Development of a web tool for Escherichia coli subtyping based on fimH alleles

Running title: Development of E. coli fimH sub-typing web-tool

Louise Roer, Veronika Tchesnokova, Rosa Lundbye Allesøe, Mariya Muradova, Sujay Chattopadhyay, Johanne Ahrenfeldt, Martin Christen Frølund Thomsen, Ole Lund, Frank Hansen, Anette Marie Hammerum, Evgeni Sokurenko, Henrik Hasman

    Research output: Contribution to journalJournal articleResearchpeer-review

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    Abstract

    The aim of this study was to construct a valid publicly available method for in silico fimH sub-typing of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multi-locus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available on https://bitbucket.org/genomicepidemiology/fimtyper, the database freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software available at https://cge.cbs.dtu.dk/services/FimTyperFimTyper was validated on three datasets; (i) containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study, (ii) whole-genome sequence data of 243 third-generation cephalosporins-resistant E. coli isolates, and (iii) a randomly chosen subset of 40 E. coli isolates from dataset (ii), which were subjected to conventional fimH sub-typing. The combination of the three datasets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 40 fimH sub-types from the Sanger sequences from dataset (i), and successfully analyzed all 243 drafted genomes from dataset (ii). FimTyper sub-typing of the Sanger sequences and WGS data from dataset (iii) were in complete agreement. Additionally, fimH sub-typing was evaluated on a phylogenetic network of 122 ST131 E. coli isolates. There were perfect concordance between the typology and fimH-based sub-clones within ST131 with accurate identification of the pandemic multidrug resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH sub-typing, highly suitable for surveillance and outbreak detection.
    Original languageEnglish
    JournalJournal of Clinical Microbiology
    Volume55
    Issue number8
    Pages (from-to)2538-2543
    ISSN0095-1137
    DOIs
    Publication statusPublished - 2017

    Keywords

    • FimH
    • E. coli
    • Typing
    • Whole genome sequencing analysis

    Cite this

    Roer, Louise ; Tchesnokova, Veronika ; Allesøe, Rosa Lundbye ; Muradova, Mariya ; Chattopadhyay, Sujay ; Ahrenfeldt, Johanne ; Thomsen, Martin Christen Frølund ; Lund, Ole ; Hansen, Frank ; Hammerum, Anette Marie ; Sokurenko, Evgeni ; Hasman, Henrik. / Development of a web tool for Escherichia coli subtyping based on fimH alleles : Running title: Development of E. coli fimH sub-typing web-tool . In: Journal of Clinical Microbiology. 2017 ; Vol. 55, No. 8. pp. 2538-2543.
    @article{4e0223efcd3f4a87b71a5291b58fa416,
    title = "Development of a web tool for Escherichia coli subtyping based on fimH alleles: Running title: Development of E. coli fimH sub-typing web-tool",
    abstract = "The aim of this study was to construct a valid publicly available method for in silico fimH sub-typing of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multi-locus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available on https://bitbucket.org/genomicepidemiology/fimtyper, the database freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software available at https://cge.cbs.dtu.dk/services/FimTyperFimTyper was validated on three datasets; (i) containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study, (ii) whole-genome sequence data of 243 third-generation cephalosporins-resistant E. coli isolates, and (iii) a randomly chosen subset of 40 E. coli isolates from dataset (ii), which were subjected to conventional fimH sub-typing. The combination of the three datasets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 40 fimH sub-types from the Sanger sequences from dataset (i), and successfully analyzed all 243 drafted genomes from dataset (ii). FimTyper sub-typing of the Sanger sequences and WGS data from dataset (iii) were in complete agreement. Additionally, fimH sub-typing was evaluated on a phylogenetic network of 122 ST131 E. coli isolates. There were perfect concordance between the typology and fimH-based sub-clones within ST131 with accurate identification of the pandemic multidrug resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH sub-typing, highly suitable for surveillance and outbreak detection.",
    keywords = "FimH, E. coli, Typing, Whole genome sequencing analysis",
    author = "Louise Roer and Veronika Tchesnokova and Alles{\o}e, {Rosa Lundbye} and Mariya Muradova and Sujay Chattopadhyay and Johanne Ahrenfeldt and Thomsen, {Martin Christen Fr{\o}lund} and Ole Lund and Frank Hansen and Hammerum, {Anette Marie} and Evgeni Sokurenko and Henrik Hasman",
    year = "2017",
    doi = "10.1128/JCM.00737-17",
    language = "English",
    volume = "55",
    pages = "2538--2543",
    journal = "Journal of Clinical Microbiology",
    issn = "0095-1137",
    publisher = "American Society for Microbiology",
    number = "8",

