In most cases, it is difficult to confidently resolve classifications for 16S data at the species or sub-species level. So, if you were specifically interested in types of Staphylococcus aureus, it might be best to use a different marker (which you could define from comparing whole genome sequences from GenBank).
That said, there are a couple options to get relatively straight-forward taxonomy information for some reference 16S sequences:
1) The RDPclassifier provides the training data, where the taxonomy information is in the FASTA header: https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/. The main RDPclassifier .jar file also has
rm-partialseq functions to filter for unique sequences.
2) NCBI provides some 16S sequences in a BLAST database. It takes a little extra work to extract the FASTA sequence from the database files (using
blastdbcmd -entry all -db 16SMicrobial > NCBI_16S.fa) and then download the taxonomy information, but BLCA provides some scripts for this pre-processing step: https://github.com/qunfengdong/BLCA
Last time I checked, the SILVA database had a different data format that was a little harder to parse, but taxonomy information is available in a format that can be used by mothur here: https://www.mothur.org/wiki/Silva_reference_files