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.
Highlights
The recent re-e mergence of multidrug-resistant pathogens through persistent misuse of antibiotics has exacerbated their threat to worldwide human public health and well- being
Such organisms, consisting of Staphylococcus aureus, Pseudomonas aeruginosa and Klebsiella species belonging to the ESKAPE pathogen group, have been flagged among the most notorious micro-organisms expressing tremendously high levels of antimicrobial resistance by the World Health Organization (WHO), and have been reported by many studies to contribute to the high frequency of nosocomial infections which have led to high morbidity and mortality rates all over the world [1,2,3]
We introduce the Rapid Microbial Analysis Pipeline, a one-stop toolbox that uses whole-genome sequencing (WGS) illumina data to characterize the resistomes of bacteria of ESKAPE origin
Summary
The recent re-e mergence of multidrug-resistant pathogens through persistent misuse of antibiotics has exacerbated their threat to worldwide human public health and well- being. Such organisms, consisting of Staphylococcus aureus, Pseudomonas aeruginosa and Klebsiella species belonging to the ESKAPE pathogen group, have been flagged among the most notorious micro-organisms expressing tremendously high levels of antimicrobial resistance by the World Health Organization (WHO), and have been reported by many studies to contribute to the high frequency of nosocomial infections which have led to high morbidity and mortality rates all over the world [1,2,3]. Rapid advances in diagnostic science and personalized medicine have seen the emergence of high- throughput next-g eneration sequencing technologies to replace conventional microbiology laboratories, and this has greatly reduced diagnostic costs and turnaround times for results for infectious pathogens as a way of keeping pace with emerging multidrug-resistant varieties. The field of microbial bioinformatics is thriving and quickly adapting to technological changes, which creates difficulties for clinical microbiologists with little or no bioinformatics background in following the complexity and increasingly obscure jargon of this field [4]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
