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  1. Article ; Online: Multidrug-resistant toxigenic

    Arcari, Gabriele / Hennart, Mélanie / Badell, Edgar / Brisse, Sylvain

    Microbial genomics

    2023  Volume 9, Issue 1

    Abstract: Antimicrobial therapy is important for case management of diphtheria, but knowledge on the emergence of multidrug-resistance ... ...

    Abstract Antimicrobial therapy is important for case management of diphtheria, but knowledge on the emergence of multidrug-resistance in
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Corynebacterium diphtheriae/drug effects ; Corynebacterium diphtheriae/genetics ; Genomic Islands ; Drug Resistance, Multiple, Bacterial
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-02-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000923
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Multidrug-resistant

    Brémont, Sylvie / Passet, Virginie / Hennart, Mélanie / Fonteneau, Laure / Toubiana, Julie / Badell, Edgar / Brisse, Sylvain

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

    2023  Volume 28, Issue 46

    Abstract: We describe 10 unlinked cases ... ...

    Abstract We describe 10 unlinked cases of
    MeSH term(s) Humans ; Corynebacterium diphtheriae/genetics ; Diphtheria/diagnosis ; Diphtheria/drug therapy ; Diphtheria/epidemiology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; France/epidemiology ; Mali
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-11-16
    Publishing country Sweden
    Document type Journal Article
    ZDB-ID 1338803-4
    ISSN 1560-7917 ; 1025-496X
    ISSN (online) 1560-7917
    ISSN 1025-496X
    DOI 10.2807/1560-7917.ES.2023.28.46.2300615
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Corynebacteria of the

    Museux, Kristina / Arcari, Gabriele / Rodrigo, Guido / Hennart, Melanie / Badell, Edgar / Toubiana, Julie / Brisse, Sylvain

    Microbiology spectrum

    2023  Volume 11, Issue 3, Page(s) e0000623

    Abstract: Corynebacteria of ... ...

    Abstract Corynebacteria of the
    MeSH term(s) Humans ; Animals ; Dogs ; Horses ; Rats ; Rhinitis ; Corynebacterium diphtheriae ; Diphtheria/microbiology ; Anti-Bacterial Agents/pharmacology ; France/epidemiology ; Mammals
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.00006-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genomic Epidemiology and Strain Taxonomy of

    Guglielmini, Julien / Hennart, Melanie / Badell, Edgar / Toubiana, Julie / Criscuolo, Alexis / Brisse, Sylvain

    Journal of clinical microbiology

    2021  Volume 59, Issue 12, Page(s) e0158121

    Abstract: Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale ... ...

    Abstract Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST gene diversity among 602 isolates from sporadic clinical cases, small clusters, or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed a short-timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500-cgMLST-mismatch threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible (https://bigsdb.pasteur.fr/diphtheria). Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae. The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies of ecology, evolution, and virulence heterogeneity among C. diphtheriae sublineages.
    MeSH term(s) Corynebacterium diphtheriae/genetics ; Diphtheria/epidemiology ; Diphtheria/microbiology ; Genome, Bacterial ; Genomics ; Humans ; Multilocus Sequence Typing ; Phylogeny
    Language English
    Publishing date 2021-09-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.01581-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains.

    Hennart, Melanie / Guglielmini, Julien / Bridel, Sébastien / Maiden, Martin C J / Jolley, Keith A / Criscuolo, Alexis / Brisse, Sylvain

    Molecular biology and evolution

    2022  Volume 39, Issue 7

    Abstract: Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are ... ...

    Abstract Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users' genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.
    MeSH term(s) Genome, Bacterial ; Genomics ; Genotype ; Klebsiella pneumoniae/genetics ; Multilocus Sequence Typing ; Phylogeny
    Language English
    Publishing date 2022-06-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msac135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Genomic Epidemiology of Corynebacterium diphtheriae in New Caledonia.

    Tessier, Eve / Hennart, Melanie / Badell, Edgar / Passet, Virginie / Toubiana, Julie / Biron, Antoine / Gourinat, Ann-Claire / Merlet, Audrey / Colot, Julien / Brisse, Sylvain

    Microbiology spectrum

    2023  Volume 11, Issue 3, Page(s) e0461622

    Abstract: An increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae. All C. diphtheriae ... ...

    Abstract An increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae. All C. diphtheriae isolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes,
    MeSH term(s) Female ; Humans ; Corynebacterium diphtheriae/genetics ; Diphtheria/epidemiology ; Diphtheria/microbiology ; Multilocus Sequence Typing ; New Caledonia/epidemiology ; Retrospective Studies ; Corynebacterium/genetics ; Genomics ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Protein Synthesis Inhibitors
    Chemical Substances Anti-Bacterial Agents ; Tetracycline (F8VB5M810T) ; Protein Synthesis Inhibitors
    Language English
    Publishing date 2023-04-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.04616-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence

    Hennart, Mélanie / Crestani, Chiara / Bridel, Sébastien / Armatys, Nathalie / Brémont, Sylvie / Carmi-Leroy, Annick / Landier, Annie / Passet, Virginie / Fonteneau, Laure / Vaux, Sophie / Toubiana, Julie / Badell, Edgar / Brisse, Sylvain

    Peer Community Journal, Vol 3, Iss , Pp - (2023)

    2023  

    Abstract: Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important ... ...

    Abstract Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.
    Keywords diphtheria ; genomic sequencing ; antimicrobial resistance ; virulence ; epidemiology ; transmission ; 2022 reemergence ; bioinformatics tool ; Archaeology ; CC1-960 ; Science ; Q
    Language English
    Publishing date 2023-08-01T00:00:00Z
    Publisher Peer Community In
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex

    Badell, Edgar / Hennart, Mélanie / Rodrigues, Carla / Passet, Virginie / Dazas, Melody / Panunzi, Leonardo / Bouchez, Valérie / Carmi-Leroy, Annick / Toubiana, Julie / Brisse, Sylvain

    Research in microbiology. 2020 Feb. 19,

    2020  

    Abstract: A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and MALDI-TOF ... ...

