection window stimulated transfer of the resistance plasmid most.
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Affiliation(s)
- Jasper M Schuurmans
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sacha A F T van Hijum
- NIZO Food Research B.V., Kernhemseweg 2, 6718 ZB Ede, The Netherlands; Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jurgen R Piet
- Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Nadine Händel
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jan Smelt
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Benno H ter Kuile
- Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Office for Risk Assessment and Research, Netherlands Food and Consumer Product Safety Authority, Catharijnesingel 59, 3511 GG Utrecht, The Netherlands.
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441
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Jansen G, Barbosa C, Schulenburg H. Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance. Drug Resist Updat 2014; 16:96-107. [PMID: 24594007 DOI: 10.1016/j.drup.2014.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibiotic treatments increasingly fail due to rapid dissemination of drug resistance. Comparative genomics of clinical isolates highlights the role of de novo adaptive mutations and horizontal gene transfer (HGT) in the acquisition of resistance. Yet it cannot fully describe the selective pressures and evolutionary trajectories that yielded today's problematic strains. Experimental evolution offers a compelling addition to such studies because the combination of replicated experiments under tightly controlled conditions with genomics of intermediate time points allows real-time reconstruction of evolutionary trajectories. Recent studies thus established causal links between antibiotic deployment therapies and the course and timing of mutations, the cost of resistance and the likelihood of compensating mutations. They particularly underscored the importance of long-term effects. Similar investigations incorporating horizontal gene transfer (HGT) are wanting, likely because of difficulties associated with its integration into experiments. In this review, we describe current advances in experimental evolution of antibiotic resistance and reflect on ways to incorporate horizontal gene transfer into the approach. We contend it provides a powerful tool for systematic and highly controlled dissection of evolutionary paths to antibiotic resistance that needs to be taken into account for the development of sustainable anti-bacterial treatment strategies.
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Affiliation(s)
- Gunther Jansen
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany.
| | - Camilo Barbosa
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany
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442
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Elliott KT, Cuff LE, Neidle EL. Copy number change: evolving views on gene amplification. Future Microbiol 2014; 8:887-99. [PMID: 23841635 DOI: 10.2217/fmb.13.53] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The rapid pace of genomic sequence analysis is increasing the awareness of intrinsically dynamic genetic landscapes. Gene duplication and amplification (GDA) contribute to adaptation and evolution by allowing DNA regions to expand and contract in an accordion-like fashion. This process affects diverse aspects of bacterial infection, including antibiotic resistance and host-pathogen interactions. In this review, microbial GDA is discussed, primarily using recent bacterial examples that demonstrate medical and evolutionary consequences. Interplay between GDA and horizontal gene transfer further impact evolutionary trajectories. Complementing the discovery of gene duplication in clinical and environmental settings, experimental evolution provides a powerful method to document genetic change over time. New methods for GDA detection highlight both its importance and its potential application for genetic engineering, synthetic biology and biotechnology.
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Affiliation(s)
- Kathryn T Elliott
- Biology Department, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA.
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443
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Zhang QG. Exposure to phages has little impact on the evolution of bacterial antibiotic resistance on drug concentration gradients. Evol Appl 2014; 7:394-402. [PMID: 24665341 PMCID: PMC3962299 DOI: 10.1111/eva.12136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/31/2013] [Indexed: 01/05/2023] Open
Abstract
The use of phages for treating bacterial pathogens has recently been advocated as an alternative to antibiotic therapy. Here, we test a hypothesis that bacteria treated with phages may show more limited evolution of antibiotic resistance as the fitness costs of resistance to phages may add to those of antibiotic resistance, further reducing the growth performance of antibiotic-resistant bacteria. We did this by studying the evolution of phage-exposed and phage-free Pseudomonas fluorescens cultures on concentration gradients of single drugs, including cefotaxime, chloramphenicol, and kanamycin. During drug treatment, the level of bacterial antibiotic resistance increased through time and was not affected by the phage treatment. Exposure to phages did not cause slower growth in antibiotic-resistant bacteria, although it did so in antibiotic-susceptible bacteria. We observed significant reversion of antibiotic resistance after drug use being terminated, and the rate of reversion was not affected by the phage treatment. The results suggest that the fitness costs caused by resistance to phages are unlikely to be an important constraint on the evolution of bacterial antibiotic resistance in heterogeneous drug environments. Further studies are needed for the interaction of fitness costs of antibiotic resistance with other factors.
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Affiliation(s)
- Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University Beijing, China
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444
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The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:211-31. [PMID: 24277302 DOI: 10.1007/978-94-007-7347-9_11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests some shortcomings of the reductionist approach. We conclude that convergence may be better defined at an integrated level, such as the genic level or even at a phenotypic level, and that integrated mechanistic models derived from systems biology may offer an interesting perspective for the analysis of convergence at all levels.
