SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data

ABSTRACT Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and...

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Autores principales: Hülya Kaya, Henrik Hasman, Jesper Larsen, Marc Stegger, Thor Bech Johannesen, Rosa Lundbye Allesøe, Camilla Koldbæk Lemvigh, Frank Møller Aarestrup, Ole Lund, Anders Rhod Larsen
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Publicado: American Society for Microbiology 2018
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spelling oai:doaj.org-article:2df8ecb99dd64b53b5ff11d8c342aa322021-11-15T15:22:02ZSCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data10.1128/mSphere.00612-172379-5042https://doaj.org/article/2df8ecb99dd64b53b5ff11d8c342aa322018-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00612-17https://doaj.org/toc/2379-5042ABSTRACT Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available. Here, we report the development and evaluation of SCCmecFinder for characterization of the SCCmec element from S. aureus WGS data. SCCmecFinder is able to identify all SCCmec element types, designated I to XIII, with subtyping of SCCmec types IV (2B) and V (5C2). SCCmec elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach. Evaluation of SCCmecFinder by using a diverse collection of clinical isolates (n = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCmecFinder can be an alternative to more laborious SCCmec typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder. IMPORTANCE SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.Hülya KayaHenrik HasmanJesper LarsenMarc SteggerThor Bech JohannesenRosa Lundbye AllesøeCamilla Koldbæk LemvighFrank Møller AarestrupOle LundAnders Rhod LarsenAmerican Society for MicrobiologyarticleMRSASCCmecbioinformaticsmecAmecCtypingMicrobiologyQR1-502ENmSphere, Vol 3, Iss 1 (2018)
institution DOAJ
collection DOAJ
language EN
topic MRSA
SCCmec
bioinformatics
mecA
mecC
typing
Microbiology
QR1-502
spellingShingle MRSA
SCCmec
bioinformatics
mecA
mecC
typing
Microbiology
QR1-502
Hülya Kaya
Henrik Hasman
Jesper Larsen
Marc Stegger
Thor Bech Johannesen
Rosa Lundbye Allesøe
Camilla Koldbæk Lemvigh
Frank Møller Aarestrup
Ole Lund
Anders Rhod Larsen
SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data
description ABSTRACT Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available. Here, we report the development and evaluation of SCCmecFinder for characterization of the SCCmec element from S. aureus WGS data. SCCmecFinder is able to identify all SCCmec element types, designated I to XIII, with subtyping of SCCmec types IV (2B) and V (5C2). SCCmec elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach. Evaluation of SCCmecFinder by using a diverse collection of clinical isolates (n = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCmecFinder can be an alternative to more laborious SCCmec typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder. IMPORTANCE SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.
format article
author Hülya Kaya
Henrik Hasman
Jesper Larsen
Marc Stegger
Thor Bech Johannesen
Rosa Lundbye Allesøe
Camilla Koldbæk Lemvigh
Frank Møller Aarestrup
Ole Lund
Anders Rhod Larsen
author_facet Hülya Kaya
Henrik Hasman
Jesper Larsen
Marc Stegger
Thor Bech Johannesen
Rosa Lundbye Allesøe
Camilla Koldbæk Lemvigh
Frank Møller Aarestrup
Ole Lund
Anders Rhod Larsen
author_sort Hülya Kaya
title SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data
title_short SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data
title_full SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data
title_fullStr SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data
title_full_unstemmed SCC<italic toggle="yes">mec</italic>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">Staphylococcus aureus</named-content> Using Whole-Genome Sequence Data
title_sort scc<italic toggle="yes">mec</italic>finder, a web-based tool for typing of staphylococcal cassette chromosome <italic toggle="yes">mec</italic> in <named-content content-type="genus-species">staphylococcus aureus</named-content> using whole-genome sequence data
publisher American Society for Microbiology
publishDate 2018
url https://doaj.org/article/2df8ecb99dd64b53b5ff11d8c342aa32
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