Computational protocol: Comparison of community-onset Staphylococcus argenteus and Staphylococcus aureus sepsis in Thailand: a prospective multicentre observational study

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Protocol publication

[…] Pulsed-field gel electrophoresis (PFGE) was performed using the SmaI restriction enzyme (New England Biolabs, UK) . Banding patterns were analysed using BioNumerics software version 6.01 (Applied Maths, Sint-Martens-Latem, Belgium) as described . A similarity coefficient of 80% was used to define PFGE types . DNA was extracted and MLST was performed as described elsewhere , , . Sequence types (ST) were assigned using the MLST database (www.mlst.net) . Phylogenetic analysis of concatenated MSLT data was performed using ClustalW for the alignment and the maximum likelihood method for construction of the phylogenetic tree in MEGA version 6. Two multiplex PCR assays were used to detect the presence of virulence and other genes (assay 1 for tst, eta, etb, sea, seb, sec, sed, see , assay 2 for mecA and pvl) . […]

Pipeline specifications

Software tools BioNumerics, Clustal W, MEGA
Databases MLST.net
Application Phylogenetics
Organisms Staphylococcus aureus, Homo sapiens, Pampus argenteus, Epipremnum aureum
Diseases Infection, Respiratory Insufficiency