RIDOMRibosomal Differentiation of Medical Microorganisms
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The spa-like (RIDOM) t267 (43strains) (corresponding to the sequence of43RIDOMSRRinclassification, and the sequence [UJGFMBBBPB] in Kreis wirth classification.
Hence monitored databases like RIDOM (http://www.ridom-rdna.de/) that has peer-reviewed entries along with extensive phenotypic and sequence data are recommended to confirm MicroSeq results which do not result in species level matches (2,25).
Consequently, there are currently 2366 spa types in the Ridom SpaServer database (http://spaserver.ridom.de).
We performed the cgMLST scheme version 2.1, considering 2,891 core genes, by using Ridom SeqSphere+ version 5.0.0 software (Ridom GmbH,_https://www.cgmlst.org) (7).
spa types were assigned using the Ridom Staph Type standard protocol (http://www.ridom.com) and the Ridom SpaServer (http://spa.ridom.de/index.
Sequence assembly was performed in Clone Manager Basic 9 (SciEd), followed by analysis of the spa tandem repeats using spa typing online software (http://spatyper.fortinbras.us/) and the Ridom Spa Server database (http://www.spaserver.ridom.de/) [29].
We imported FASTA files into SeqSphere+ software version 4.1 (Ridom GmbH, http://www.ridom.de/seqsphere) for analysis (9).
In order to characterize the MRSA strains, different molecular typing methods were used including SCCmec typing, spa-typing and the corresponding multilocus sequence typing (MLST) and clonal complex based on the spa types in the Ridom StaphType database.
Spa types were assigned a StaphType (e.g., t008, t002) using the Ridom SpaServer database (http:// www.spaserver.ridom.de).
We analyzed DNA sequences using RidomStaphType and SeqSphere+ (Ridom GmbH, Munster, Germany).
(20,21) The sequences were analyzed using the Ridom Staph Type software (Ridom, Germany) to determine the spa types.
We conducted bioinformatics analyses using the Ridom SeqSphere+ software version 3.1.0-2016-01 (Ridom GmbH, Munster, Germany).