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.

CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes

“…Several pipelines have been developed for bacterial genome analyses, especially in recent years ( Quijada et al, 2019 ; Petit and Read, 2020 ; Xavier et al, 2020 ; Sserwadda and Mboowa, 2021 ). Every pipeline has strengths and limitations in the analyses they provide, data visualization, execution, and updating policy.…”

“…Some pipelines that run on the user’s local machine do not infer quality, like Torme ( Quijada et al, 2019 ). Most of them do sequence quality filtering ( Quijada et al, 2019 ; Petit and Read, 2020 ; Xavier et al, 2020 ; Sserwadda and Mboowa, 2021 ), but we choose not to do this step once the parameters adopted can be very relative and strict filtering may cause loss of essential genes. We think that the user can evaluate FastQC intuitive reports and decide to run, or not, the pipeline.…”

“…We think that the user can evaluate FastQC intuitive reports and decide to run, or not, the pipeline. Analyses performed by our pipeline are species identification (not performed by rMAP and Bacpipe; Xavier et al, 2020 ; Sserwadda and Mboowa, 2021 ), assembly quality (not performed by rMAP; Sserwadda and Mboowa, 2021 ), and point mutations detection in specific AMR genes for K. pneumoniae, P. aeruginosa , A. baumannii , and E. cloacae subsp. cloacae (not performed by the other aforementioned pipelines; Quijada et al, 2019 ; Petit and Read, 2020 ; Xavier et al, 2020 ; Sserwadda and Mboowa, 2021 ).…”

“…Analyses performed by our pipeline are species identification (not performed by rMAP and Bacpipe; Xavier et al, 2020 ; Sserwadda and Mboowa, 2021 ), assembly quality (not performed by rMAP; Sserwadda and Mboowa, 2021 ), and point mutations detection in specific AMR genes for K. pneumoniae, P. aeruginosa , A. baumannii , and E. cloacae subsp. cloacae (not performed by the other aforementioned pipelines; Quijada et al, 2019 ; Petit and Read, 2020 ; Xavier et al, 2020 ; Sserwadda and Mboowa, 2021 ). Furthermore, regarding updating of the evaluated pipelines, the most recent version varies from 2019 (Bacpipe), 2020 (rMAP), 2021 (Torme), and 2022 (Bactopia).…”

“…Although a few pipelines and websites have been developed for bacterial genome analyses ( Quijada et al, 2019 ; Vallenet et al, 2019 ; Petit and Read, 2020 ; Sserwadda and Mboowa, 2021 ), we bring some additional advantages, focusing on clinically applied aspects, easy execution, and functional visualization. The analyses include reads quality; coverage estimation; species identification; de novo genome assembly; assembly quality; genome annotation; MLST assignment; search for genes related to AMR, virulence, and plasmids and point mutations detection in specific AMR genes.…”