Antimicrobial Resistance

Analysing antimicrobial resistance phenotypes in the collection view.

About the Resistance Tables

The resistance predictions from the antimicrobial resistance (AMR) prediction module are displayed in the final set of three tabs: "Antimicrobials | SNPs | Genes".

Within each tab it is possible to display the distribution of resistance in both the Tree Viewer and the Map View by clicking on the relevant column header. Holding the command or control button will allow you to select multiple columns, this showing the distribution of multi-drug resistant phenotypes or genotypes.

The Tables

Antibiotics Table

The first tab contains the simple resistance profile, based on the aggregation of the all the resistance genes and variants identified. For full details on how this profile is constructed visit the resistance module description. The antibiotic is given as a short three letter name, while mousing over will reveal the complete name. Resistance is indicated by a red circle, partial resistance is yellow, and inducible resistance is orange.

SNPs Table

Individual resistance-associated mutations are listed in the SNPs tab. Mutations are grouped by the antibiotic they give resistance to, so a mutation that provides resistance to more than one antibiotic may be listed more than once. The mutations are further grouped by the gene they are found in, with the gene name in an empty column to the left of the mutation. Gene names are always followed by an underscore, while mutation names are given in the tradition wild-type:position:mutation notation, e.g. R78Q. Mutations may be given as amino acids (protein encoding genes), or nucleotides (RNA genes). Variants that individually are indicative of a resistant phenotype are show with a red circle, elements that contribute either in combination with other genes or variants are yellow, inducible resistance is marked orange, while suppressing mechanisms are teal

A yellow determinant marker does not indicate clinical resistance of any level by itself. The phenotype is determined from the combination of identified markers

Genes Table

Individual resistance-associated genes are grouped by the antibiotics they give resistance to. Genes that confer resistance to more than one antimicrobial will be shown more than once in the table. Presence of an acquired resistance determinant is marked with a circle coloured according to the same rules of the SNPs table.