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

Abstract

The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) using WGS data generated from Illumina's sequencing platforms. rMAP is designed for individuals with little bioinformatics expertise, and automates the steps required for WGS analysis directly from the raw genomic sequence data, including adapter and low-quality sequence read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, phylogenetic inference by maximum likelihood, antimicrobial resistance (AMR) profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis and insertion sequence characterization (IS). Once the analysis is finished, rMAP generates an interactive web-like html report. rMAP installation is very simple, it can be run using very simple commands. It represents a rapid and easy way to perform comprehensive bacterial WGS analysis using a personal laptop in low-income settings where high-performance computing infrastructure is limited.

Keywords: ESKAPE; command line; pipeline; rMAP; rapid microbial analysis; whole-genome sequencing.

Fig. 1.

Schematic graphical representation of rMAP pipeline workflow and associated tools.

Fig. 2.

Selected interactive Enterococcus species HTML reports. (a) Genome assembly summary statistics for the different Enterococcus species isolates. These include common genome analysis key metrics for checking assembly quality. (b) Table of multi-locus sequence typing (MLST) distribution. (c) SNP-based approximately maximum-likelihood phylogenetic tree. Three different formats are available, i.e circular (phylogram), circular (cladogram) and rectangular (phylogram). An approximately maximum-likelihood phylogenetic tree is computed based on SNPs detected via read mapping against a reference genome and stored in a standard Newick file format. (d) Pangenome analysis including a schematic representation of gene presence (colour) or absence (blank) between samples. (e) Antibiotic resistance profile. Presence/absence of antibiotic resistance genes (coverage and identity >90 %) for each sample. An antibiotic resistance profile is computed based on Resfinder, CARD, ARG-ANNOT, NCBI and MEGARES annotations for each isolate and transformed into an overview that allows a rapid resistome comparison of all analysed isolates.