Molecular Typing of MRSA Isolates

Using the primers listed in Table 8, all the investigated MRSA isolates (n = 34) were subjected to a PCR assay for amplification of the polymorphic repeat region (X region) of the spa gene as described elsewhere^{90 (link)}. The spa amplicons were then purified using a Qiagen DNA purification kit (Qiagen GmbH, Hilden, Germany) and sequenced by Macrogen® (Seoul, South Korea) using capillary electrophoresis. spa typing was conducted as described by Harmsen et al.^{91 (link)}, and the resulting spa types were then clustered into related spa clonal complexes (spa-CCs) using the BURP algorithm implemented in the Ridom StaphType software version 2.2.1 (Ridom GmbH, Würzburg, Germany). The default parameters of the BURP algorithm (exclusion of spa types shorter than 5 repeats and clustering of spa types if cost is less or equal to 5) were applied in this analysis, in order to prevent the formation of spa clusters that are too large or non-specific^{92 (link)}. The spa type that could not be assigned to a cluster was considered as a singleton. Due to the high concordance between spa typing and MLST^{24 (link)}, the MLST clonal complexes (CC) corresponding to the respective spa-CCs were deduced from the data on the Ridom SpaServer (http://spaserver.ridom.de, last accessed on 15 November 2016) and by literature search.