X. Didelot

Presence of phage-plasmids in multiple serovars of Salmonella enterica

This study identifies phage-plasmids in multiple Salmonella serovars, showing their prevalence and serovar-specific distribution, with implications for antimicrobial resistance transmission.

Emergence of Acinetobacter baumannii International Clone 10 predominantly found in the Middle East

The paper reports genomic and epidemiological data on a novel Acinetobacter baumannii international clone, IC10, predominantly found in the Middle East.

Inference of multiple mergers while dating a pathogen phylogeny

This paper develops a method to detect multiple merger events in pathogen phylogenies and improves dating by incorporating these events, validated on simulated and real datasets.

The inter-continental population dynamics of Neisseria gonorrhoeae

This study reconstructs the global population dynamics of Neisseria gonorrhoeae using phylogenomic analysis, revealing expanding effective population size and distinct transmission patterns between Norway and Victoria, Australia.

Inference of infectious disease transmission using multiple genomes per host

This paper introduces a method to infer infectious disease transmission networks using multiple genomes per host, showing improved accuracy with more genomes and applying it to real outbreaks.

Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data

This paper estimates the fitness cost and benefit of antimicrobial resistance using genomic data from Neisseria gonorrhoeae, showing that fluoroquinolone resistance could be safely used in a minority of cases.

Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease

This paper introduces a method to distinguish imported from locally acquired infectious disease cases using genomic data from a single location, showing good sensitivity and specificity.

Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks

This study shows that incorporating within-host genetic diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

Phylogenetic analysis of the origin and spread of plague in Madagascar

This study uses Bayesian phylogenetics to trace the origin and spread of plague in Madagascar, identifying two independent reintroductions from the Central Highlands to Mahajanga in the early 1980s.

The bounded coalescent model: conditioning a genealogy on a minimum root date

The paper introduces a new algorithm for simulating the bounded coalescent model directly, showing improved computational efficiency and providing methods to calculate probabilities under this model.

A scalable analytical approach from bacterial genomes to epidemiology

The paper presents a scalable approach for genomic epidemiology analyses of bacterial pathogens, emphasizing the construction of dated phylogenies and computational efficiency.

Bayesian inference of clonal expansions in a dated phylogeny

The paper develops a Bayesian model to infer clonal expansions in phylogenies and applies it to simulated and real datasets.

A two-hit epistasis model prevents core genome disharmony in recombining bacteria

The paper shows that recombination in bacteria can overcome genomic disharmony through a two-hit epistasis model, allowing beneficial gene combinations to be reinstated in new genetic backgrounds.

Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

This study investigates antimicrobial resistance in Corynebacterium diphtheriae by analyzing genomic and phenotypic data from 247 strains, identifying resistance mechanisms and plasmids.

The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies

This study identifies three ancient, toxigenic genomospecies within C. difficile using global phylogenomic analysis, reshaping its taxonomy and understanding of toxin gene evolution.

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

This paper reclassifies Pseudorhizobium species based on genomic analysis and identifies key functions for adaptation to extreme environments.

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

The paper investigates a hospital outbreak of carbapenem-resistant Enterobacteriales, identifying an OXA-48 plasmid in E. coli ST399 as the main driver, with evidence of plasmid conjugation and clonal expansion.

Speeding up Inference of Homologous Recombination in Bacteria

The paper improves inference under the ClonalOrigin model by applying a new computational method to address the limitations of the Reversible-Jump Markov Chain Monte Carlo algorithm.

Identification of hidden population structure in time-scaled phylogenies

This paper introduces a statistical test to detect hidden population structure in time-scaled phylogenies and applies it to HIV-1 and Neisseria gonorrhoeae data to identify outbreaks and antimicrobial resistance patterns.

Vaccination against antibiotic resistant gonorrhoea for men who have sex with men in England: a modelling study

This study models vaccination strategies for antibiotic-resistant gonorrhoea in MSM in England, showing that even partially protective vaccines could significantly reduce incidence under various resistance scenarios.

The speciation and hybridization history of the genus Salmonella

This study investigates the speciation and hybridization history of Salmonella, identifying eleven phylogroups and revealing complex hybridization events that challenge traditional speciation models.

Why panmictic bacteria are rare

The paper estimates recombination scaled effective population size in 21 bacterial species and finds only two show signs of panmixia, suggesting panmixia is unstable in bacteria.

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

The paper investigates the evolutionary history of Clostridium difficile RT078, finding that tetracycline resistance genes, particularly tetM, were acquired independently in multiple clonal expansions, contributing to its increased prevalence.

The global distribution and spread of the mobilized colistin resistance gene mcr-1

The paper analyzes the global spread of the mcr-1 gene by sequencing isolates and phylogenetic analysis, finding all mcr-1 elements originated from a single mobilization event in the mid-2000s.

Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

The paper introduces non-parametric models for estimating pathogen population size dynamics and links growth rates to antibiotic use, showing a correlation between S. aureus growth and beta-lactam prescriptions.

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination

This paper introduces a phylogenetic method for microbial GWAS that accounts for population structure and recombination, showing improved power and specificity over existing methods.

Quantifying The Fitness Benefit And Cost Of Cefixime Resistance In Neisseria gonorrhoeae To Inform Prescription Policy

This study estimates the fitness costs and benefits of cefixime resistance in Neisseria gonorrhoeae using a model of transmission dynamics in MSM, finding that resistance provides a fitness benefit when cefixime is used.