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www.ccrbtyping.net – a web-based typing tool for staphylococci

Abstract number: P2233

Santos M.D., Milheiriço C., Oliveira D.C., Vinga S., Oliveira A., de Lencastre H., Carriço J.A.

Objectives: ccrB typing, based on the DNA sequencing of an internal fragment of ccrB, was developed as a potential first-line SCCmec typing strategy for meticillin resistant Staphylococcus aureus, since the ccrB sequence is part of the ccrAB locus, whose allotypes are used for the definition of SCCmec types. Clustering of ccrB sequences has been shown to properly discriminate between different SCCmec types (I, II, III, IV and VI) (Oliveira et al, J. Antimicrob Chemother 58:23–30). To make this approach available to the general public, a web based typing tool interface was developed so that users can submit ccrB sequences and obtain an automatic assignment to a ccrB allele and presumptive SCCmec type classification.

Methods: The website serves as a front-end for a database and user management system, coupled with two sequence alignment programmes (MUSCLE and Clustal) and an alignment and tree viewer software (Jalview). For each SCCmec type, a set of known sequences are defined as a prototypes. The user submitted ccrB sequences are then, after an automatic trimming, compared by multiple sequence alignment with the defined prototypes, and the most similar prototype defines the ccrB allele, allowing the inference of ccrAB allotype and SCCmec type.

Results: The website (www.ccrbtyping.net) is being used since late October 2007. At the website launch date the database had 98 ccrB sequences, including 17 prototype sequences, with references and with other important isolate information. All the public information can be easily extracted to csv format and an online tutorial explains the users how to work with the web tool. The data can be saved privately or it can be submitted to the public database after being reviewed by a system curator.

Conclusion: Web-based applications have proved to be the best approach for the comparison of sequence based typing methodologies results. Anyone with internet connection can contribute with their data to the public database and help to validate and improve the typing methodology. The implemented website has demonstrated its usefulness for ccrB typing giving good results for several staphylococci species, allowing for an expanding database of curated ccrB sequences. Additionally the web based typing tool interface was implemented to be rapidly configurable, and can be used as a framework for other sequence based typing methods based either on direct sequence similarity or on the comparison of repeated patterns.

Session Details

Date: 19/04/2008
Time: 00:00-00:00
Session name: 18th European Congress of Clinical Microbiology and Infectious Diseases
Subject:
Location: Barcelona, Spain
Presentation type:
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