Biology subjects

Pena-Miller, R.

Publications and source records attributed to Pena-Miller, R..

10 recordsLinked to original sources

bioRxiv2026

Fitness effects of antimicrobial resistance genes in changing environments

The evolutionary success of antimicrobial resistance (AMR) genes is generally seen as a trade-off between their function in the presence and their cost in the absence of antibiotics. Mobile integrons are genetic elements that recruit and disseminate dozens of AMR genes among Gram-negative pathogens. Here, we have measured the fitness effects of 136 integron genes conferring resistance against several antibiotic families. We have found a significant proportion having neutral and positive effects in the absence of antibiotics. We confirmed this using a mouse model, where we also observed cases of changes in the sign of fitness effects. This led us to unveil that oxygen availability modulates the cost of AMR genes. Using a stochastic model, we show that fluctuating aerobic/anaerobic conditions can rescue AMR genes in the absence of selective pressure. Here we provide a comprehensive analysis of the cost of AMR at the gene level challenging the traditional fitness-resistance trade-off hypothesis.

microbiology↗

bioRxiv2025

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate

Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacterial ecology and evolution. Theory suggests that plasmids might evolve faster than chromosomes, as the mutation rate per gene should proportionally increase with plasmid copy number. However, the segregation of plasmid copies to daughter cells is random, introducing an additional layer of genetic drift, known as segregational drift, that might delay plasmid evolution. The interplay between plasmid mutational supply and segregational drift determines the evolutionary rate of plasmid-encoded genes, yet the relative contribution of these opposite forces in plasmid evolution remains unclear. Here, we took a classical population genetics framework to devise a mathematical approximation that predicts the fate of plasmid mutations in bacterial populations. We then validate these predictions by integrating computational, experimental, and bioinformatic approaches. Our findings show that plasmid mutation rates scale logarithmically with copy number: while increasing copy number elevates the mutation rate, the effect diminishes at higher copy numbers, where additional copies yield only marginal increases. Nonetheless, the supply of new mutations consistently surpasses the impact of segregational drift across all copy number levels. These results underscore plasmids as powerful platforms for bacterial evolvability and help explain their remarkable prevalence across microbial phylogeny.

microbiology↗

bioRxiv2025

Conditional filamentation enhances bacterial survival in toxic environments

Bacterial phenotypic plasticity enables rapid adaptation to fluctuating environments. Filamentation, a shape-shifting response commonly observed under stress, has often been viewed as a byproduct of cellular damage. However, filamentation might also confer survival advantages by influencing toxin accumulation dynamics. In this study, we examined the adaptive value of filamentation in Escherichia coli using a genetically controlled, SOS-independent induction system to compare isogenic, yet phenotypically distinct cells. By integrating mathematical modeling, single-cell microfluidics, and time-resolved flow cytometry, we evaluate bacterial survival under heavy metal and {beta} -lactam antibiotic stress. Our results show that filamentation can improve survival by decreasing the surface area-to-volume ratio, which slows intracellular toxin accumulation and extends the time available for stress response activation or for external toxin levels to dissipate. These findings suggest that filamentation serves as an effective morphological strategy to transiently withstand environmental toxicity, reinforcing its broader role in bacterial stress adaptation.

microbiology↗

bioRxiv2023

Differences in vertical and horizontal transmission dynamics shape plasmid distribution in clinical enterobacteria

Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild type enterobacterial strains isolated from hospitalized patients. Our results reveal significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities. Significance statementConjugative plasmids disseminate AMR genes across bacterial pathogens. Understanding the rules governing plasmid dynamics in bacterial communities is therefore crucial to controlling the global AMR crisis. In this study, we analyzed the dynamics of an AMR plasmid of great clinical relevance, pOXA-48, in a collection of wild type bacteria recovered from hospitalized patients. We reported a high degree of variability in two key plasmid-associated phenotypes, AMR level and conjugation ability, across the collection of clinical bacteria. Using simulations based on the experimental results, we studied how successful associations between AMR plasmids and clinical strains can arise in bacterial communities. Our results revealed that accounting for variability in plasmid-associated phenotypes help to understand the evolution of AMR in clinical settings.

microbiology↗

bioRxiv2022

Antibiotic heteroresistance generated by multi-copy plasmids

Heteroresistance - in which a clonal bacterial population contains a cell subpopulation with higher resistance to antibiotics than the main population - is a growing clinical problem that complicates susceptibility determination and threatens therapeutic success. Despite the high prevalence of heteroresistance in clinical settings, the underlying genetic mechanisms that stably maintain heterogeneous bacterial populations are poorly understood. Using fluorescence microscopy, single-cell microfluidics, and quantitative image analysis, we show that random replication and segregation of multicopy plasmids produce populations of bacterium Escherichia coli MG1655 in which cells with low-and high-plasmid copy numbers stably co-exist. By combining stochastic simulations of a computational model with high-throughput single-cell measurements of blaTEM-1 expression, we show that copy number variability confers the bacterial population with transient resistance to a lethal concentration of a {beta} -lactam antibiotic. Moreover, this surviving, high plasmid copy minority is capable of regenerating a heterogeneous bacterial population with low and high plasmid copy numbers through segregational instability, rapidly alleviating the fitness burden of carrying large numbers of plasmids. Our results provide further support for the tenet that plasmids are more than simple vehicles for horizontal transmission of genetic information between cells, as they can also drive bacterial adaptation in dynamic environments by providing a platform for rapid amplification and attenuation of gene copy number that can accelerate the rate of resistance adaptation and can lead to treatment failure.

