Basic Info

The spaTyper service predicts the Staphylococcus aureus spa type from genome sequences

More Details

spa typing is the sequencing of the 24-bp (21 to 30 bp) repeat region of the Staphylococcus protein A gene (spa). Repeats are assigned a numerical code, and the spa type is determined from the order of these repeats.The traditional method of spa typing is by PCR amplification of the spa repeat region followed by Sanger sequencing. Nowadays, the Staphylococcus aureus spa type can be predicted from genome sequences using modern spa typing methods. Spa type sequences are used as queries to perform BLAST searches against a database containing genome sequences. Subsequently, it matches the 5' and 3' ends of the spa type sequences that have 100% identity starting at position 1.

What's New

NA

Additional Information

Related links:

https://github.com/genomicepidemiology/spatyper/

https://spa.ridom.de/index.shtml

Literature

Bartels MD, Petersen A, Worning P, et al. Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus. J Clin Microbiol. 2014;52(12):4305-4308. doi:10.1128/JCM.01979-14

Harmsen D, Claus H, Witte W, et al. Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol. 2003;41(12):5442-5448. doi:10.1128/JCM.41.12.5442-5448.2003