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  1. Article ; Online: Genotype-phenotype maps and the predictability of evolution: Comment on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics" by Susanna Manrubia et al.

    de Visser, J Arjan G M

    Physics of life reviews

    2021  Volume 39, Page(s) 79–81

    MeSH term(s) Biological Evolution ; Genotype ; Phenotype
    Language English
    Publishing date 2021-08-23
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2021.08.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory.

    Ruelens, Philip / Wynands, Thomas / de Visser, J Arjan G M

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2023  Volume 378, Issue 1877, Page(s) 20220051

    Abstract: What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. ... ...

    Abstract What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. Additionally, pleiotropy may promote repeatability by allowing large fitness benefits of single mutations via adaptive combinations of phenotypic effects. Yet, this latter evolutionary potential may be reaped solely by specific types of mutations able to realize optimal combinations of phenotypic effects while avoiding the costs of pleiotropy. Here, we address the interaction of gene pleiotropy and mutation type on evolutionary repeatability in a meta-analysis of experimental evolution studies with
    MeSH term(s) Genetic Pleiotropy ; Mutation ; Phenotype ; Escherichia coli/genetics ; Alleles
    Language English
    Publishing date 2023-04-03
    Publishing country England
    Document type Meta-Analysis ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2022.0051
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Population dynamics of cross-protection against β-lactam antibiotics in droplet microreactors.

    Zhao, Xinne / Ruelens, Philip / Farr, Andrew D / de Visser, J Arjan G M / Baraban, Larysa

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1294790

    Abstract: Introduction: Bacterial strains that are resistant to antibiotics may protect not only themselves, but also sensitive bacteria nearby if resistance involves antibiotic degradation. Such cross-protection poses a challenge to effective antibiotic therapy ... ...

    Abstract Introduction: Bacterial strains that are resistant to antibiotics may protect not only themselves, but also sensitive bacteria nearby if resistance involves antibiotic degradation. Such cross-protection poses a challenge to effective antibiotic therapy by enhancing the long-term survival of bacterial infections, however, the current understanding is limited.
    Methods: In this study, we utilize an automated nanoliter droplet analyzer to study the interactions between
    Results: We observed a cross-protection window of CTX concentrations for the sensitive strain, extending up to approximately 100 times its minimal inhibitory concentration (MIC). Through both microscopy and enzyme activity analyses, we demonstrate that bacterial filaments, triggered by antibiotic stress, contribute to cross-protection.
    Discussion: The antibiotic concentration window for cross-protection depends on the difference in β-lactamase activity between co-cultured strains: larger differences shift the 'cross-protection window' toward higher CTX concentrations. Our findings highlight the dependence of opportunities for cross-protection on the relative resistance levels of the strains involved and suggest a possible specific role for filamentation.
    Language English
    Publishing date 2023-12-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1294790
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations.

    Farr, Andrew D / Pesce, Diego / Das, Suman G / Zwart, Mark P / de Visser, J Arjan G M

    mBio

    2023  Volume 14, Issue 3, Page(s) e0009823

    Abstract: Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness ... ...

    Abstract Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; beta-Lactamases/genetics ; Cefotaxime/pharmacology ; Drug Resistance, Microbial/genetics ; Selection, Genetic ; Mutation
    Chemical Substances Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6) ; Cefotaxime (N2GI8B1GK7)
    Language English
    Publishing date 2023-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.00098-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets.

    Ruelens, Philip / de Visser, J Arjan G M

    Genes

    2021  Volume 12, Issue 2

    Abstract: Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments ... ...

    Abstract Experimental evolution studies have provided key insights into the fundamental mechanisms of evolution. One striking observation is that parallel and convergent evolution during laboratory evolution can be surprisingly common. However, these experiments are typically performed with well-mixed cultures and large effective population sizes, while pathogenic microbes typically experience strong bottlenecks during infection or drug treatment. Yet, our knowledge about adaptation in very small populations, where selection strength and mutation supplies are limited, is scant. In this study, wild-type and mutator strains of the bacterium
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Cefotaxime/pharmacology ; Directed Molecular Evolution ; Escherichia coli/genetics ; Escherichia coli/growth & development ; Escherichia coli Proteins/genetics ; Mutation/genetics ; Mutation Rate ; Selection, Genetic/genetics
    Chemical Substances Anti-Bacterial Agents ; Escherichia coli Proteins ; Cefotaxime (N2GI8B1GK7)
    Language English
    Publishing date 2021-02-04
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12020223
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Choice of β-Lactam Resistance Pathway Depends Critically on Initial Antibiotic Concentration.

    Ruelens, Philip / de Visser, J Arjan G M

    Antimicrobial agents and chemotherapy

    2021  Volume 65, Issue 8, Page(s) e0047121

    Abstract: Antibiotic resistance trajectories with different final resistance may critically depend on the first mutation, due to epistatic interactions. Here, we study the effect of mutation bias and the concentration-dependent effects on fitness of two clinically ...