    }

    Roer, L, Tchesnokova, V, Allesøe, RL, Muradova, M, Chattopadhyay, S, Ahrenfeldt, J, Thomsen, MCF, Lund, O, Hansen, F, Hammerum, AM, Sokurenko, E & Hasman, H 2017, 'Development of a web tool for Escherichia coli subtyping based on fimH alleles: Running title: Development of E. coli fimH sub-typing web-tool ', Journal of Clinical Microbiology, vol. 55, no. 8, pp. 2538-2543. https://doi.org/10.1128/JCM.00737-17

    Development of a web tool for Escherichia coli subtyping based on fimH alleles : Running title: Development of E. coli fimH sub-typing web-tool . / Roer, Louise; Tchesnokova, Veronika; Allesøe, Rosa Lundbye; Muradova, Mariya; Chattopadhyay, Sujay; Ahrenfeldt, Johanne; Thomsen, Martin Christen Frølund; Lund, Ole; Hansen, Frank; Hammerum, Anette Marie; Sokurenko, Evgeni; Hasman, Henrik.

    In: Journal of Clinical Microbiology, Vol. 55, No. 8, 2017, p. 2538-2543.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Development of a web tool for Escherichia coli subtyping based on fimH alleles

    T2 - Running title: Development of E. coli fimH sub-typing web-tool

    AU - Roer, Louise

    AU - Tchesnokova, Veronika

    AU - Allesøe, Rosa Lundbye

    AU - Muradova, Mariya

    AU - Chattopadhyay, Sujay

    AU - Ahrenfeldt, Johanne

    AU - Thomsen, Martin Christen Frølund

    AU - Lund, Ole

    AU - Hansen, Frank

    AU - Hammerum, Anette Marie

    AU - Sokurenko, Evgeni

    AU - Hasman, Henrik

    PY - 2017

    Y1 - 2017

    N2 - The aim of this study was to construct a valid publicly available method for in silico fimH sub-typing of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multi-locus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available on https://bitbucket.org/genomicepidemiology/fimtyper, the database freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software available at https://cge.cbs.dtu.dk/services/FimTyperFimTyper was validated on three datasets; (i) containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study, (ii) whole-genome sequence data of 243 third-generation cephalosporins-resistant E. coli isolates, and (iii) a randomly chosen subset of 40 E. coli isolates from dataset (ii), which were subjected to conventional fimH sub-typing. The combination of the three datasets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 40 fimH sub-types from the Sanger sequences from dataset (i), and successfully analyzed all 243 drafted genomes from dataset (ii). FimTyper sub-typing of the Sanger sequences and WGS data from dataset (iii) were in complete agreement. Additionally, fimH sub-typing was evaluated on a phylogenetic network of 122 ST131 E. coli isolates. There were perfect concordance between the typology and fimH-based sub-clones within ST131 with accurate identification of the pandemic multidrug resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH sub-typing, highly suitable for surveillance and outbreak detection.

    AB - The aim of this study was to construct a valid publicly available method for in silico fimH sub-typing of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multi-locus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available on https://bitbucket.org/genomicepidemiology/fimtyper, the database freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software available at https://cge.cbs.dtu.dk/services/FimTyperFimTyper was validated on three datasets; (i) containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study, (ii) whole-genome sequence data of 243 third-generation cephalosporins-resistant E. coli isolates, and (iii) a randomly chosen subset of 40 E. coli isolates from dataset (ii), which were subjected to conventional fimH sub-typing. The combination of the three datasets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 40 fimH sub-types from the Sanger sequences from dataset (i), and successfully analyzed all 243 drafted genomes from dataset (ii). FimTyper sub-typing of the Sanger sequences and WGS data from dataset (iii) were in complete agreement. Additionally, fimH sub-typing was evaluated on a phylogenetic network of 122 ST131 E. coli isolates. There were perfect concordance between the typology and fimH-based sub-clones within ST131 with accurate identification of the pandemic multidrug resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH sub-typing, highly suitable for surveillance and outbreak detection.

    KW - FimH

    KW - E. coli

    KW - Typing

    KW - Whole genome sequencing analysis

    U2 - 10.1128/JCM.00737-17

    DO - 10.1128/JCM.00737-17

    M3 - Journal article

    VL - 55

    SP - 2538

    EP - 2543

    JO - Journal of Clinical Microbiology

    JF - Journal of Clinical Microbiology

    SN - 0095-1137

    IS - 8

    ER -