Download Resistance Database

Download Resistance Database enables download of databases for use with the Find Resistance with Nucleotide Database, Find Resistance with PointFinder and Find Resistance with ShortBRED tools.

To run the tool, go to:

        Tools | Microbial Genomics Module () | Databases () | Drug Resistance Analysis () | Download Resistance Database ()

The available databases fall into four categories:

ShortBRED Marker Databases

These databases can be used with Find Resistance with ShortBRED (Find Resistance with ShortBRED). The databases are marker databases, containing peptide fragments that uniquely characterize sets of similar proteins, rather than a specific gene.

• QMI-AR Peptide Marker Database. The QIAGEN Microbial Insight - Antimicrobial Resistance database is a curated database containing peptide markers derived from the following source databases: CARD [Alcock et al., 2023] (https://card.mcmaster.ca/), ARG-ANNOT [Gupta et al., 2014] (https://www.mediterranee-infection.com/acces-ressources/base-de-donnees/arg-annot-2/), NCBI Bacterial Antimicrobial Resistance Reference Gene Database (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047), ResFinder (https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/).

• CARD Peptide Marker Database. Peptide markers derived from the Comprehensive Antibiotic Resistance Database [Alcock et al., 2023] (https://card.mcmaster.ca/).

• ARG-ANNOT Peptide Marker Database. Protein markers from the ARG-ANNOT database [Gupta et al., 2014] (https://www.mediterranee-infection.com/acces-ressources/base-de-donnees/arg-annot-2/).

Nucleotide Databases

These databases can be used with Find Resistance with Nucleotide Database (Find Resistance with Nucleotide Database). The databases contain nucleotide gene sequences.

• QMI-AR Nucleotide Database. The QIAGEN Microbial Insight - Antimicrobial Resistance database is a curated database containing nucleotide sequences compiled from the following source databases: CARD [Alcock et al., 2023] (https://card.mcmaster.ca/), ARG-ANNOT [Gupta et al., 2014] (https://www.mediterranee-infection.com/acces-ressources/base-de-donnees/arg-annot-2/), NCBI Bacterial Antimicrobial Resistance Reference Gene Database (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047), ResFinder (https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/).

• VFDB. Nucleotide sequences compiled from the Virulence Factor database core dataset (https://www.mgc.ac.cn/VFs/main.htm).

• CARD Nucleotide Database. Nucleotide sequences compiled from the Comprehensive Antibiotic Resistance Database (CARD) (https://card.mcmaster.ca/).

• ResFinder Nucleotide Database. Nucleotide sequences from the ResFinder database (https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/).

Point Mutation Databases

These databases are used with Find Resistance with PointFinder (Find Resistance with PointFinder).

• PointFinder. Organism-specific databases containing wild type genes and known resistance conferring mutations [Zankari et al., 2017] (https://bitbucket.org/genomicepidemiology/).