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  1. Article ; Online: A novel cgMLST for genomic surveillance of

    Le Guern, Anne-Sophie / Savin, Cyril / Chereau, Fanny / Tessier, Sabrina / Guglielmini, Julien / Brémont, Sylvie / Pizarro-Cerdá, Javier

    Microbiology spectrum

    2024  , Page(s) e0050424

    Abstract: Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen : Importance: We describe here the new typing method used for molecular surveillance ... ...

    Abstract Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen
    Importance: We describe here the new typing method used for molecular surveillance of
    Language English
    Publishing date 2024-04-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.00504-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences

    Bigot, Thomas / Guglielmini, Julien / Criscuolo, Alexis

    Data in Brief. 2019 Aug., v. 25

    2019  

    Abstract: Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when ... ...

    Abstract Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences.
    Keywords amino acids ; genomics ; phylogeny ; statistical analysis
    Language English
    Dates of publication 2019-08
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2019.104212
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences.

    Bigot, Thomas / Guglielmini, Julien / Criscuolo, Alexis

    Data in brief

    2019  Volume 25, Page(s) 104212

    Abstract: Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when ... ...

    Abstract Estimating the number of substitution events per site that have occurred during the evolution of a pair of amino acid sequences is a common task in phylogenetics and comparative genomics that often requires quite slow maximum-likelihood procedures when taking into account explicit evolutionary models. Data presented in this article are large sets of numbers of substitution events and associated numbers of observed differences between pairs of aligned amino acid sequences that have been generated through a simulation procedure of sequence evolution under a broad range of evolutionary models. These data are available at https://zenodo.org/record/2653704 (doi:10.5281/zenodo.2653704). They are accompanied in this paper by figures showing the strong relationship between the corresponding evolutionary and uncorrected distances, as well as estimated numerical constants that determine non-linear functions that fit the simulated data. These numerical constants can be useful to quickly estimate pairwise evolutionary distances directly from uncorrected distances between aligned amino acid sequences.
    Language English
    Publishing date 2019-07-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2019.104212
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Diversity and evolution of B-family DNA polymerases.

    Kazlauskas, Darius / Krupovic, Mart / Guglielmini, Julien / Forterre, Patrick / Venclovas, Česlovas

    Nucleic acids research

    2020  Volume 48, Issue 18, Page(s) 10142–10156

    Abstract: B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and ...

    Abstract B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.
    MeSH term(s) Archaea/enzymology ; Bacteria/enzymology ; DNA Polymerase beta/chemistry ; DNA Polymerase beta/classification ; DNA Viruses/enzymology ; Databases, Protein ; Eukaryota/enzymology ; Evolution, Molecular
    Chemical Substances DNA Polymerase beta (EC 2.7.7.-)
    Language English
    Publishing date 2020-10-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkaa760
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
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  5. Article: Phylogeny of the

    Woo, Anthony C / Gaia, Morgan / Guglielmini, Julien / Da Cunha, Violette / Forterre, Patrick

    Frontiers in microbiology

    2021  Volume 12, Page(s) 704052

    Abstract: Double-stranded DNA viruses of the ... ...

    Abstract Double-stranded DNA viruses of the realm
    Language English
    Publishing date 2021-07-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.704052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. 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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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1188: Show issues Location:
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  7. Article ; Online: First Description of a Yersinia pseudotuberculosis Clonal Outbreak in France, Confirmed Using a New Core Genome Multilocus Sequence Typing Method.

    Savin, Cyril / Le Guern, Anne-Sophie / Chereau, Fanny / Guglielmini, Julien / Heuzé, Guillaume / Demeure, Christian / Pizarro-Cerdá, Javier

    Microbiology spectrum

    2022  Volume 10, Issue 4, Page(s) e0114522

    Abstract: Yersinia pseudotuberculosis is an enteric pathogen causing mild enteritis that can lead to mesenteric adenitis in children and septicemia in elderly patients. Most cases are sporadic, but outbreaks have already been described in different countries. We ... ...

    Abstract Yersinia pseudotuberculosis is an enteric pathogen causing mild enteritis that can lead to mesenteric adenitis in children and septicemia in elderly patients. Most cases are sporadic, but outbreaks have already been described in different countries. We report for the first time a Y. pseudotuberculosis clonal outbreak in France, that occurred in 2020. An epidemiological investigation based on food queries pointed toward the consumption of tomatoes as the suspected source of infection. The
    MeSH term(s) Aged ; Child ; Disease Outbreaks ; Humans ; Multilocus Sequence Typing/methods ; Retrospective Studies ; Yersinia pseudotuberculosis/genetics ; Yersinia pseudotuberculosis Infections/epidemiology ; Yersinia pseudotuberculosis Infections/microbiology
    Language English
    Publishing date 2022-07-06
    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.01145-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. 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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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2137: Show issues Location:
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  9. Article ; Online: Correction: Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.

    Guglielmini, Julien / Bourhy, Pascale / Schiettekatte, Olivier / Zinini, Farida / Brisse, Sylvain / Picardeau, Mathieu

    PLoS neglected tropical diseases

    2020  Volume 14, Issue 8, Page(s) e0008673

    Abstract: This corrects the article DOI: 10.1371/journal.pntd.0007374.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pntd.0007374.].
    Language English
    Publishing date 2020-08-21
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 2429704-5
    ISSN 1935-2735 ; 1935-2727
    ISSN (online) 1935-2735
    ISSN 1935-2727
    DOI 10.1371/journal.pntd.0008673
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Reply to Ku and Sun: Ancestors of modern giant and large eukaryotic dsDNA viruses infected proto-eukaryotes.

    Guglielmini, Julien / Woo, Anthony C / Krupovic, Mart / Forterre, Patrick / Gaia, Morgan

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 6, Page(s) 2749–2750

    MeSH term(s) Eukaryota ; Eukaryotic Cells ; Viruses
    Language English
    Publishing date 2020-01-28
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1920855117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1148: Show issues Location:
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