rMAP

rMAP performs comprehensive resistome and genomic profiling of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) from Illumina whole-genome sequencing (WGS) data.

Key Features:

• Illumina WGS support: Processes Illumina whole-genome sequencing (WGS) data for downstream genomic analyses.
• Adapter and quality trimming: Performs adapter and low-quality sequence read trimming.
• De novo genome assembly: Performs de novo genome assembly.
• Genome annotation: Performs genome annotation on assembled sequences.
• SNP variant calling: Performs single-nucleotide polymorphism (SNP) variant calling.
• Phylogenetic inference: Constructs phylogenies using maximum likelihood methods.
• Antimicrobial resistance (AMR) profiling: Performs AMR profiling to identify resistance determinants.
• Plasmid profiling: Performs plasmid profiling to identify mobile genetic elements.
• Virulence factor determination: Determines presence of virulence factors.
• Multi-locus sequence typing (MLST): Performs MLST for strain differentiation and epidemiology.
• Pangenome analysis: Performs pangenome analysis to assess genomic diversity within species.
• Insertion sequence (IS) characterization: Characterizes insertion sequences (IS) contributing to genomic variability.

Scientific Applications:

• Antimicrobial resistance surveillance: Monitoring the evolution and distribution of antimicrobial resistance determinants across ESKAPE pathogens.
• Epidemiological investigations: Supporting outbreak tracing and transmission-pathway analysis through comparative genomics and phylogenetics.
• Clinical and translational research: Informing clinical decision-making by identifying resistance patterns, sequence types, and potential therapeutic targets.

Methodology:

Explicit computational steps include adapter and low-quality read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, maximum likelihood phylogenetic inference, antimicrobial resistance profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis, and insertion sequence (IS) characterization.