Find Resistance with ResFinder

Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. The Find Resistance with ResFinder 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 http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=De_novo_assembly.html. Alternatively, use the Type a Known Species or Type among Multiple Species template workflows as described in the chapter Workflow templates.

The Find Resistance with ResFinder tool 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's aim is to quantify the occurrence of entire resistance conferring genes, whether they break down (e.g. beta-lactamases) or expel (e.g. efflux-pumps) antibiotic compounds.

To perform resistance typing, go to:

        Metagenomics | Drug Resistance Analysis | Find Resistance with ResFinder (Image find_resistance_16_h_p)

Select the input genome or contigs (figure 8.4).

Image resfinder1
Figure 8.4: 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 8.5).

Image resfinder2
Figure 8.5: Select database and settings for resistance typing.

The output of the Find Resistance with ResFinder 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), the location where the gene was found (contig name, and position in the contig) as well as a link to NCBI. To add the obtained resistance types to your Result Metadata Table, see the section Add to Result Metadata Table.