F. Blanquart

Persistent, Private and Mobile genes: a model for gene dynamics in evolving pangenomes

This paper introduces a model for bacterial pangenome evolution and applies it to Salmonella genomes to classify genes based on their evolutionary dynamics.

Evolution of Virulence in Emerging Epidemics: From Theory to Experimental Evolution and Back

This study combines experimental, theoretical, and statistical approaches to improve the quantitative validation of models predicting virulence evolution in bacteriophages.

Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time series

This study tracks E. coli dynamics in a human gut over 20 years, showing how strain properties and environmental factors influence diversity and persistence.

Residence-colonization trade-off and niche differentiation enable the coexistence of Escherichia coli phylogroups in healthy humans

The paper identifies a residence-colonization trade-off and niche differentiation among E. coli phylogroups in healthy humans, enabling their coexistence through equalizing and stabilizing mechanisms.

Within-host density and duration of colonization of multidrug-resistant Enterobacterales acquired during travel to the tropics

The paper studies within-host dynamics of multidrug-resistant Enterobacterales in travelers, finding that resistant strains coexist with sensitive ones for months before abrupt clearance.

A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance

This paper develops a stochastic model to analyze how antibiotic dose, mode of action, and bacterial competition influence resistance evolution, finding that resistance survival depends on density regulation and drug type.

The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

This study identifies genetic determinants of Escherichia coli's ability to cause bloodstream infections using genomic and machine learning analyses of clinical isolates.

Genetic determinism of phage-bacteria coevolution in natural populations

The paper investigates phage-bacteria coevolution in natural populations, finding that phage and host genomes exhibit gene content variation and that negative-frequency dependent selection drives coevolutionary dynamics.

Success of Escherichia coli O25b:H4 ST131 clade C associated with a decrease in virulence

This study compares virulence and colonization abilities of antibiotic-susceptible clade B and multidrug-resistant clade C ST131 E. coli strains, finding clade C strains have reduced virulence and are outcompeted by clade B in vivo.

Epidemiological dynamics of bacteriocin competition and antibiotic resistance

This study examines bacteriocin dynamics and their link to antibiotic resistance in epidemiological models, finding that diversity can be maintained through competition-colonisation trade-offs rather than rock-paper-scissors dynamics.

The effect of habitat choice on evolutionary rescue in subdivided populations

This study models how habitat choice affects evolutionary rescue in subdivided populations, finding that dispersal rates and immigration biases influence rescue probability in three distinct phases.

Evolution of virulence in emerging epidemics: inference from an evolution experiment

The paper estimates epidemiological parameters of two bacteriophage strains from an evolution experiment to understand virulence evolution in epidemics.

On the evolutionary ecology of multidrug resistance in bacteria

This paper explains high multidrug resistance frequencies in bacteria through ecological models of strain competition, showing that resistance to different antibiotics often co-occurs due to stable coexistence rather than competitive exclusion.