Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance

2013 ◽  
Vol 16 (6) ◽  
pp. 96-107 ◽  
Author(s):  
Gunther Jansen ◽  
Camilo Barbosa ◽  
Hinrich Schulenburg
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Efficient Tool

scholarly journals Evolution of Cost-Free Resistance under Fluctuating Drug Selection in Pseudomonas aeruginosa

mSphere ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Anita H. Melnyk ◽  
Nicholas McCloskey ◽  
Aaron J. Hinz ◽  
Jeremy Dettman ◽  
Rees Kassen
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Antibiotic Treatment ◽  
Experimental Evolution ◽  
Public Health Problem ◽  
Content Type ◽  
Compensatory Evolution ◽  
High Fitness ◽  
Treatment Conditions ◽  
Resistant Strains

ABSTRACT Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide. Antibiotic resistance evolves rapidly in response to drug selection, but it can also persist at appreciable levels even after the removal of the antibiotic. This suggests that many resistant strains can both be resistant and have high fitness in the absence of antibiotics. To explore the conditions under which high-fitness, resistant strains evolve and the genetic changes responsible, we used a combination of experimental evolution and whole-genome sequencing to track the acquisition of ciprofloxacin resistance in the opportunistic pathogen Pseudomonas aeruginosa under conditions of constant and fluctuating antibiotic delivery patterns. We found that high-fitness, resistant strains evolved readily under fluctuating but not constant antibiotic conditions and that their evolution was underlain by a trade-off between resistance and fitness. Whole-genome sequencing of evolved isolates revealed that resistance was gained through mutations in known resistance genes and that second-site mutations generally compensated for costs associated with resistance in the fluctuating treatment, leading to the evolution of cost-free resistance. Our results suggest that current therapies involving intermittent administration of antibiotics are contributing to the maintenance of antibiotic resistance at high levels in clinical settings. IMPORTANCE Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide.

scholarly journals A large-scale comparison shows that genetic changes causing antibiotic resistance in experimentally evolved Pseudomonas aeruginosa predict those in naturally evolved bacteria

2019 ◽  
Author(s):  
Samuel J. T. Wardell ◽  
Attika Rehman ◽  
Lois W. Martin ◽  
Craig Winstanley ◽  
Wayne M. Patrick ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Large Scale ◽  
Genetic Basis ◽  
Clinical Isolates ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Health Crisis ◽  
Wide Range

AbstractPseudomonas aeruginosa is an opportunistic pathogen that causes a wide range of acute and chronic infections. An increasing number of isolates have acquired mutations that make them antibiotic resistant, making treatment more difficult. To identify resistance-associated mutations we experimentally evolved the antibiotic sensitive strain P. aeruginosa PAO1 to become resistant to three widely used anti-pseudomonal antibiotics, ciprofloxacin, meropenem and tobramycin. Mutants were able to tolerate up to 2048-fold higher concentrations of antibiotic than strain PAO1. Genome sequences were determined for thirteen mutants for each antibiotic. Each mutant had between 2 and 8 mutations. There were at least 8 genes mutated in more than one mutant per antibiotic, demonstrating the complexity of the genetic basis of resistance. Additionally, large deletions of up to 479kb arose in multiple meropenem resistant mutants. For all three antibiotics mutations arose in genes known to be associated with resistance, but also in genes not previously associated with resistance. To determine the clinical relevance of mutations uncovered in experimentally-evolved mutants we analysed the corresponding genes in 457 isolates of P. aeruginosa from patients with cystic fibrosis or bronchiectasis as well as 172 isolates from the general environment. Many of the genes identified through experimental evolution had changes predicted to be function-altering in clinical isolates but not in isolates from the general environment, showing that mutated genes in experimentally evolved bacteria can predict those that undergo mutation during infection. These findings expand understanding of the genetic basis of antibiotic resistance in P. aeruginosa as well as demonstrating the validity of experimental evolution in identifying clinically-relevant resistance-associated mutations.ImportanceThe rise in antibiotic resistant bacteria represents an impending global health crisis. As such, understanding the genetic mechanisms underpinning this resistance can be a crucial piece of the puzzle to combatting it. The importance of this research is that by experimentally evolving P. aeruginosa to three clinically relevant antibiotics, we have generated a catalogue of genes that can contribute to resistance in vitro. We show that many (but not all) of these genes are clinically relevant, by identifying variants in clinical isolates of P. aeruginosa. This research furthers our understanding of the genetics leading to resistance in P. aeruginosa and provides tangible evidence that these genes can play a role clinically, potentially leading to new druggable targets or inform therapies.

