J. Corander

Basic reproduction number for pandemic Escherichia coli clones varies markedly and can be comparable to pandemic influenza viruses

The paper estimates the basic reproduction number (R0) for pandemic E. coli clones and finds that ST131-A has an R0 comparable to pandemic influenza viruses.

Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork

This paper develops a genomic autogenous vaccine for poultry to reduce Campylobacter, showing reduced extra-intestinal survival genes and meat surface survival in vaccinated flocks.

Plasmid-driven strategies for clone success in Escherichia coli

The paper uses long-read sequencing to analyze plasmids and chromosomes in E. coli over two decades, revealing long-term plasmid-lineage associations and success strategies.

Multi-drug resistant E. coli displace commensal E. coli from the intestinal tract, a trait associated with elevated levels of genetic diversity in carbohydrate metabolism genes.

This study shows that multi-drug resistant E. coli outcompetes non-MDR E. coli in the gut, linked to higher genetic diversity in carbohydrate metabolism genes.

The population-level impact of Enterococcus faecalis genetics on intestinal colonisation and extraintestinal infection

This study investigates the genetic factors influencing E. faecalis intestinal colonization and extraintestinal infection using GWAS and heritability analysis across 750 isolates.

The highly diverse and complex plasmid population found in Escherichia coli colonising travellers to Laos and their role in antimicrobial resistance gene carriage

This study characterizes the diverse plasmid population in ESBL-producing E. coli from travellers to Laos, revealing AMR gene carriage and potential for global AMR spread.

Strong pathogen competition in neonatal gut colonisation

This study quantifies strain-level colonisation dynamics of gut pathogens in neonates, finding strong competition and some synergies, and reveals pathogenic potential differences among ExPEC clones.

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

The paper introduces Panstripe, a method to robustly analyze gene gain and loss rates in prokaryotic pangenomes, accounting for sampling bias and annotation errors.

Evolution of chlorhexidine susceptibility and of the EfrEF operon among Enterococcus faecalis from diverse environments, clones and time spans

This study examines CHX susceptibility and ChlR-EfrEF variability in E. faecalis isolates from diverse environments, finding increased tolerance in food chain and recent human isolates.

One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment

This study models Klebsiella transmission across human, animal, and environmental sources, finding limited AMR spread outside clinical settings and human-to-human transmission dominance.

A high-throughput multiplexing and selection strategy to complete bacterial genomes

This paper evaluates a high-throughput multiplexing strategy using Oxford Nanopore Technologies to complete bacterial genomes, showing improved assembly contiguity and completeness.

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 analysis of Legionella pneumophila reveals the basis of resistance to complement-mediated killing

This study identifies the gene lag-1 as a key determinant of Legionella pneumophila's resistance to complement-mediated killing through population genomic and functional analyses.

Co-evolutionary signals from Burkholderia pseudomallei genomics identify its survival strategies and highlight improving environmental health as prevention policy

This study identifies co-selected gene pairs in Burkholderia pseudomallei genomes that enhance survival under nutrient stress, linking environmental factors to melioidosis prevalence.

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

The paper tests whether negative frequency-dependent selection and asymmetrical recombination can explain the stability of multi-strain bacterial populations using simulations and genomic data.

The binding mechanism of Streptococcus suis accessory virulence factor and adhesin SadP to globotetraosylceramide

This study identifies the molecular mechanism by which SadP adhesin subtype PN binds Gb4, revealing a key role for Asn-285 in this interaction and its potential for targeted intervention against invasive S. suis strains.

The effect of recombination on the evolution of a population of Neisseria meningitidis

This study analyzes 2,839 Neisseria meningitidis genomes to show recombination's role in genome dynamics and population structure, with implications for vaccine effectiveness and public health surveillance.

Predicting evolution using frequency-dependent selection in bacterial populations

The paper predicts changes in pneumococcal populations after vaccination by analyzing accessory gene frequencies under negative frequency-dependent selection.

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions

The paper tracks MDR-GN colonization in travelers in real time, finding frequent transient acquisitions and strain replacement.

Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions

This paper introduces a joint modeling framework for bacterial GWAS that improves statistical power and phenotype prediction while maintaining interpretability and computational efficiency.

Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

This paper describes two new Klebsiella species, K. spallanzanii and K. pasteurii, based on genomic and biochemical analyses of phylogroups Ko3 and Ko4, with type strains isolated from various sources.

Designing ecologically-optimised vaccines using population genomics

This paper shows that vaccines designed using population genomics and ecological models can better reduce IPD and antibiotic-resistant disease by preventing serotype replacement.

Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

The paper identifies strong signatures of positive selection in Neisseria gonorrhoeae by analyzing fine-scale haplotype structure and linkage patterns between nonsynonymous alleles.

Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

This study identifies negative frequency-dependent selection in Escherichia coli ST131 as a key driver of its evolutionary success and adaptation to different ecological niches.

Genomic determinants of sympatric speciation of the Mycobacterium tuberculosis complex across evolutionary timescales.

This study identifies genomic factors driving sympatric speciation in Mycobacterium tuberculosis complex across evolutionary timescales, highlighting the role of phoR in virulence and adaptation.

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

The paper introduces mlplasmids, an SVM-based tool to classify short-read WGS contigs as plasmid- or chromosome-derived in bacterial species, achieving high accuracy across three species.

PANINI: Pangenome Neighbor Identification for Bacterial Populations

PANINI identifies bacterial population neighbours using machine learning, integrating core and accessory genome data with metadata for epidemiological analysis.

The contribution of genetic variation of Streptococcus pneumoniae to the clinical manifestation of invasive pneumococcal disease

This study identifies pneumococcal genetic variants associated with specific clinical outcomes of invasive pneumococcal disease using genome-wide association studies and validation in multiple cohorts.

Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis

The paper analyzes global Yersinia pseudotuberculosis genomes to show phylogeographic splits and lineage formation driven by CRISPR clusters, with limited genetic exchange between lineages.

Weak epistasis may drive adaptation in recombining bacteria

This study shows that weak epistasis can influence adaptation in recombining bacteria, even when recombination is frequent, due to limited transfer of genetic segments.