Find Resistance with Nucleotide Database

Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. The Find Resistance with Nucleotide Database tool may be used for resistance typing of pre-assembled, complete or partial genomes simple contig sequences assembled using the de novo assembly algorithm of CLC Genomics Workbench (see

Alternatively, use the Type a Known Species or Type among Multiple Species template workflows as described in Workflow templates.

Find Resistance with Nucleotide Database is inspired by [Zankari et al., 2017] and uses BLAST for identification of acquired antimicrobial resistance genes within whole-genome sequencing (WGS) data. The tool detects resistance conferring genes, whether they break down (e.g. beta-lactamases) or expel (e.g. efflux-pumps) antimicrobial compounds.

Nucleotide resistance databases for use with the tool can be downloaded using Download Resistance Database (Download Resistance Database).

To perform resistance typing, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Drug Resistance Analysis (Image resistance_folder_closed_16_n_p) | Find Resistance with Nucleotide Database (Image find_resistance_16_h_p)

Select the input genome or contigs (figure 12.3).

Image resfinder1
Figure 12.3: Pre-assembled and complete- or partial genomes simple contig sequences may be used as input for resistance typing.

You can then specify the settings for the tool (figure 12.4).

Image resfinder2
Figure 12.4: Select database and settings for resistance typing.

The output of the Find Resistance with Nucleotide Database tool is a table listing all the possible resistance genes and predicted phenotypes found in the input genome or contigs, as well as additional information such as degrees of similarity between the gene found in the genome and the reference (% identity and query /HSB values) and the location where the gene was found (contig name, and position in the contig). Depending on the type of database used, additional columns with link to resources may also be present in the table. To add the obtained resistance types to your Result Metadata Table, see the section Extend Result Metadata Table.