Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(51)

Published: Dec. 14, 2023

Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR are widespread clinical settings, but their distribution is not random, and certain associations between clones particularly successful. For example, globally spread carbapenem plasmid pOXA-48 can use wide range enterobacterial species as hosts, it usually associated with small number specific

Language: Английский

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Encounter rates and engagement times limit the transmission of conjugative plasmids

PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(2), P. e1011560 - e1011560

Published: Feb. 7, 2025

Plasmid conjugation is a major route for the dissemination of antibiotic resistances and adaptive genes among bacterial populations. Obtaining precise rates thus key to understanding how spread. typically modeled as density-dependent process, where formation new transconjugants depends on rate encounters between donor receptor cells. By analyzing dynamics at different cell concentrations, here we show that this assumption only holds very low densities. At higher becomes limited by engagement time, interval required two successful matings. therefore follows Holling´s Type II functional response, characterized encounter which represent, respectively, density frequency-dependent limits plasmid transmission. Our results demonstrate these parameters are characteristic transfer machinery, rather than entire genome, they robust environmental transcriptional perturbation. Precise parameterization will contribute better propagation antimicrobial resistances.

Language: Английский

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Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Molecular Systems Biology, Journal Year: 2022, Volume and Issue: 19(2)

Published: Dec. 27, 2022

Abstract Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal conjugation. When considered individually, improvements in either mode of can promote how well a plasmid spreads persists. Together, however, the metabolic cost conjugation could create tradeoff that constrains evolution. Here, we present evidence for presence, consequences, molecular basis conjugation‐growth across 40 plasmids derived from clinical Escherichia coli pathogens. We discover most operate below efficiency threshold major growth effects, indicating strong natural selection vertical transfer. Below this threshold, E. demonstrates remarkable tolerance to over four orders magnitude change efficiency. This fades as nutrients become scarce attracts greater share host resources. Our results provide insight into evolutionary constraints directing strategies combat spread antibiotic resistance.

Language: Английский

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A mathematician’s guide to plasmids: an introduction to plasmid biology for modellers

Microbiology, Journal Year: 2023, Volume and Issue: 169(7)

Published: July 28, 2023

Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role genetics evolution. Our understanding of plasmid biology has been furthered greatly by the development mathematical models, there are many questions about plasmids that models would be useful answering. In this review, we present introductory, yet comprehensive, overview suitable for modellers unfamiliar with who want to get up speed begin working on plasmid-related models. addition reviewing diversity genes they carry, their key physiological functions, interactions between host, also highlight selected topics may particular interest areas where is a need theoretical development. The world holds great variety subjects will biologists, introducing new subject help expand existing body theory.

Language: Английский

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Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Dec. 1, 2023

Abstract The ability to effectively represent microbiome dynamics is a crucial challenge in their quantitative analysis and engineering. By using autoencoder neural networks, we show that microbial growth can be compressed into low-dimensional representations reconstructed with high fidelity. These embeddings are just as effective, if not better, than raw data for tasks such identifying bacterial strains, predicting traits like antibiotic resistance, community dynamics. Additionally, demonstrate essential dynamical information of these systems captured far fewer variables traditional mechanistic models. Our work suggests machine learning enable the creation concise high-dimensional facilitate gain new biological insights.

Language: Английский

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Programming Dynamic Division of Labor Using Horizontal Gene Transfer

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(4), P. 1142 - 1151

Published: April 3, 2024

The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. introduction a complex, multistep pathway often imposes substantial burden on the host cell, restraining accumulation productive biomass limiting efficiency. One strategy to alleviate is division labor (DOL) in which different subpopulations carry out parts work together convert substrate into final product. However, maintenance engineered challenging due competition convoluted interstrain population dynamics. Through modeling, we show that dynamic (DDOL), define as DOL between indiscrete populations capable reversible interchange, can overcome these limitations enable robust burdensome, pathways. We propose DDOL be mediated by horizontal gene transfer (HGT) use plasmid genomics uncover evidence utilized natural microbial communities. Our suggests bioengineers harness HGT stabilize synthetic pathways communities, enabling development systems for deployment variety contexts.

Language: Английский

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Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil–plant system

Environmental Geochemistry and Health, Journal Year: 2024, Volume and Issue: 46(11)

Published: Sept. 24, 2024

Language: Английский

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Fitness and adaptive evolution of a Rhodococcus sp. harboring dioxin-catabolic plasmids

World Journal of Microbiology and Biotechnology, Journal Year: 2025, Volume and Issue: 41(2)

Published: Jan. 27, 2025

Language: Английский

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Should I stay or should I go: transmission trade-offs in phages and plasmids

Trends in Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence antibiotic resistance in bacterial populations. For reproductive success, MGEs must balance horizontal vertical transmission. Yet, the cost transmission (metabolic burden or host death) puts these modes at odds. Using virulence-transmission trade-off (VTT) theory, we identify three groups environmental variables affecting between transmission: density, physiology, competitors. We find that general theoretical predictions optimal response to cues align with experimental evidence on regulation by phages plasmids. further highlight gaps theory experiments, differences suggest areas for future research.

Language: Английский

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A bayesian approach for parameterizing and predicting plasmid conjugation dynamics

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 3, 2025

Population dynamic models that explain and predict the spread of conjugative plasmids are pivotal for understanding microbial evolution engineering microbiomes. However, prediction uncertainty these has rarely been assessed. We adopt a Bayesian approach, employing Markov Chain Monte Carlo (MCMC), to parameterize model plasmid conjugation dynamics. This approach treats parameters as random variables whose probability distributions informed by data on population These allow us estimate credible intervals model's predictions. validated this using synthetic with known parameter values experimental mini-RK2, miniaturized counterpart well-characterized widely used RK2 plasmid. Our methodology accurately estimated data, predictions were robust across time scales initial conditions. Incorporating long-term enhances precision estimates related loss accuracy For correctly explained predicted most trends, albeit broader intervals. also improves ranges parameters. in some cases, such growth cells plasmid, inclusion can lead stronger correlations potential identifiability issues between key Overall, our method allows deeper investigation dynamics could potentially be generalized study other mobile genetic elements.

Language: Английский

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