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Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections.
Berwa, Aimé; Caspar, Yvan.
Afiliación
  • Berwa A; Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, Grenoble, France.
  • Caspar Y; Laboratoire de Bactériologie-Hygiène Hospitalière, CHU Grenoble Alpes, Grenoble, France; Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, CEA, IBS, Grenoble, France. Electronic address: YCaspar@chu-grenoble.fr.
J Glob Antimicrob Resist ; 39: 153-158, 2024 Sep 13.
Article en En | MEDLINE | ID: mdl-39278463
ABSTRACT

OBJECTIVES:

Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia.

METHODS:

We built a bioinformatics pipeline consisting of the following sequential tools Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed.

RESULTS:

The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were blaCTX-M-15 (62.1%) and blaCTX-M-27 (13.6%).

CONCLUSIONS:

The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: J Glob Antimicrob Resist Año: 2024 Tipo del documento: Article País de afiliación: Francia Pais de publicación: Países Bajos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: J Glob Antimicrob Resist Año: 2024 Tipo del documento: Article País de afiliación: Francia Pais de publicación: Países Bajos