SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data.
SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data.
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DOI：
10.1128/msphere.00612-17
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发表时间：
2018-01
期刊：
影响因子：
4.8
通讯作者：
Larsen AR
中科院分区：
文献类型：
--
作者：
Kaya H;Hasman H;Larsen J;Stegger M;Johannesen TB;Allesøe RL;Lemvigh CK;Aarestrup FM;Lund O;Larsen AR
MRSA中的SCCmec被认为是重要的，不仅因为它含有mecA或mecC基因，而且还因为葡萄球菌适应不同的环境，例如，在医院、社区和牲畜中。由于SCCmec的异质性，通过PCR技术对其进行分型具有挑战性，而全基因组测序仅部分解决了这一问题，因为没有良好的生物信息学工具可用。在这篇文章中，我们描述了一种新的生物信息学工具，SCCmeclampus，其中包括大部分的感染控制专业人员和研究人员关于SCCmec元素的解释的需求的发展。该软件可检测葡萄球菌盒式染色体元件分类国际工作组接受的所有SCCmec元件，如果上传了分歧和潜在的新元素，用户将得到提示。此外，SCCmecket将随着新元素的发现而进行策划和更新，并且易于使用和免费访问。耐甲氧西林金黄色葡萄球菌（MRSA）的分型在感染控制和监测中非常重要。MRSA的当前命名法包括通过多位点序列分型（MLST）或等效方法（如spa分型和携带mecA或mecC基因的移动的遗传元件葡萄球菌盒式染色体mec（SCCmec）分型）确定的金黄色葡萄球菌菌株的遗传背景。MLST和spa分型相对简单，而SCCmec的分型由于其异质性而不那么简单。全基因组测序（WGS）为遗传背景和SCCmec的分型提供了必要的数据，但到目前为止，还没有用于SCCmec分型的生物信息学工具。在这里，我们报告了SCCmeclase的开发和评价，用于表征来自金黄色葡萄球菌WGS数据的SCCmec元素。SCCmectin能够识别所有SCCmec元素类型，指定为I至XIII，具有SCCmec类型IV（2B）和V（5C2）的亚型。SCCmec元件的特征在于两种不同的基因预测方法，以实现正确的注释，基于基本局部比对搜索工具（BLAST）的方法和基于k-mer的方法。通过使用临床分离株的不同集合（n = 93）对SCC meclampsia进行评估，显示出96.7%的高分型性水平，在修改默认设置后，该水平增加到98.9%。总而言之，SCCmectin可以作为更费力的SCCmec分型方法的替代方法，并且可以在www.example.com上免费获得。重要性众所周知，MRSA中的SCCmec非常重要，不仅因为它含有mecA或mecC基因，而且还因为它有助于葡萄球菌适应不同的环境，例如，在医院、社区和牲畜中。由于SCCmec的异质性，通过PCR技术对其进行分型具有挑战性，而全基因组测序仅部分解决了这一问题，因为没有良好的生物信息学工具可用。在这篇文章中，我们描述了一种新的生物信息学工具，SCCmeclampus，其中包括大部分的感染控制专业人员和研究人员关于SCCmec元素的解释的需求的发展。该软件可检测葡萄球菌盒式染色体元件分类国际工作组接受的所有SCCmec元件，如果上传了分歧和潜在的新元素，用户将得到提示。此外，SCCmecket将随着新元素的发现而进行策划和更新，并且易于使用和免费访问。
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. 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.