Resistome
What is AMRFinder+?
The AMRFinderPlus software and the accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein sequences.
AMRFinderPlus uses an AMR protein database, HMMs, a hierarchy of AMR protein families, and a custom rule set to identify AMR genes and point mutations, stress response genes, and virulence genes.
The database is highly curated with hierarchical structure for AMR proteins, manually curated cutoffs, and associated hierarchical names. It also includes point mutations, stress response and virulence genes, and it contains additional descriptive fields for each gene or point mutation.
References:
How to access to the Antibiotic Resistance predictions?
AMRFinderPlus predictions can be accessed via the Resistome page, located in the Comparative Genomics section of the main navigation menu. Results can also be queried through the “Search by Keywords” page under “Resistome results” in the Search/Export section.
How to read AMRFinderPlus results?
AMRFinderPlus is ran with the protein sequences as input using the ‘plus’ option and the ‘organism’ option.
the ‘plus’ option provides results from “Plus” genes such as virulence factors, stress-response genes, etc.
the ‘organism’ option delivers optimized organism-specific results (only for organisms which have been curated). It screens for point mutations, filter out non-informative genes and indentify specific features such as stx type in Escherichia or pbp proteins in Streptococcus pneumoniae or Neisseria gonorrhoeae.
All result fields are described in detail in the official AMRFinderPlus documentation. We recommand checking this page for more details.
Method: Type of hit detected by AMRFinderPlus (ALLELEP, EXACTP, PARTIALP, PARTIAL_CONTIG_ENDP, BLASTP, HMM, POINTP). The “P” suffix denotes that the analysis was performed using protein sequences.
AMRFinderPlus Element Symbol: Gene or gene-family symbol for protein or nucleotide hit, with a link to its entry in the Reference Gene Catalog.
AMRFinderPlus Element Name: Full-text name for the protein, RNA, or point mutation.
Scope: The AMRFinderPlus database is split into ‘core’ AMR proteins that are expected to have an effect on resistance and ‘plus’ proteins of interest added with less stringent inclusion criteria. These may or may not be expected to have an effect on phenotype.
Type and Subtype: These fields describe the classification of the AMRFinderPlus gene. “Element type” is split into 3 categories, AMR, STRESS, or VIRULENCE. “Element subtype” is a duplicate of “Element type” unless a more specific category has been defined.
Class: For AMR genes this is the class of drugs that this gene is known to contribute to resistance of.
Subclass: If more specificity about drugs within the drug class is known it is elaborated here.
Closest Reference Accession: RefSeq accession for reference hit by BLAST if a blast alignment was detected otherwise NA. The link directs to the corresponding entry in NCBI.
Closest Reference Name: Full name assigned to the closest reference hit if a blast alignment was detected, otherwise NA.
HMM accession: Accession for the HMM, with a link to its entry in the Reference HMM Catalog.
HMM description: The family name associated with the HMM.
Query Length: The length of the query protein or gene.
Subject Length: The length of the Reference protein in the database if a blast alignment was detected.
Coverage: % of reference covered by blast hit if a blast alignment was detected.
Identity: % amino-acid identity to reference protein if a blast alignment was detected.
Alignment length: Length of BLAST alignment in amino-acids if a blast alignment was detected.
For all tables, you can export the genes by clicking on Export to Gene Cart.