Role of bacterial motility in differential resistance mechanisms of silver nanoparticles and silver ions

Nature Nanotechnology, Journal Year: 2021, Volume and Issue: 16(9), P. 996 - 1003

Published: June 21, 2021

Language: Английский

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

eLife, Journal Year: 2019, Volume and Issue: 8

Published: Sept. 13, 2019

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

Language: Английский

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Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

EMBO Reports, Journal Year: 2019, Volume and Issue: 20(8)

Published: July 24, 2019

Review24 July 2019Open Access Microbial Experimental Evolution – a proving ground for evolutionary theory and tool discovery Michael J McDonald Corresponding Author [email protected] orcid.org/0000-0002-5735-960X School of Biological Sciences, Monash University, Melbourne, Vic., Australia Search more papers by this author Information *,1 1School *Corresponding author. Tel: +61 3 9905 1697; E-mail: EMBO Reports (2019)20:e46992https://doi.org/10.15252/embr.201846992 See the Glossary abbreviations used in article. PDFDownload PDF article text main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract experimental evolution uses controlled laboratory populations study mechanisms evolution. The molecular analysis evolved enables empirical tests that can confirm predictions theory, but also lead surprising discoveries. As with other fields life sciences, microbial has become tool, deployed as part suite techniques available biologist. Here, I provide review general findings evolution, especially those relevant microbiologists are new field. relate these results design considerations an experiment suggest future directions working at intersection biology. clonal interference slowed rates fixation asexual population due competition between lineages each carry beneficial mutation coverage length concatenated DNA-sequence read data divided genome de novo occurs spontaneously during period fixed state which allele given genetic locus is frequency 1 barcode short DNA sequence identify individual or lineage haplotype set variants physically linked on single chromosome HGT horizontal gene transfer individuals share common ancestor within time LN natural log LTEE long-term N size parallel similar phenotypes genotypes independently evolving selection coefficient(s) quantitative representation relative fitness reproductive success standing variation present before considered observer Introduction studies now constitute one foundations 1. In particular, bring greater power precision studies, providing means out elaborate explore ideas biology 2. A typical starts culture, just like any microbiology laboratory. Cells inoculated into media left grow until culture reaches high density. Instead throwing using all resultant population, evolutionist transfers dilutes allow continued growth division. This cycle be indefinitely, generations accumulate, will drive adapt environment. simple process carried range systems, summarised Fig Figure Mechanisms propagation evolution(A) Batch requires regular dilution fresh media. These experiments relatively easy establish, since vessels commonly batch culture. scaled large number replicates, example when 96-well plates. (B) Chemostat systems include constant supply medium. provides continuous cultures without fluctuations phase. (C) Microfluidics most precise control over supplements cell cultures. may need custom designed, replicates limited. (D) Emulsion take advantage small cell-containing vesicles form mixing oil, surfactant cells. cells vesicle determined ratio cell, oil. mixed back vortexing centrifuging solution. One select yield per-vesicle rather than rapid 144. (E) Mutation accumulation introduces regular, single-cell bottleneck replicate population. achieved streaking petri dish then choosing colony (founded cell) streak next plate. (F) introduced model organism, often plant mouse, propagate it recovered from organism. analysed subjected further mode allows testing unanticipated organism-specific features environment difficult Download figure PowerPoint Long- short-term approaches Perhaps striking microbes access long scales. generation times up tens pass every day. limited only how experimentalist maintain transfers. easily stored freezer, indefinite period, so saved frozen snapshot restart inevitable accidents happen. longest running, probably famous, (LTEE). comprised 12 E. coli, started 1987 still passaged daily 68,000 later (see here recent 4). What learned running long? Twenty years ago, biologist might have predicted coli would reached optimal after few thousand generations. However, we know continues 61,500 5, 6. key been utilisation citrate (cit+ phenotype), carbon source buffer phenotype significant because species-defining characteristic unable utilised under oxidising conditions 7. effect mutations explicitly cause cit+ dependent "potentiating" do not seem directly influence occurred first 20,000 8. words, particular trait unlikely experiment. there quicker routes many An alternative propagating term evolve shorter time. strong, rapidly. Adapting temperatures, Tenaillon et al propagated 115 2,000 9. Increasing another magnitude, Lang 1,000 Saccharomyces cerevisiae 10, 11. massive replication confers statistical detect change, hundreds shows some questions highly replicated cannot address; however, trends emerging consistent across both long- 12, 13, reviewed below. Repeatability, diminishing returns diversification: predictable Parallel same phenotypes, sometimes mutations, 14. Parallelism driven observed short- species 11, 15-19 (Fig 2A). Repeatability interesting suggests phenotypic outcomes could predictable. To anticipate response environmental changes major goal 20, capacity make accurate desirable. unclear whether about ever enough useful, subject ongoing models 21, 22. Three experiments(A) Genetic parallelism. signature repeated genes independent populations. expected multi-hit mutated six hypothetical 1000-generation (grey shaded) (orange line) Diminishing epistasis. negatively correlated background (figure adapted 25). Stable polymorphism evolve, whereby multiple ecotypes, different niche microcosm, coexist 27. possible outcome successive sweeps mutation, occasionally hampered (D). At onset