Computational protocol: MRSA Clonal Complex 22 Strains Harboring Toxic Shock Syndrome Toxin (TSST-1) Are Endemic in the Primary Hospital in Gaza, Palestine

Similar protocols

Protocol publication

[…] All 215 S. aureus isolates were characterized by staphylococcal protein A (spa) typing []; 2008 isolates were spa typed using the Ridom StaphType software [,], while 2012 isolates were spa typed using eGenomics software [,], with Ridom assignments made using the Spa Server website (http://spa.ridom.de/). In order to avoid confusion, both designations are used throughout this manuscript, with eGenomics spa types prefaced by the term “spa”, and Ridom spa types shown in parentheses. All MRSA isolates were subjected to staphylococcal cassette chromosome (SCC)mec typing; 2012 isolates were typed using multiplex real-time PCR [], while 2008 isolates were typed using both multiplex conventional [] and real-time [] PCR. Multilocus sequence typing (MLST) was performed as described previously [] on a representative subset of 42 isolates, with clonal complexes inferred via eBURST analysis []; all other clonal complexes were inferred from spa typing data as described previously [], using both the Ridom Spa Server website and our own internal eGenomics database. Clonal complex sub-groups with distinct genotypic signatures were classified as individual CCs [], e.g. ST239 strains were classified as CC239 rather than CC8; ST34 strains were classified as CC34 rather than CC30; and ST291 strains were classified as CC291 rather than CC398. […]

Pipeline specifications

Software tools StaphType, BURST
Application WGS analysis
Organisms Staphylococcus aureus, Epipremnum aureum
Diseases Staphylococcal Infections, Drug-Related Side Effects and Adverse Reactions
Chemicals Clindamycin, Erythromycin, Gentamicins, Tetracycline, Fluoroquinolones, beta-Lactams