    Abstract A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and MALDI-TOF mass spectrometry. The six isolates were negative for the diphtheria toxin gene. Phylogenetic analyses showed that the six isolates (including FRC0190T) are clearly demarcated from C. diphtheriae, C. belfantii, C. ulcerans and C. pseudotuberculosis. The average nucleotide identity of FRC0190T with C. diphtheriae NCTC11397T was 92.6%, and was 91.8% with C. belfantii FRC0043T. C. diphtheriae subsp. lausannense strain CHUV2995T appeared to be a later heterotypic synonym of C. belfantii (ANI, 99.3%). Phenotyping data revealed an atypical negative or heterogeneous intermediate maltose fermentation reaction for the six isolates. MALDI-TOF mass spectrometry differentiated the new group from the other Corynebacterium taxa by the presence of specific spectral peaks. rpoB sequences showed identity to atypical, maltose-negative C. diphtheriae biovar Belfanti isolates previously described from two cats in the USA. We propose the name Corynebacterium rouxii sp. nov. for the novel group, with FRC0190T (= CIP 111752T = DSM 110354T) as type strain.
    Keywords Corynebacterium diphtheriae ; Corynebacterium pseudotuberculosis ; Corynebacterium ulcerans ; cats ; diphtheria toxin ; dogs ; fermentation ; genes ; humans ; maltose ; matrix-assisted laser desorption-ionization mass spectrometry ; new species ; peritoneum ; phenotype ; phylogeny ; sequence analysis ; United States
    Language English
    Dates of publication 2020-0219
    Publishing place Elsevier Masson SAS
    Document type Article
    Note Pre-press version
    ZDB-ID 1004220-9
    ISSN 1769-7123 ; 0923-2508
    ISSN (online) 1769-7123
    ISSN 0923-2508
    DOI 10.1016/j.resmic.2020.02.003
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Population genomics and antimicrobial resistance in Corynebacterium diphtheriae.

    Hennart, Melanie / Panunzi, Leonardo G / Rodrigues, Carla / Gaday, Quentin / Baines, Sarah L / Barros-Pinkelnig, Marina / Carmi-Leroy, Annick / Dazas, Melody / Wehenkel, Anne Marie / Didelot, Xavier / Toubiana, Julie / Badell, Edgar / Brisse, Sylvain

    Genome medicine

    2020  Volume 12, Issue 1, Page(s) 107

    Abstract: Background: Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population ... ...

    Abstract Background: Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen.
    Methods: Here, we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production, and genomic features in C. diphtheriae. We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories.
    Results: Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production and a largely toxin gene-negative Gravis lineage with few toxin-producing isolates including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Seventeen (10.4%) prospective isolates were multidrug-resistant (≥ 3 antimicrobial categories), including four isolates resistant to penicillin and macrolides. Homologous recombination was frequent (r/m = 5), and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Gene pbp2m is widespread in other Corynebacterium species, and its expression in C. glutamicum demonstrated its effect against several beta-lactams. A novel 73-kb C. diphtheriae multiresistance plasmid was discovered.
    Conclusions: This work uncovers the dynamics of antimicrobial resistance in C. diphtheriae in the context of phylogenetic structure, biovar, and diphtheria toxin production and provides a blueprint to analyze re-emerging diphtheria.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Corynebacterium diphtheriae/classification ; Corynebacterium diphtheriae/drug effects ; Corynebacterium diphtheriae/genetics ; Corynebacterium diphtheriae/isolation & purification ; DNA, Bacterial/genetics ; Diphtheria/microbiology ; Diphtheria Toxin/genetics ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Genome-Wide Association Study ; Genomics ; Humans ; Macrolides/pharmacology ; Metagenomics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Phylogeny ; Prospective Studies
    Chemical Substances Anti-Bacterial Agents ; DNA, Bacterial ; Diphtheria Toxin ; Macrolides
    Language English
    Publishing date 2020-11-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2484394-5
    ISSN 1756-994X ; 1756-994X
    ISSN (online) 1756-994X
    ISSN 1756-994X
    DOI 10.1186/s13073-020-00805-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex.

    Badell, Edgar / Hennart, Mélanie / Rodrigues, Carla / Passet, Virginie / Dazas, Melody / Panunzi, Leonardo / Bouchez, Valérie / Carmi-Leroy, Annick / Toubiana, Julie / Brisse, Sylvain

    Research in microbiology

    2020  Volume 171, Issue 3-4, Page(s) 122–127

    Abstract: A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and MALDI-TOF ... ...

    Abstract A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and MALDI-TOF mass spectrometry. The six isolates were negative for the diphtheria toxin gene. Phylogenetic analyses showed that the six isolates (including FRC0190
    MeSH term(s) Bacterial Typing Techniques ; Corynebacterium/chemistry ; Corynebacterium/classification ; Corynebacterium/genetics ; Corynebacterium Infections/microbiology ; Corynebacterium diphtheriae/chemistry ; Corynebacterium diphtheriae/classification ; Corynebacterium diphtheriae/genetics ; Humans ; Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Whole Genome Sequencing
    Language English
    Publishing date 2020-02-28
    Publishing country France
    Document type Journal Article
    ZDB-ID 1004220-9
    ISSN 1769-7123 ; 0923-2508
    ISSN (online) 1769-7123
    ISSN 0923-2508
    DOI 10.1016/j.resmic.2020.02.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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