experiment, adaptation tends slows down 23. LTEE, rate increase follows law, no attained 5. explained epistatic interactions effects lower better 24. Experiments show engineered low-fitness larger if they high-fitness 2B). "diminishing returns" epistasis M. extorquens S. 25, well 26. While return makes specific does robust made although true experiencing fluctuating complex environments. Most use unicellular organisms adapting defined-nutrient diverse, co-existing subpopulations niches, evident 6, 27, 28 2C). Diverse heterogeneity experimenter, called eco-evolutionary feedback 29. happens populations, altered production waste products consumption modifications change ecology alters selective pressures experienced 30. observation emphasises its importance real communities mechanism experiments. facilitate fundamental parameters evolution: environment, Understanding, manipulating, factors benefit exerted size, founding genotype determines therefore drives while manipulating variable potentially subtle effects. interpreting setting discussed Population (N) strength forces minimum detected selection, expressed coefficient (s), 1/N, where "N" ineffective Ns < 31. likely experience drift, random sampling frequencies chance deleterious loss mutations. consequence expect slower and, extreme cases, extinction 32. Some designed consequences 33-36, deliberately 1–10 1). If avoid 103–104 recommended. Variation experimenter vary much variation, "fuel" supplied 37. proportional amount 38. start amounts 39-41, founded clone 3, 28, 42 adaptive must fuelled 43, 44, elevated artificially induced supplementing mutagen deleting required mismatch repair. antimicrobial resistance antibiotic global health challenge that, sits disciplines biology, microbiology, genomics 20. measure costs underlie 45-49, probability 49. Mutations occur important biological functions reduction viability 50. Fitness assays Box 1: How fitness) shown confer actually 47, 51-53, always come cost. When costly, resistant microbe secondary compensate primary 54. Since processes, strategies amelioration resistance, drugs, should account 55. promising line research characterise susceptibilities multidrug-resistant strains. order attain strains several compensatory It less able additional Knowledge multidrug targeted drug combinations based clinical pathogenic organism contribute offspring generation. determine degree validate experimentally wide assays. Growth 145, total carrying capacity, biomass 105 speed boundary expansion 141 measures gold standard measurement competitive starting point assay obtain construct marked reference strain. typically modified readily distinguished nature marker accuracy For instance, fluorescent differentiate strain, proportions measured flow cytometry 10 10s thousands counted ratios. Alternatively, mixture spread onto agar plates containing distinction 146, counting Initially, strain 1:1 ratio. Even care taken mix competitors ratio, very initial frequency, difference calculations fitness. Once portion aside competing diluted incubated time, allowing two compete. After competition, again. calculated measurements dividing individuals. done final point. (LN) quotient gives performance compared value passed points, yielding per-generation (s). chosen carefully. too long, extinction, thus reducing calculation s. short, changed detection differences genotypes. bacteriophages Bacteriophages therapies 56, bacteriophage provided insights genetics 57. Bacteriophage genomes small, whole-genome sequencing phage was rise next-generation technologies 58. head exploited 19, 59, 60. ease bacteria co-culture led co-evolutionary dynamics. infecting isolation 61, 62. diverse bacteriophage, increases types 63. bind membrane protein gain entry cell. facilitated detailed λ site 64, 65. Conversely, bacterial modifying encodes protein. conferred efflux pumps, hypothesised targets such pump tandem comprise "evolution proof" treatment strategy 56. principle demonstrated drove MEX pump, thereby restoring sensitivity P. aeruginosa 66. trait. applications. introduction useful properties reductions 67. yeast, crossed "wild-type" promote recombinants possess productivity fast-growing 68. Continuous passaging widely restore ethanol xylose 69-71. example, C321 replace UAG codons UAA. ideal biotechnological applications, incorporation non-standard amino acids code. engineering caused slow growth. 1,000-generation resulted restored rates. Moreover, re-sequencing revealed mutational causes reduced founder 72. novel hosts, conditions. Wolbachia quickly among their hosts conferring infected females. addition, induce insect pathogens. devised Dengue virus amongst mosquitos originally discovered D. melanogaster. suited dispersal mosquito A. aegypti mosquito's intracellular 2 years. newly establish stable infection 73 thereafter eventual public dengue 74. Next, introduce describing full historical recommend books 1, reviews 75-77 exhaustive treatments earlier periods non-microbial 78-81 aspects You get what you for: choices Setting beyond normally adaptation. Adaptation described, including temperatures 9, 82, gradients 55 even levels ionising radiation 83. imagination. parameter pressure differential survival relied upon regardless pressure, adaptations predict. Wildenberg 84 fluorescence-activated sorter brightest 24 h. anticipated expression modulate fluorescence. Instead, periodically multicellular clusters increased brightness advantage. unpredicted did diminish elegance serves demonstrate unpredictability thwart outcomes. general, complicated regime, unpredictable noted complicated, well-designed, elicit selection. sought traits selecting against germ progenitor cooperative mats fluorescens. Although were unexpected, successfully applied 85. Simple environments function Natural expose microorganisms nutrients stresses spatial temporal complexity reflected numbers utilise respond stress. Laboratory 86, inactivate superfluous 87. Many contain source, usually glucose. glucose sole concentration limits 3. h "lag time", enter via pykF, became 88. specialisation cost sources. Studies showed rbs operon, proteins ribose 89, disrupted deleted Measurements ~1% 90. then, disruption genes, sources, maltose, minimal Other yeast concentrations glucose, Genes 91. Whole-genome half disrupt encode negative regulators RAS/PKA pathway ac

