Genetic Characterization of Staphylococcus aureus

Initially, S. aureus isolates were screened by PCR for identification of CC398 [24 (link)] and in all accessory gene regulator (agr) allotypes were determined [25 (link)]. Amongst CC398 isolates discrimination between human and animal clade was performed [26 (link)].
spa typing was performed [27 (link)] and spa-types were determined by using the Ridom StaphType software v.2.1.1 (Ridom GmbH) [28 (link)]. The BURP algorithm was used to assign spa-types into spa-clonal complexes (spa-CCs) with defined default parameters "exclude spa-types shorter than 5 repeats" and "cluster spa-types into the same group if cost distances are less than 4" [29 (link)].
Multilocus Sequence Typing (MLST) was performed on selected isolates, 36 MRSA and 62 MSSA [30 (link)]. At least one isolate per each spa-type detected in each source of material was analyzed. The sequence type (ST) was also determined for three non-spa-typeable isolates. Allele numbers and STs were assigned through the S. aureus MLST database (http://saureus.mlst.net).
Clonal complexes, CCs, were determined using the eBURSTv3 algorithm (http://saureus.mlst.net/eburst) and restricted to STs that share five or more alleles of seven loci examined with founder or subfounders, within each predicted clonal group [31 (link)]. The analysis was performed on April 29^th, 2016.