Q1: How to Change the Printer in Ridom StaphType ?
There is no possibility to change the printer in Ridom StaphType. We use for printing Adobe Reader. All documents are sent to the printer that is configured as the default printer of the computer operation system (OS; e.g. Windows). Therefore, if you want to print to another printer you have to change this configuration in the OS.
Q2: When I click a link in the “View StaphType Statistics” the program CMD.exe tries to get access to the Internet
We start the OS dependent default WWW browser by issuing a command line command. This command is “translated” under Windows by CMD.exe.
Q3: A New Repeat is not detected by Ridom StaphType. It is not highlighted green or violet in the sequence editor, and the button above the region is labelled as 'GAP'
Detecting spa-repeats with Ridom StaphType is a two-step process. The software first searches for repeats using an ambiguous match-pattern and then it examines whether the repeat is already known or not. On rare occasions it is possible that you detect a totally new sort of repeat that is currently not detected by our ambiguous match-pattern. If this is the case we request you to send the chromatograms to us since we would wish to inspect the chromatograms and, if necessary, extend our match-pattern. Please use this New Repeat Form to send your sequences.
Q4: What primers should be used for PCR and sequencing of the spa gene?
This is indeed an important question. Our software searches for 5'- and 3'-signatures at the begin and end of the repeat region to ensure that no leading or ending repeat is missed (e.g., due to bad quality at the start and end of the determined sequence). It is therefore important that both PCR primers anneal far enough from the signature regions, so that a reliable sequence of them can be determined. Many different spa-primers can be found in the literature (e.g., Frenay, Kreiswirth, Enright, or our JCM 2003). We recommend currently the primers spa-1113f (5'- TAA AGA CGA TCC TTC GGT GAG C -3'; 1092-1113) and spa-1514r (5'- CAG CAG TAG TGC CGT TTG CTT -3'; 1534-1514) for amplification and sequencing, because they gave in our hands the best results (the primers are numbered from the 3' end of the primer with respect to the S. aureus GenBank accession no. J01786). Please note, that these are slightly different and improved primers than the ones stated in our J. Clin. Microbiol. (41:5442-5448, 2003) publication.
