Work

Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections

Year: 2024

Type: article

Abstract: • Bacterial WGS is still rarely performed in routine clinical microbiology. • Easy to use open-source tools are required for clinical microbiologist (CM). • Open-access galaxy web browser provides a graphical interface and easy to use tools. • Galaxy platform allows for comprehensive and reproducible analysis in a few steps. • It facilitates WGS analysis by CM without advanced bioinformatics skills. 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. 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. 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 bla CTX−M-15 (62.1%) and bla CTX−M-27 (13.6%). 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.

Source: Journal of Global Antimicrobial Resistance

DOI: 10.1016/j.jgar.2024.08.012

Authors: Aimé Berwa, Yvan Caspar