Microbial Resistance, Plasmid and Virulence (RPV) identification

Table of Contents

• Microbial Resistance, Plasmid and Virulence (RPV) identification
  • Table of Contents
  • Introduction
  • Description
  • Dependencies
  • Installation
    • Environment
    • Databases
  • Usage
    • rpv.py
    • rpv.py command
  • References

Introduction

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Monitoring the evolution of resistance, plasmid and virulence of bacterial strains is essential in epidemiology. This tool allows the identification of resistance, plasmid and virulence genes. Several tools and databases are available. For this, we rely on three public and regularly updated databases. ResFinder for resistance data, PlasmidFinder for plasmid data and VirulenceFactors(VFDB) database for virulence data.

Description

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The program has been developed for use in a command line under a linux system. So some basics are necessary. You will have a simple guide to make the program work without being a linux expert

RVP is a python script that takes as input:

• A database in fasta format
• One or more nucleotide sequences of the assambled strains (the contigs in fasta format)

And it returns a table mentioning the genes identified for each strain.

Dependencies

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• Linux
• Python >= 3.7
• Databases : ResFinder_db, PlasmidFinder_db, VFDB
• Install requierements : Python packages
• blat

Installation

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Environment

• Install python virtual environnement

  python3 -m venv /path/to/new/virtual/environment

• Install python packages

  pip install -r requierements.txt

• Install RPV

  git clone https://github.com/ATCHON/rpv.git

Or download it in .zip format

Databases

Create a directory for downloading last databases updates.

• ResFinder database

  git clone https://[email protected]/genomicepidemiology/resfinder_db.git
  cd resfinder_db
  bash RPV/scr/rmv_dup_seq.sh named_temporary_database.db named_finaly_database.db

• PlasmiFinder database

  git clone https://[email protected]/genomicepidemiology/plasmidfinder_db.git
  cd resfinder_db
  bash rpv/content/scr/rmv_dup_seq.sh named_temporary_database.db named_finaly_database.db

• Virulence Factor database

  • Go to Download page
  • Select "DNA sequences of dataset"
  • Remove duplicate sequences

  gunzip VFDB_setA_nt.fas.gz
  awk '/^>/{f=!d[$1];d[$1]=1}f' VFDB_setA_nt.fas > named_finaly_database.db
  

Default databases are available in rpv/content/databases.
The update date corresponds to the values following the database name in the format "database_name_creation_date.db".

Default databases are available for use in rpv/content/databases

Usage

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rpv.py

Usage:

$ rpv.py [OPTIONS] COMMAND [ARGS]...

Commands:

• plasmid: Search plasmid genes
• resistance: Search resistance genes
• virulence: Search virulence genes

rpv.py command

Usage:

$ rpv.py command [OPTIONS] DATABASE SEQUENCES...

Arguments:

• DATABASE: Database in fasta format [required]
• SEQUENCES...: Sequence(s) in fasta format. [required]

Options:

• --output PATH: Output file path of the result (.tsv).
• --identity INTEGER RANGE: Minimum percentage of sequence identity [default: 90]
• --coverage INTEGER RANGE: Minimum percentage of sequence identity. [default: 80]
• --help: Show this message and exit.

References

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• Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020 Dec 1;75(12):3491-3500. doi: 10.1093/jac/dkaa345. PMID: 32780112; PMCID: PMC7662176.
• PlasmidFinder and pMLST: in silico detection and typing of plasmids. Carattoli A, Zankari E, Garcia-Fernandez A, Volby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H. Antimicrob. Agents Chemother. 2014. April 28th.
• Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022 Jan 7;50(D1):D912-D917. doi: 10.1093/nar/gkab1107. PMID: 34850947; PMCID: PMC8728188.