    Abstract Antibiotic resistance trajectories with different final resistance may critically depend on the first mutation, due to epistatic interactions. Here, we study the effect of mutation bias and the concentration-dependent effects on fitness of two clinically important mutations in TEM-1 β-lactamase in initiating alternative trajectories to cefotaxime resistance. We show that at low cefotaxime concentrations, the R164S mutation (a mutation of arginine to serine at position 164), which confers relatively low resistance, is competitively superior to the G238S mutation, conferring higher resistance, thus highlighting a critical influence of antibiotic concentration on long-term resistance evolution.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Cefotaxime/pharmacology ; Drug Resistance, Microbial ; Escherichia coli/genetics ; Mutation ; beta-Lactam Resistance ; beta-Lactamases/genetics
    Chemical Substances Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6) ; Cefotaxime (N2GI8B1GK7)
    Language English
    Publishing date 2021-07-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/AAC.00471-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  7. Article ; Online: Stochastic establishment of β-lactam-resistant

    Saebelfeld, Manja / Das, Suman G / Hagenbeek, Arno / Krug, Joachim / de Visser, J Arjan G M

    Proceedings. Biological sciences

    2022  Volume 289, Issue 1974, Page(s) 20212486

    Abstract: For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Comprehending the stochastic factors that influence mutant establishment is crucial for a quantitative ... ...

    Abstract For antibiotic resistance to arise, new resistant mutants must establish in a bacterial population before they can spread via natural selection. Comprehending the stochastic factors that influence mutant establishment is crucial for a quantitative understanding of antibiotic resistance emergence. Here, we quantify the single-cell establishment probability of four
    MeSH term(s) Agar/pharmacology ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Microbial Sensitivity Tests ; beta-Lactams/pharmacology
    Chemical Substances Anti-Bacterial Agents ; beta-Lactams ; Agar (9002-18-0)
    Language English
    Publishing date 2022-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209242-6
    ISSN 1471-2954 ; 0080-4649 ; 0962-8452 ; 0950-1193
    ISSN (online) 1471-2954
    ISSN 0080-4649 ; 0962-8452 ; 0950-1193
    DOI 10.1098/rspb.2021.2486
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1364: Show issues Location:
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  8. Article: High-Throughput Gel Microbeads as Incubators for Bacterial Competition Study.

    Nguyen-Le, Trang Anh / Zhao, Xinne / Bachmann, Michael / Ruelens, Philip / Visser, J Arjan G M de / Baraban, Larysa

    Micromachines

    2023  Volume 14, Issue 3

    Abstract: Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, ... ...

    Abstract Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled
    Language English
    Publishing date 2023-03-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2620864-7
    ISSN 2072-666X
    ISSN 2072-666X
    DOI 10.3390/mi14030645
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  9. Article ; Online: Minimal Surviving Inoculum in Collective Antibiotic Resistance.

    Geyrhofer, Lukas / Ruelens, Philip / Farr, Andrew D / Pesce, Diego / de Visser, J Arjan G M / Brenner, Naama

    mBio

    2023  Volume 14, Issue 2, Page(s) e0245622

    Abstract: A common strategy used by bacteria to resist antibiotics is enzymatic degradation or modification. This reduces the antibiotic threat in the environment and is therefore potentially a collective mechanism that also enhances the survival of nearby cells. ... ...

    Abstract A common strategy used by bacteria to resist antibiotics is enzymatic degradation or modification. This reduces the antibiotic threat in the environment and is therefore potentially a collective mechanism that also enhances the survival of nearby cells. Collective resistance is of clinical significance, yet a quantitative understanding at the population level is still incomplete. Here, we develop a general theoretical framework of collective resistance by antibiotic degradation. Our modeling study reveals that population survival crucially depends on the ratio of timescales of two processes: the rates of population death and antibiotic removal. However, it is insensitive to molecular, biological, and kinetic details of the underlying processes that give rise to these timescales. Another important aspect of antibiotic degradation is the degree of cooperativity, related to the permeability of the cell wall to antibiotics and enzymes. These observations motivate a coarse-grained, phenomenological model, with two compound parameters representing the population's race to survival and single-cell effective resistance. We propose a simple experimental assay to measure the dose-dependent minimal surviving inoculum and apply it to Escherichia coli expressing several types of β-lactamase. Experimental data analyzed within the theoretical framework corroborate it with good agreement. Our simple model may serve as a reference for more complex situations, such as heterogeneous bacterial communities.
    MeSH term(s) Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Drug Resistance, Microbial ; Bacteria/metabolism ; beta-Lactamases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Drug Resistance, Bacterial
    Chemical Substances Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.02456-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in

    Duxbury, Sarah J N / Alderliesten, Jesse B / Zwart, Mark P / Stegeman, Arjan / Fischer, Egil A J / de Visser, J Arjan G M

    Proceedings. Biological sciences

    2021  Volume 288, Issue 1962, Page(s) 20212027

    Abstract: Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal ... ...

    Abstract Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified
    MeSH term(s) Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome ; Plasmids/genetics
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2021-11-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209242-6
    ISSN 1471-2954 ; 0080-4649 ; 0962-8452 ; 0950-1193
    ISSN (online) 1471-2954
    ISSN 0080-4649 ; 0962-8452 ; 0950-1193
    DOI 10.1098/rspb.2021.2027
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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