ARES Database

The ARES Database has three table views:

The database also comes with an overview report summarizing its content.

The Nucleotide Marker table

The Nucleotide Marker Table (Image nucleotide_gene_table_16_n_p) lists AMR marker genes together with AMR related information annotated with CARD Antibiotic Resistance Ontology (ARO) accession numbers (figure 22.2).

Image nuclmarkertable
Figure 22.2: A Nucleotide Marker Table.

The table contains the following columns:

From this table, it is possible to Create a Nucleotide Sequence List with unique sequences that can be used as a database for the Find Resistance with Nucleotide DB tool. Note that the underlying sequences can be the same for two different species.

The Protein Marker table

The Protein Marker Table (Image protein_gene_table_16_n_p) lists the protein products corresponding to the sequences of the Nucleotide Marker Table (figure 22.3). The Marker Id shows the connection between nucleotide and protein markers. Note that selections in the nucleotide and protein tables are synchronized when both views are open simultaneously.

Image protmarkertable
Figure 22.3: A Protein Marker Table.

The table contains the following information:

From this table, it is possible to Create a Protein Sequence List, i.e., an annotated protein sequence list of gene markers for the proteins and species of interest. Furthermore, the button Performance Indicators opens another table with the performance statistics obtained from experimental data.

The Point Mutation Marker table

The Point Mutation Marker table (Image pointfinder_table_16_n_p) gives an overview of resistance conferring single-nucleotide polymorphisms (SNP's) and their performance data (figure 22.4).

Image pointmarkertable
Figure 22.4: A Point Mutation Marker Table.

The columns of the Point Mutation Marker Table are:

From this table it is possible to create a sequence list which can be used as a database for the Find Resistance with PointFinder tool by pressing the Create Point Mutation Database button and each mutation is associated with performance data which can be accessed by clicking the button Performance Indicators.

The Performance Indicators table

Microbial susceptibility to various compounds may depend on a combination of multiple genetic factors and/or be specific to certain organism. As such, the presence of a single gene or variant marker is not a clear indication of whether an isolate is resistant to compound or class or class of compounds. The ARES Performance Indicators table (figure 22.5) provides a measure for how well a given gene marker is expected to perform for a given compound and species. The gene marker statistics is not only calculated for the species the marker was originally identified in, but for other species as well.

Image performancetable
Figure 22.5: A Performance Table.

The ARES Performance Indicators tables were derived by identifying the gene markers in a large collection of isolates with known resistance profiles. Based on the presence of the gene markers in the isolates, confusion matrix statistics ( were calculated for a large number of marker, species, and compound combinations. In confusion matrix terms, resistant isolates are considered 'positives' and susceptible isolates are considered 'negatives'. For example, a resistant isolate with a given gene marker is considered a 'true positive', and a resistant isolate without a given gene marker is a 'false negative'.

The table with performance data is synchronized with the protein table and a selection made in the former will trigger a selection in the latter.

The ARES Database Overview Report

The ARES database overview contains some summary statistics on the content of the ARES database (figure 22.6).

Image aresreport
Figure 22.6: An example of ARES Database Overview Report.