The implementation of the new clustering algorithm Based Upon Repeat Pattern (BURP) into the Ridom StaphType software tool enables clustering based on spa typing data for Staphylococcus aureus. We compared clustering results obtained by spa typing/BURP to those obtained by currently well-established methods, i.e., SmaI macrorestriction analysis and multilocus sequence typing/eBURST. A total of 99 clinical S. aureus strains, including MRSA and representing major clonal lineages associated with important kinds of infections which have been prevalent in Germany and Central Europe during the last 10 years, were used for comparison. SmaI macrorestriction analysis revealed the highest discriminatory power, and clustering results for all three methods resulted in concordance values ranging from 96.8% between the two sequence-based methods to 93.4% between spa typing/BURP and SmaI macrorestriction/cluster analysis. The results of this study indicate that spa typing, together with BURP clustering, is a useful tool in S. aureus epidemiology, especially because of ease of use and the advantages of unambiguous sequence analysis as well as reproducibility and exchange of typing data.Staphylococcus aureus is one of the most frequent nosocomial pathogens. The emergence and spread of epidemic strains of methicillin-resistant S. aureus in hospitals (hMRSA) and, independent from the nosocomial setting, in the community (cMRSA) require special attention of infection control. Typing is an important prerequisite for targeted control measures. For about 30 years, phage typing has been widely used for strain typing. More recently, SmaI macrorestriction analysis (pulsedfield gel electrophoresis [PFGE]) was introduced as a typing method with high discriminatory power. PFGE is still regarded the "gold standard" of molecular typing of MRSA, despite insufficient comparability of results obtained from different laboratories (21). During the past 5 years, DNA sequencebased typing has become more popular due to progress in large-scale sequencing methodology, ease of data transfer, and excellent comparability of results (2). This first became evident by the application of multilocus sequence typing (MLST) to MRSA (4, 5). At present, however, MLST is not suitable for routine infection control due to high cost, labor intensity, and lack of broad access to high-throughput DNA sequencing.Several S. aureus typing schemes targeting polymorphic DNA repeat regions in genes for microbial surface components recognizing adhesive matrix molecules have been described previously (7,9,16,27,30). They also include typing methods based on the length polymorphism in spa amplimers (9) or, more recently, on polymorphisms in multiple fragments amplified in a multiplex PCR approach for variable-number tandem repeats (7, 27). Among sequence-based approches, spa typing was the most promising (8,12,13,15,31). The X region of the protein A gene (spa) consists of direct repeats exhibiting an extensive polymorphism based on point mutations, deletions, duplications, and i...
