Sequence types (STs) were calculated according to the multilocus sequence typing (MLST) scheme of the Public databases for molecular typing and microbial genome diversity (PubMLST)3 using Ariba v2.6.2 (Hunt et al., 2017 (link)). A simple diversity index (SDI; Gastmeier et al., 2006 (link)) was applied to analyze population diversity. Core genome MLST (cgMLST), consisting of 1861 targets for S. aureus provided by SeqSphere+3.5.0 (Ridom, Münster, Germany), was performed with the 137 sequenced isolates. Additionally, ST398 isolates from this study were analyzed using cgMLST together with a collection of 239 S. aureus of this ST downloaded from the NCBI database using “chromosome” and “complete” as filtering criteria for assembly level and the absence of mec genes as the genotypic criterion.
El Mammery A., Ramírez de Arellano E., Cañada-García J.E., Cercenado E., Villar-Gómara L., Casquero-García V., García-Cobos S., Lepe J.A., Ruiz de Gopegui Bordes E., Calvo-Montes J., Larrosa Escartín N., Cantón R., Pérez-Vázquez M., Aracil B, & Oteo-Iglesias J. (2023). An increase in erythromycin resistance in methicillin-susceptible Staphylococcus aureus from blood correlates with the use of macrolide/lincosamide/streptogramin antibiotics. EARS-Net Spain (2004–2020). Frontiers in Microbiology, 14, 1220286.
ChromosomeGenesGenome Genotypic Microbial genome S aureus
Corresponding Organization :
Other organizations :
Instituto de Salud Carlos III, Centro Nacional de Microbiologia, Centro de Investigación Biomédica en Red, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Hospital General Universitario Gregorio Marañón, Agencia Española de Medicamentos y Productos Sanitarios, Hospital Universitario Virgen del Rocío, Hospital Universitario Son Espases, Instituto de Investigación Marqués de Valdecilla, Vall d'Hebron Hospital Universitari, Hospital Universitario Ramón y Cajal
Sequence types (STs) calculated according to the multilocus sequence typing (MLST) scheme of the Public databases for molecular typing and microbial genome diversity (PubMLST) using Ariba v2.6.2
Core genome MLST (cgMLST), consisting of 1861 targets for S. aureus provided by SeqSphere+3.5.0 (Ridom, Münster, Germany), performed with the 137 sequenced isolates
ST398 isolates from this study analyzed using cgMLST together with a collection of 239 S. aureus of this ST downloaded from the NCBI database using 'chromosome' and 'complete' as filtering criteria for assembly level and the absence of mec genes as the genotypic criterion
dependent variables
Simple diversity index (SDI) applied to analyze population diversity
control variables
Positive and negative controls not explicitly mentioned
Annotations
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