rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Multidrug-resistant pathogens pose a significant global public health threat.
• Whole-genome sequencing (WGS) generates vast amounts of data for pathogen analysis.
• Limited bioinformatics expertise and infrastructure can hinder WGS data utilization.

Purpose of the Study:

• To develop a user-friendly pipeline (rMAP) for comprehensive WGS analysis of ESKAPE pathogens.
• To automate complex WGS analysis steps for researchers with limited bioinformatics experience.
• To facilitate rapid antimicrobial resistance profiling and pathogen characterization.

Main Methods:

• Development of the Rapid Microbial Analysis Pipeline (rMAP).
• Automation of WGS data processing: trimming, assembly, annotation, variant calling, and phylogenetic inference.
• Integration of modules for antimicrobial resistance profiling, plasmid analysis, virulence factors, MLST, pangenome, and insertion sequences.

Main Results:

• rMAP successfully profiles resistomes and other genomic features of ESKAPE pathogens from Illumina WGS data.
• The pipeline automates complex analyses, producing an interactive HTML report.
• rMAP is easily installed and executable on a personal laptop, requiring minimal bioinformatics expertise.

Conclusions:

• rMAP provides a rapid, accessible, and comprehensive solution for bacterial WGS analysis.
• The pipeline empowers researchers, particularly in low-resource settings, to combat antimicrobial resistance.
• rMAP facilitates timely insights into pathogen evolution and public health surveillance.