S. Brisse

Phenotypic and genomic changes in enteric Klebsiella populations during long-term ICU patient hospitalization: The role of RamR regulation

This study tracks genomic and phenotypic changes in Klebsiella populations in ICU patients, identifying a ramR mutation linked to antimicrobial resistance and persistence.

Life Identification Numbers: A bacterial strain nomenclature approach

The paper proposes the Life Identification Number (LIN) system as a stable, multilevel strain taxonomy for bacterial pathogens based on core genome MLST to improve epidemiological tracking and nomenclature consistency.

Triplex real-time PCR ZKIR-T assay for simultaneous detection of the Klebsiella pneumoniae species complex and identification of K. pneumoniae sensu stricto

The paper develops a triplex real-time PCR assay (ZKIR-T) to detect all Klebsiella pneumoniae species complex members and specifically identify K. pneumoniae sensu stricto.

A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence

The paper develops a bioinformatics pipeline to analyze C. diphtheriae genomes, revealing virulence and resistance heterogeneities and emerging threats.

Corynebacterium of the diphtheriae complex in companion animals: clinical and microbiological characterization of 64 cases from France

This paper characterizes 64 cases of Corynebacteria of the diphtheriae complex (Cdc) infections in companion animals, identifying C. ulcerans as a zoonotic risk and highlighting the need for improved detection and management.

Genomic epidemiology of Corynebacterium diphtheriae in New Caledonia

This study analyzes C. diphtheriae isolates in New Caledonia, identifying tox-positive strains linked to travel and local transmission, while most isolates are non-toxigenic and antibiotic-susceptible.

Phages against non-capsulated Klebsiella pneumoniae: broader host range, slower resistance

This study isolates and compares phages targeting capsule-deficient Klebsiella pneumoniae strains, finding they have broader host ranges and slower resistance emergence than phages targeting capsule-expressing strains.

Is it the same strain? Defining genomic epidemiology thresholds tailored to individual outbreaks

This paper introduces a framework to determine genomic relatedness thresholds for outbreak strains based on outbreak-specific parameters, improving accuracy in identifying clusters.

Genomic library of Bordetella

The paper creates a unified genomic library of Bordetella strains, revealing new species and phylogenetic insights, and provides resources for studying Bordetella evolution and epidemiology.

High prevalence of Klebsiella pneumoniae in European food products: a multicentric study comparing culture and molecular detection methods

The paper identifies high prevalence of Klebsiella pneumoniae in European chicken meat and salad samples using culture and molecular methods, revealing genetic diversity and potential transmission within the food sector.

Transmission of Klebsiella strains and plasmids within and between Grey-headed flying fox colonies

This study identifies transmission clusters and plasmid exchange among Klebsiella strains in Grey-headed flying foxes, showing gene flow between bat and human-associated isolates.

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

The paper curates 37 strain-specific genome-scale metabolic models for Klebsiella pneumoniae species complex isolates, revealing strain-specific metabolic differences and gene essentiality.

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 dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains

The paper introduces a dual barcoding system for bacterial strain classification using Klebsiella pneumoniae genomes, defining sublineages with genetic dissimilarity thresholds and providing a publicly accessible taxonomy platform.

Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae

This study develops a cgMLST scheme for C. diphtheriae to track outbreaks and reveals cryptic transmission chains and sublineages.

Leakiness at the human-animal interface in Southeast Asia and implications for the spread of antibiotic resistance

The paper identifies antibiotic resistance elements shared between humans and animals in Cambodia, highlighting the need to address human-animal interface leaks to combat antimicrobial resistance.

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 ZKIR Assay, a novel Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples

The paper develops the ZKIR assay, a real-time PCR method for detecting Klebsiella pneumoniae in environmental samples, showing it is more sensitive than culture-based methods and reveals genetic differences between environmental and clinical isolates.

Description of Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex

The paper describes a new Corynebacterium species, C. rouxii, based on genomic and phenotypic analysis of six isolates previously classified as C. diphtheriae biovar Belfanti.

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.

Optimization and validation of a quadruplex real-time PCR assay for the diagnosis of diphtheria

The paper improves a quadruplex real-time PCR assay for diphtheria diagnosis by adding an internal control and validates its performance across multiple labs and platforms.

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.

Carriage of a single strain of non-toxigenic Corynebacterium diphtheriae biovar Belfanti (Corynebacterium belfantii) in four patients with cystic fibrosis

This study identifies a non-toxigenic C. belfantii strain persistently colonizing four CF patients and transmitted within a CF care center over six years.

Description of Klebsiella africanensis sp. nov., Klebsiella variicola subsp. tropicalensis subsp. nov. and Klebsiella variicola subsp. variicola subsp. nov.

The paper describes three new bacterial taxa within the Klebsiella genus based on genomic and biochemical analyses.

Identification of Klebsiella pneumoniae complex members using MALDI-TOF mass spectrometry

This study identifies MALDI-TOF mass spectrometry biomarkers for distinguishing Klebsiella pneumoniae complex phylogroups with high sensitivity and specificity.

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

The paper analyzes the prevalence and evolution of yersiniabactin-encoding mobile elements in Klebsiella pneumoniae using whole genome sequences, identifying diverse lineages and novel dispersal mechanisms.

Gene composition as a potential barrier to large recombinations in the bacterial pathogen Klebsiella pneumoniae

This study analyzes 834 Klebsiella pneumoniae genomes to investigate the frequency, distribution, and dynamics of large recombination events, finding that gene composition influences the success of such events.

Outbreak of invasive wound mucormycosis in a burn unit due to multiple strains of Mucor circinelloides f. circinelloides resolved by whole genome sequencing

This study used whole genome sequencing to investigate an outbreak of invasive wound mucormycosis in a burn unit, revealing multiple strains from an environmental reservoir rather than direct patient-to-patient transmission.