Computational protocol for analyzing whole-genome sequencing data from Staphylococcus aureus clinical isolates

被引：0

作者：

Sanchez-Osuna, Miquel ^{[1
,2
]}

Erill, Ivan ^{[3
,4
]}

Gasch, Oriol ^{[5
]}

Pich, Oscar Q. ^{[1
,2
]}

机构：

[1] Univ Autonoma Barcelona, Hosp Univ Parc Tauli, Inst Invest & Innovacio Parc Tauli I3PT CERCA, Lab Recerca Microbiol & Malalties Infeccioses, Sabadell 08208, Barcelona, Spain

[2] Univ Autonoma Barcelona, Inst Biotecnol & Biomed, Cerdanyola Del Valles 08193, Barcelona, Spain

[3] Univ Maryland, Dept Biol Sci, Baltimore, MD 21250 USA

[4] Univ Autonoma Barcelona, Dept Engn Informacio Comunicac, Cerdanyola Del Valles 08193, Barcelona, Spain

[5] Univ Autonoma Barcelona, Hosp Univ Parc Tauli, Inst Invest & Innovacio Parc Tauli I3PT CERCA, Serv Malalties Infeccioses, Sabadell 08208, Barcelona, Spain

来源：

STAR PROTOCOLS | 2025年 / 6卷 / 01期

关键词：

isolates; Stepwise framework; genomes; virulence factors; prophages; Accessible protocol; bioinformatics; expertise;

D O I：

10.1016/j.xpro.2025.103613

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Analyzing whole-genome sequencing (WGS) data from bacterial isolates is pivotal for understanding virulence and predicting clinical outcomes through association studies. Herein, we present a computational protocol for the detailed analysis of WGS data from Staphylococcus aureus clinical isolates generated with Illumina sequencing. We describe steps for de novo assembly, functional annotation, and genetic characterization of chromosomal and extrachromosomal elements. This approach paves the way for an improved understanding of the interplay between virulence factors, resistome, strain type, and disease severity. For complete details on the use and execution of this protocol, please refer to Sa<acute accent>nchez-Osuna et al.1

引用

页数：12

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