Experimental Evolution of Antibiotic Resistance in Bacteria

2007 ◽  
Vol 69 (2) ◽  
pp. 94-97 ◽  
Author(s):  
Amy C. Krist ◽  
Sasha A. Showsh
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution

scholarly journals Phenotypic Suppression of Streptomycin Resistance by Mutations in Multiple Components of the Translation Apparatus

2015 ◽  
Vol 197 (18) ◽  
pp. 2981-2988 ◽  
Author(s):  
Jennifer F. Carr ◽  
Hannah J. Lee ◽  
Joshua B. Jaspers ◽  
Albert E. Dahlberg ◽  
Gerwald Jogl ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Long Range ◽  
Experimental Evolution ◽  
Thermus Thermophilus ◽  
Thermophilic Bacterium ◽  
Streptomycin Resistance ◽  
Resistance Mutations ◽  
Content Type ◽  
Translation Apparatus ◽  
Antibiotic Resistance Mutations

ABSTRACTThe bacterial ribosome and its associated translation factors are frequent targets of antibiotics, and antibiotic resistance mutations have been found in a number of these components. Such mutations can potentially interact with one another in unpredictable ways, including the phenotypic suppression of one mutation by another. These phenotypic interactions can provide evidence of long-range functional interactions throughout the ribosome and its functional complexes and potentially give insights into antibiotic resistance mechanisms. In this study, we used genetics and experimental evolution of the thermophilic bacteriumThermus thermophilusto examine the ability of mutations in various components of the protein synthesis apparatus to suppress the streptomycin resistance phenotypes of mutations in ribosomal protein S12, specifically those located distant from the streptomycin binding site. With genetic selections and strain constructions, we identified suppressor mutations in EF-Tu or in ribosomal protein L11. Using experimental evolution, we identified amino acid substitutions in EF-Tu or in ribosomal proteins S4, S5, L14, or L19, some of which were found to also relieve streptomycin resistance. The wide dispersal of these mutations is consistent with long-range functional interactions among components of the translational machinery and indicates that streptomycin resistance can result from the modulation of long-range conformational signals.IMPORTANCEThe thermophilic bacteriumThermus thermophilushas become a model system for high-resolution structural studies of macromolecular complexes, such as the ribosome, while its natural competence for transformation facilitates genetic approaches. Genetic studies ofT. thermophilusribosomes can take advantage of existing high-resolution crystallographic information to allow a structural interpretation of phenotypic interactions among mutations. Using a combination of genetic selections, strain constructions, and experimental evolution, we find that certain mutations in the translation apparatus can suppress the phenotype of certain antibiotic resistance mutations. Suppression of resistance can occur by mutations located distant in the ribosome or in a translation factor. These observations suggest the existence of long-range conformational signals in the translating ribosome, particularly during the decoding of mRNA.

scholarly journals Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens

mBio ◽  
2021 ◽  
Author(s):  
Jaime E. Zlamal ◽  
Semen A. Leyn ◽  
Mallika Iyer ◽  
Marinela L. Elane ◽  
Nicholas A. Wong ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Bacterial Pathogens ◽  
Genome Rearrangements ◽  
Microbial Populations ◽  
Gram Negative ◽  
Evolutionary Trajectories ◽  
Ciprofloxacin Resistance