Language: Английский

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Parallel Evolution of Tobramycin Resistance across Species and Environments

mBio, Journal Year: 2020, Volume and Issue: 11(3)

Published: May 25, 2020

Different species exposed to a common stress may adapt by mutations in shared pathways or unique systems, depending on how past environments have molded their genomes. Understanding diverse bacterial pathogens evolve response an antimicrobial treatment is pressing example of this problem, where discovery molecular parallelism could lead clinically useful predictions. Evolution experiments with containing antibiotics, combined periodic whole-population genome sequencing, can be used identify many contending routes resistance. We separately propagated two relevant Gram-negative pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii, increasing concentrations tobramycin different each: planktonic biofilm. Independently the pathogen, populations adapted selection parallel evolution fusA1, encoding elongation factor G, ptsP, phosphoenolpyruvate phosphotransferase. As neither gene direct target aminoglycoside, either are unexpected underreported causes Additionally, both acquired antibiotic resistance-associated that were more prevalent biofilm lifestyle than lifestyle; these electron transport chain components A. baumannii lipopolysaccharide biosynthesis enzymes P. populations. Using existing databases, we discovered site-specific fusA1 extends across phyla clinical isolates. This study suggests strong selective pressures, such as treatment, result high levels predictability targets evolution, despite differences between organisms' genetic backgrounds environments.IMPORTANCE The rise resistance leading medical threat, motivating efforts forecast its evolutionary dynamics causes. Aminoglycosides major class antibiotics disrupt translation, but occur number mechanisms. Here, show repeated aminoglycoside via nitrogen-specific phosphotransferase system. Laboratory sequencing targets, at identical amino acid positions also found published genomes identified other mechanisms associated growth biofilms likely interfere drug binding uptake. Characterizing multiple presence new, repeatable predicted counteracted alternative treatment.

