Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. The Find Resistance with Nucleotide DB 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 Workflow templates.
Find Resistance with Nucleotide DB 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 () | Drug Resistance Analysis () | Find Resistance with Nucleotide DB ()
Select the input genome or contigs (figure 14.3).
You can then specify the settings for the tool (figure 14.4).
- Database Select a nucleotide resistance database.
- Minimum Identity % is the threshold for the minimum percentage of nucleotides that are identical between the best matching resistance gene in the database and the corresponding sequence in the genome.
- Minimum Length % reflect the percentage of the total resistance gene length that a sequence must overlap a resistance gene to count as a hit for that gene. Here represented as a percentage of the total resistance gene length.
- Filter overlaps: will perform extra filtering of results per contig, where one hit is contained by the other with a preference for the hit with the higher number of aligned nucleotides (length * identity).
The output of the Find Resistance with Nucleotide DB 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.