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445
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Deris JB, Kim M, Zhang Z, Okano H, Hermsen R, Groisman A, Hwa T. The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science 2013; 342:1237435. [PMID: 24288338 DOI: 10.1126/science.1237435] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To predict the emergence of antibiotic resistance, quantitative relations must be established between the fitness of drug-resistant organisms and the molecular mechanisms conferring resistance. These relations are often unknown and may depend on the state of bacterial growth. To bridge this gap, we have investigated Escherichia coli strains expressing resistance to translation-inhibiting antibiotics. We show that resistance expression and drug inhibition are linked in a positive feedback loop arising from an innate, global effect of drug-inhibited growth on gene expression. A quantitative model of bacterial growth based on this innate feedback accurately predicts the rich phenomena observed: a plateau-shaped fitness landscape, with an abrupt drop in the growth rates of cultures at a threshold drug concentration, and the coexistence of growing and nongrowing populations, that is, growth bistability, below the threshold.
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Affiliation(s)
- J Barrett Deris
- Department of Physics, University of California at San Diego, La Jolla, CA 92093-0374, USA
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446
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Nourmohammad A, Held T, Lässig M. Universality and predictability in molecular quantitative genetics. Curr Opin Genet Dev 2013; 23:684-93. [PMID: 24291213 DOI: 10.1016/j.gde.2013.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/14/2013] [Accepted: 11/01/2013] [Indexed: 12/15/2022]
Abstract
Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent developments in evolutionary theory and experiments that are expected to become building blocks of a quantitative genetics of molecular traits. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least partially unknown. We show that universal measurements can be used to infer selection on a quantitative trait, which determines its evolutionary mode of conservation or adaptation. Furthermore, universality is closely linked to predictability of trait evolution across lineages. We argue that universal trait statistics extends over a range of cellular scales and opens new avenues of quantitative evolutionary systems biology.
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Affiliation(s)
- Armita Nourmohammad
- Joseph-Henri Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
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447
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Malaria life cycle intensifies both natural selection and random genetic drift. Proc Natl Acad Sci U S A 2013; 110:20129-34. [PMID: 24259712 DOI: 10.1073/pnas.1319857110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Analysis of genome sequences of 159 isolates of Plasmodium falciparum from Senegal yields an extraordinarily high proportion (26.85%) of protein-coding genes with the ratio of nonsynonymous to synonymous polymorphism greater than one. This proportion is much greater than observed in other organisms. Also unusual is that the site-frequency spectra of synonymous and nonsynonymous polymorphisms are virtually indistinguishable. We hypothesized that the complicated life cycle of malaria parasites might lead to qualitatively different population genetics from that predicted from the classical Wright-Fisher (WF) model, which assumes a single random-mating population with a finite and constant population size in an organism with nonoverlapping generations. This paper summarizes simulation studies of random genetic drift and selection in malaria parasites that take into account their unusual life history. Our results show that random genetic drift in the malaria life cycle is more pronounced than under the WF model. Paradoxically, the efficiency of purifying selection in the malaria life cycle is also greater than under WF, and the relative efficiency of positive selection varies according to conditions. Additionally, the site-frequency spectrum under neutrality is also more skewed toward low-frequency alleles than expected with WF. These results highlight the importance of considering the malaria life cycle when applying existing population genetic tools based on the WF model. The same caveat applies to other species with similarly complex life cycles.
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448
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Affiliation(s)
- Stephen P. Ellner
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca; New York; 14853-2701; USA
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449
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Okumus B, Yildiz S, Toprak E. Fluidic and microfluidic tools for quantitative systems biology. Curr Opin Biotechnol 2013; 25:30-8. [PMID: 24484878 DOI: 10.1016/j.copbio.2013.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/22/2013] [Indexed: 11/18/2022]
Abstract
Understanding genes and their functions is a daunting task due to the level of complexity in biological organisms. For discovering how genotype and phenotype are linked to each other, it is essential to carry out systematic studies with maximum sensitivity and high-throughput. Recent developments in fluid-handling technologies, both at the macro and micro scale, are now allowing us to apply engineering approaches to achieve this goal. With these newly developed tools, it is now possible to identify genetic factors that are responsible for particular phenotypes, perturb and monitor cells at the single-cell level, evaluate cell-to-cell variability, detect very rare phenotypes, and construct faithful in vitro disease models.
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Affiliation(s)
- Burak Okumus
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Sadik Yildiz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Erdal Toprak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods 2013; 95:401-14. [PMID: 24029734 DOI: 10.1016/j.mimet.2013.08.011] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/13/2013] [Accepted: 08/13/2013] [Indexed: 02/07/2023]
Abstract
High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is therefore becoming more widely used to study whole communities of prokaryotes in many niches. This review discusses these techniques, including nucleic acid extraction from different environments, sample preparation and high-throughput sequencing platforms. We also discuss commonly used and recently developed bioinformatic tools applied to microbiomes, including analyzing amplicon sequences, metagenome shotgun sequences and metatranscriptome sequences. This field is relatively new and rapidly evolving, thus we hope that this review will provide a baseline for understanding these methods of microbiome analyses. Additionally, we seek to stimulate others to solve the many problems that still exist with the sensitivity, specificity and interpretation of high throughput microbiome sequence analysis.
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Affiliation(s)
- Julia M Di Bella
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
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