SCCFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome in Using Whole-Genome Sequence Data

Typing of methicillin-resistant (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the strain determined by multilocus sequence typing (MLST) or equivalent methods like typing and typing of the mobile genetic element staphylococcal cassette chromosome (SCC), which carries the or gene. Whereas MLST and typing are relatively simple, typing of SCC is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCC, but so far, no bioinformatic tools for SCC typing have been available. Here, we report the development and evaluation of SCCFinder for characterization of the SCC element from WGS data. SCCFinder is able to identify all SCC element types, designated I to XIII, with subtyping of SCC types IV (2B) and V (5C2). SCC elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a -mer-based approach. Evaluation of SCCFinder by using a diverse collection of clinical isolates ( = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCFinder can be an alternative to more laborious SCC typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder. SCC in MRSA is acknowledged to be of importance not only because it contains the or gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCC 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, SCCFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCC elements. The software detects all of the SCC 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, SCCFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.