spa typing was performed according to Harmsen et al.9 (link) Nucleotide sequencing of the repeat-containing region of the spa gene was conducted on both DNA strands of the PCR product by GenoMed (St Louis, MO, USA), using BigDye Terminator Ready Reaction Cycle Sequencing Kit. The spa types were identified with Ridom StaphType software v.2.1.1 (Ridom GmbH, Münster, Germany),9 (link) and grouped using BURP, Ridom StaphType software. spa types were clustered if the cost between members of a given group was less than or equal to four. The BURP algorithm was used to assign spa types into spa clonal complexes (spa-CCs) with defined default parameters “exclude spa types shorter than five repeats” and “cluster spa types into the same group if cost distances are less than four”.10 (link) Since the results of spa typing and MLST are highly concordant,7 (link) the spa typing data could be easily mapped on the MLST types using SpaServer database (http://spaserver.ridom.de/ ).
Protocol detail
Standardized spa Typing and Clustering
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BigDye Terminator Ready Reaction Cycle Sequencing Kit
Ridom StaphType software v.2.1.1
Ridom StaphType software
Burp
Clonal
Gene
Corresponding Organization :
Other organizations : Gdańsk Medical University, Wroclaw University of Environmental and Life Sciences, Narodowy Instytut Leków
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Variable analysis
independent variables
- Spa typing was performed according to Harmsen et al.9
- Nucleotide sequencing of the repeat-containing region of the spa gene was conducted on both DNA strands of the PCR product by GenoMed (St Louis, MO, USA), using BigDye Terminator Ready Reaction Cycle Sequencing Kit
- The spa types were identified with Ridom StaphType software v.2.1.1 (Ridom GmbH, Münster, Germany),9 and grouped using BURP, Ridom StaphType software
- Spa types
- Spa types shorter than five repeats were excluded from the BURP algorithm to assign spa types into spa clonal complexes (spa-CCs)
- The cost between members of a given spa type group was less than or equal to four
- None specified
- None specified
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