Sylvain Brisse

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

Cumulative cgMLST provides increased discrimination of nested phylogenetic groups

This paper introduces a cumulative cgMLST approach to improve discrimination of nested phylogenetic groups by adding conserved loci, showing increased allelic distances and utility for epidemiological analysis.

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.

Modified Elek test improves in-vitro detection of diphtheria toxin

The study modifies the Elek test to improve detection of diphtheria toxin in Corynebacterium species, identifying more toxigenic isolates previously classified as non-toxigenic.

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports co-existence of diverse lineages

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

Pangenome structure and ecological adaptation in the Klebsiella pneumoniae species complex: insights from a geographically and time limited multi-habitat study

This study analyzes the pangenome structure and ecological adaptation of Klebsiella pneumoniae species complex across different habitats, revealing phylogroup- and niche-specific genomic features.

Life identification number (LIN) codes for the genomic taxonomy of Corynebacterium diphtheriae strains

This paper introduces a hierarchical genomic taxonomy system for Corynebacterium diphtheriae using cgMLST-based Life Identification Number (LIN) codes to classify strains at multiple levels of resolution.

No innocent bystanders: pertussis vaccination epitomizes evolutionary parallelisms between Bordetella parapertussis and B. pertussis

This paper shows that Bordetella parapertussis evolved similarly to Bordetella pertussis after pertussis vaccination, including loss of pertactin and changes in regulatory regions.

Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing

This study evaluates ONT R10.4.1 long-read sequencing for accurate genotyping of three respiratory pathogens, showing error rates below 1% for cgMLST.

Genomic Epidemiology and Microevolution of the Zoonotic Pathogen Corynebacterium ulcerans

This study develops a cgMLST scheme for high-resolution genotyping of C. ulcerans and identifies genetic clusters linked to transmission and geographical spread.

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

This study analyzes KpSC populations across human, animal, and marine sources in Norway, showing distinct yet overlapping populations with limited recent transmission between niches.

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.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae

The paper analyzes the genetic diversity and functionality of rmpADC variants in Klebsiella pneumoniae to understand their role in virulence and antimicrobial resistance.

A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex

This paper constructs a comprehensive pangenome-scale metabolic model for the Klebsiella pneumoniae species complex, showing improved accuracy in growth predictions compared to previous models.

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.

Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae

This study evaluates ONT-only assemblies for genomic surveillance of Klebsiella pneumoniae, showing reliable MLST, K type, and AMR detection but challenges in cluster detection.

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

This paper analyzes the genomic evolution of Klebsiella pneumoniae clonal group 147, identifying its global spread and resistance mechanisms through comparative genomics and phylogenetic analysis.

Emergence and global spread of Listeria monocytogenes main clinical clonal complex

This study traces the global spread of Listeria monocytogenes clonal complex 1 (Lm-CC1) through historical data, identifying two waves of expansion linked to livestock trade and cattle farming.

Spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis

The paper analyzes B. pertussis genotype dynamics post-vaccine policy changes, showing fitness shifts and regional diversity patterns.

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

The paper introduces Pathogenwatch, a web tool for genomic surveillance of Klebsiella, showing it identifies drug-resistant clones and vaccine candidate O-types in genomes from low- and middle-income countries.

Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry

The paper introduces a web-based tool for identifying Klebsiella isolates at species complex and phylogroup levels using MALDI-TOF mass spectrometry data.

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

This study identifies and tracks virulence loci encoding siderophore synthesis in K. pneumoniae using genomic surveillance tools.

Population genomics of hypervirulent Klebsiella pneumoniae clonal group 23 reveals early emergence and rapid global dissemination

This study analyzes the population genomics of hypervirulent Klebsiella pneumoniae clonal group 23, revealing its early emergence and global spread through genomic analysis of 98 isolates.

Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

This paper analyzes the genomic diversity and epidemiology of Elizabethkingia anophelis using whole-genome sequencing, revealing sublineages, antimicrobial resistance genes, and CRISPR-based strain subtyping tools.