The challenge of spreading antibiotic resistance calls for systematic efforts to develop more “irresistible” drugs based on a deeper understanding of dynamics and mechanisms of antibiotic resistance acquisition. To address this challenge, we have established a comparative resistomics approach which combines experimental evolution in a continuous-culturing device, the morbidostat, with ultradeep sequencing of evolving microbial populations to identify evolutionary trajectories (mutations and genome rearrangements) leading to antibiotic resistance over a range of target pathogens.

scholarly journals Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Alfonso Santos-Lopez ◽  
Christopher W Marshall ◽  
Michelle R Scribner ◽  
Daniel J Snyder ◽  
Vaughn S Cooper
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Drug Targets ◽  
Evolutionary Dynamics ◽  
Selective Sweeps ◽  
Resistance Level ◽  
Bacterial Populations ◽  
Collateral Sensitivity ◽  
Genetic Mechanisms ◽  
Evolution Of Resistance

Bacterial populations vary in their stress tolerance and population structure depending upon whether growth occurs in well-mixed or structured environments. We hypothesized that evolution in biofilms would generate greater genetic diversity than well-mixed environments and lead to different pathways of antibiotic resistance. We used experimental evolution and whole genome sequencing to test how the biofilm lifestyle influenced the rate, genetic mechanisms, and pleiotropic effects of resistance to ciprofloxacin in Acinetobacter baumannii populations. Both evolutionary dynamics and the identities of mutations differed between lifestyle. Planktonic populations experienced selective sweeps of mutations including the primary topoisomerase drug targets, whereas biofilm-adapted populations acquired mutations in regulators of efflux pumps. An overall trade-off between fitness and resistance level emerged, wherein biofilm-adapted clones were less resistant than planktonic but more fit in the absence of drug. However, biofilm populations developed collateral sensitivity to cephalosporins, demonstrating the clinical relevance of lifestyle on the evolution of resistance.

scholarly journals Integron activity accelerates the evolution of antibiotic resistance

2020 ◽  
Author(s):  
Célia Souque ◽  
José A. Escudero ◽  
R.Craig MacLean
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Expression System ◽  
Genomic Integrity ◽  
Resistance Evolution ◽  
On Demand ◽  
Accelerated Evolution ◽  
Gentamicin Resistance ◽  
The Impact ◽  
Target Effects

AbstractMobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to ‘evolve on demand’ in response to antibiotic pressure. To test this hypothesis, we inserted a custom three cassette integron into P. aeruginosa, and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.

scholarly journals Evolving Antibiotics against Resistance: a Potential Platform for Natural Product Development?

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Kristofer Wollein Waldetoft ◽  
James Gurney ◽  
Joseph Lachance ◽  
Paul A. Hoskisson ◽  
Sam P. Brown
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution ◽  
Rational Design ◽  
Antibiotic Production ◽  
Molecular Targets ◽  
Resistance Mechanisms ◽  
Mechanisms Of Resistance ◽  
Complex Functions ◽  
Evolution Of Resistance ◽  
Antibiotic Discovery

ABSTRACT To avoid an antibiotic resistance crisis, we need to develop antibiotics at a pace that matches the rate of evolution of resistance. However, the complex functions performed by antibiotics—combining, e.g., penetration of membranes, counteraction of resistance mechanisms, and interaction with molecular targets—have proven hard to achieve with current methods for drug development, including target-based screening and rational design. Here, we argue that we can meet the evolution of resistance in the clinic with evolution of antibiotics in the laboratory. On the basis of the results of experimental evolution studies of microbes in general and antibiotic production in Actinobacteria in particular, we propose methodology for evolving antibiotics to circumvent mechanisms of resistance. This exploits the ability of evolution to find solutions to complex problems without a need for design. We review evolutionary theory critical to this approach and argue that it is feasible and has important advantages over current methods for antibiotic discovery.

scholarly journals Experimental evolution selects clinically relevant antibiotic resistance in biofilms but with collateral tradeoffs

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Eleftheria Trampari ◽  
Emma Holden ◽  
Gregory Wickham ◽  
Anuradha Ravi ◽  
Filippo Prischi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Experimental Evolution
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