Quantifying the genomic determinants of fitness inE. coliST131 using phylodynamics DOI Creative Commons
Lenora Kepler, Manuel López Jara, Bejan Mahmud

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 10, 2024

Abstract Antimicrobial resistant pathogens such as Escherichia coli sequence type 131 (ST131) pose a serious threat to public health globally. In the United States, ST131 acquired multiple antimicrobial resistance (AMR) genes and rapidly grew its current high prevalence in healthcare settings. Notably, this coincided with introduction widespread use of antibiotics fluoroquinolones, suggesting AMR major driver ST131’s expansion. Yet, within ST131, there remains considerable diversity between strains profiles their repertoires virulence factors, stress plasmids, other accessory elements. Understanding which genomic features contribute competitive advantage relative effects on population-level fitness therefore poses challenge. Here we phylodynamic birth-death models estimate different lineages from bacterial phylogenies. By extending these methods allow shape fitness, further quantify contribution individual fitness. Our analysis indicates that while many elements, including various genes, have all contributed substantially rapid growth, increases are largely attributable mutations gyrase A confer fluoroquinolones. Author summary is pandemic lineage E. has spread globally now responsible for large percentage blood urinary tract infections cannot be treated common antibiotics. While antibiotic undoubtedly given edge, importance compared factors shaping pathogen’s growth or transmission potential (i.e. fitness) often difficult measure natural Here, present method allows us look at entire spectrum determining each component overall results suggest widely used class antibiotics, provides disproportionately more moderate effects. what determines insights can curb monitor emerging due shared enhancing attributes.

Язык: Английский

Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria DOI Creative Commons
Aída Alonso-del Valle, Laura Toribio-Celestino, Anna Quirant

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(51)

Опубликована: Дек. 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

Язык: Английский

Процитировано

28
Vertical and horizontal gene transfer tradeoffs direct plasmid fitness DOI Creative Commons
Jonathan H. Bethke, Helena Riuró, Ryan Tsoi

и другие.

Molecular Systems Biology, Год журнала: 2022, Номер 19(2)

Опубликована: Дек. 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.

Язык: Английский

Процитировано

39
A mathematician’s guide to plasmids: an introduction to plasmid biology for modellers DOI
Ian Dewan, Hildegard Uecker

Microbiology, Год журнала: 2023, Номер 169(7)

Опубликована: Июль 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.

Язык: Английский

Процитировано

19
Understanding bacterial ecology to combat antibiotic resistance dissemination DOI
Dongbo Wang, Xiangming Zhou, Qizi Fu

и другие.

Trends in biotechnology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

1
Encounter rates and engagement times limit the transmission of conjugative plasmids DOI Creative Commons
Jorge Rodríguez-Grande, Yelina Ortiz, Daniel Garcia-Lopez

и другие.

PLoS Genetics, Год журнала: 2025, Номер 21(2), С. e1011560 - e1011560

Опубликована: Фев. 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.

Язык: Английский

Процитировано

1
Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics DOI Creative Commons

Yasa Baig,

Helena Riuró, Helen Xu

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 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.

Язык: Английский

Процитировано

14
Programming Dynamic Division of Labor Using Horizontal Gene Transfer DOI
Grayson S. Hamrick, Rohan Maddamsetti,

Hye-In Son

и другие.

ACS Synthetic Biology, Год журнала: 2024, Номер 13(4), С. 1142 - 1151

Опубликована: Апрель 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.

Язык: Английский

Процитировано

6
Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil–plant system DOI

Lei Wang,

Lina Yu, Baiyan Cai

и другие.

Environmental Geochemistry and Health, Год журнала: 2024, Номер 46(11)

Опубликована: Сен. 24, 2024

Язык: Английский

Процитировано

5
IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in Escherichia coli DOI Creative Commons
Margaux Allain, Thibaut Morel‐Journel, Bénédicte Condamine

и другие.

Antimicrobial Agents and Chemotherapy, Год журнала: 2024, Номер 68(10)

Опубликована: Авг. 28, 2024

It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contributes to global plasmid fitness. As conjugative IncC plasmids are important for the spread of multidrug resistance (MDR), in a broad range bacterial hosts, we investigated two multidrug-resistant according their backbones MDR-region rearrangements, upon entry into new host. We observed genome deletions after conjugation three diverse natural

Язык: Английский

Процитировано

3
The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells DOI

Heather D. Curtsinger,

Sofía Martínez‐Absalón,

Yuchang Liu

и другие.

BioEssays, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 11, 2024

Abstract Bacterial conjugation, wherein DNA is transferred between cells through direct contact, highly prevalent in complex microbial communities and responsible for spreading myriad genes related to human environmental health. Despite their importance, much remains unknown regarding the mechanisms driving spread persistence of these plasmids situ. Studies have demonstrated that transferring, acquiring, maintaining a plasmid imposes significant metabolic burden on host. Simultaneously, emerging evidence suggests presence conjugative can also provide both obvious unexpected benefits host local community. Combined, this highlights continuous cost‐benefit tradeoff at population level, likely contributing overall abundance long‐term persistence. Yet, while burdens causes, are widely studied, attendant potential advantages less clear. Here, we summarize current perspectives plasmids’ then highlight lesser‐appreciated yet critical plasmid‐mediated may provide. We argue largely unexplored fundamental theory populations engineering applications therefore warrants further detailed study.

Язык: Английский

Процитировано

3