microbiology↗

bioRxiv2022

Plasmid stability in fluctuating environments:population genetics of multi-copy plasmids

Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial sub-stances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, non-transmissible plasmids tend to be carried in multiple copies per cell, with the added benefit of exhibiting increased gene dosage and resistance levels. But carrying multiple copies also results in a high metabolic burden to the bacterial host, therefore reducing the overall fitness of the population. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? In this manuscript, we address this question by postulating and analyzing a population genetics model to evaluate the interaction between selective pressure, the number of plasmid copies carried by each cell, and the metabolic burden associated with plasmid bearing in the absence of selection for plasmid-encoded traits. Parameter values of the model were estimated experimentally using Escherichia coli K12 carrying a multicopy plasmid encoding for a fluorescent protein and blaTEM-1, a gene conferring resistance to {beta}-lactam antibiotics. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we show that plasmid copy number is a highly optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.

evolutionary biology↗

bioRxiv2020

The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities

Introductory paragraphPlasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the distribution of fitness effects (DFE) for the major antibiotic resistance plasmid pOXA-48 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48 produced an overall reduction in bacterial fitness, the DFE was dominated by quasi-neutral effects, and beneficial effects were observed in several isolates. Incorporating these data into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. Moreover, genomic results showed a link between plasmid fitness effects and bacterial phylogeny, helping to explain pOXA-48 epidemiology. Our results provide a simple and general explanation for plasmid persistence in natural bacterial communities.

microbiology↗

bioRxiv2020

Dynamic phenotypic heterogeneity generated by delayed genetic oscillations

Eukaryotes and prokaryotes exploit the ability of genetically identical cells to exhibit different phenotypes in order to enhance their survival. However, the mechanisms by which cells transition from one phenotype to another remain unclear. Canonical models of this dynamic posit that molecular fluctuations provide the noise that drives the cell out of one stable state and into another. Stochastic processes generated by canonical models should, therefore, be good descriptors of phenotype dynamics and between-state transitions should become more likely at greater noise amplitude, for instance at higher extracellular temperatures. To test these predictions, we observed temporal expression dynamics of the promoter of a flagellum gene, fliC, in a microfluidic device using Salmonella enterica serovar Typhimurium and green fluorescent protein (GFP). Our observations show that while cells can exhibit multistable phenotypes, including stable fliC-OFF and fliC-ON states characterised by low and high GFP levels, respectively, between-state transitions can exhibit oscillatory dynamics whose return statistics do not conform to canonical theories. For example, here the fliC-ON state was more frequent following a temperature increase. To better understand our data we developed different dynamical frameworks to predict fliC expression data. We conclude that a stochastic dynamical system tailored to the genetic network of fliC is better suited to our data than prior theories where dynamical features, like oscillations and pulsing, are driven by inevitable delays in the post-translational regulation of fliC. Thus, while transcriptional noise promotes phenotypic heterogeneity, as we show here, regular features like oscillatory heterogeneity can result from delays that fundamental molecular processes impose upon a cells gene regulatory architecture.

systems biology↗

bioRxiv2019

Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria

Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium and, as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. Moreover, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalogue of genes encoded on MGEs, dictating bacterial evolution through HGT.

microbiology↗

bioRxiv2019

Canonical host-pathogen tradeoffs subverted by mutations with dual benefits

Tradeoffs between life history traits impact diverse biological phenomena, including the maintenance of biodiversity. We sought to study two canonical tradeoffs in a model host-parasite system consisting of bacteriophage lambda and Escherichia coli: i) parasite resistance for growth and ii) phage infectivity for host-range. We report that these previously hypothesised tradeoffs are, in fact, tradeups. While the observation of tradeups was surprising, they should be expected because if traits X and Y tradeoff, so too traits Y and Z, then X and Z will tradeup. By considering five different E. coli trait correlations we uncovered several tradeups and tradeoffs. Using mathematical models, we establish that tradeups need not inhibit biodiversity, as previously thought, and can help maintain it through high-dimensional trait interactions. We provide a mechanistic explanation for how tradeups emerge and give reasons for why tradeups can even evolve in well-adapted genomes.\n\nAll data will be posted at https://github.com/rebear217 and mirrored at http://people.exeter.ac.uk/reb217/rebHomePage/data.html on acceptance.

evolutionary biology↗