Language: Английский

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Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs

npj Biofilms and Microbiomes, Journal Year: 2021, Volume and Issue: 7(1)

Published: Jan. 11, 2021

Abstract Most bacteria in nature exist biofilms, which are inherently tolerant to antibiotics. There is currently very limited understanding of how biofilms evolve response sub-lethal concentrations antimicrobials. In this study, we use a biofilm evolution model study the effects sub-inhibitory three antibiotics on Salmonella Typhimurium biofilms. We show that rapidly resistance each antibiotic they exposed to, demonstrating strong selective pressure from low concentrations. While all tested select for clinical resistance, there no common mechanism. Adaptation antimicrobials, however, has marked cost other clinically important phenotypes, including formation and virulence. Cefotaxime selects mutants with greatest deficit followed by azithromycin then ciprofloxacin. Understanding impacts exposure will help understand evolutionary trajectories may guide best context. Experimental combination whole-genome sequencing powerful tool prediction associated

Language: Английский

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Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(11), P. 2097 - 2112

Published: Aug. 28, 2024

Language: Английский

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Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(6), P. e1011154 - e1011154

Published: June 20, 2024

Lager yeasts are limited to a few strains worldwide, imposing restrictions on flavour and aroma diversity hindering our understanding of the complex evolutionary mechanisms during yeast domestication. The recent finding diverse S . eubayanus lineages from Patagonia offers potential for generating new lager with different profiles. Here, we leverage natural genetic expand repertoire by including three distinct Patagonian lineages. We used experimental evolution selection desirable traits enhance fermentation profiles novel cerevisiae x hybrids. Our analyses reveal an intricate interplay pre-existing diversity, species-specific mitochondria, de-novo mutations, gene copy variations in sugar metabolism genes, resulting high ethanol production unique Hybrids mitochondria exhibited greater superior fitness post-evolution, analogous commercial Using genome-wide screens parental subgenomes, identified changes IRA2 , IMA1 MALX genes that influence maltose metabolism, increase glycolytic flux consumption evolved Functional validation transcriptome confirmed increased maltose-related expression, influencing maltotriose This study demonstrates industrially viable hybrids wild strains. hybridization, evolution, mitochondrial approach produced capacity expands beer brewing options.

Language: Английский

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Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles

Journal of Molecular Biology, Journal Year: 2019, Volume and Issue: 431(23), P. 4749 - 4759

Published: Feb. 12, 2019

Language: Английский

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Experimental Evolution as a Tool to Investigate Natural Processes and Molecular Functions

Trends in Microbiology, Journal Year: 2019, Volume and Issue: 27(7), P. 623 - 634

Published: March 23, 2019

Language: Английский

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Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

mSystems, Journal Year: 2020, Volume and Issue: 5(3)

Published: June 15, 2020

Our work demonstrated that the specific microbial strains used to construct a microbiome could impact species composition, perturbation responses, and functional outputs of system. These findings suggest 16S rRNA gene taxonomic profiles alone may have limited potential predict dynamics communities because they usually do not capture strain-level diversity. Observations from our synthetic also diversity has drive variability in aesthetics quality surface-ripened cheeses.

Language: Английский

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