KEGG Pathogen Resource

KEGG Pathogen is an interface to pathogen genomes and infectious diseases in KEGG for understanding molecular mechanisms of pathogenicity and antimicrobial resistance (AMR) from genomic information. It summarizes various datasets stored in the GENOME, GENES, PATHWAY, DISEASE and DRUG databases.

Pathogen genomes Disease pathways Drug resistance pathway Disease entries Antimicrobial drugs Toxins

Antimicrobial Resistance

Efforts are being undertaken to define characteristic genes and gene sets in pathogen genomes that would have diagnostic values for detecting AMR. First, known AMR genes are collected in the Addendum category of the GENES database. Second, finely classified KOs, called tight KOs, are defined for these genes, so that substrate specificity and other features relevant to AMR can be distinguished. Third, signature KOs and signature modules (sets of KOs) are defined whenever they have diagnostic values.

Using BlastKOALA to detect AMR

The BlastKOALA automatic annotation server can now be used to detect AMR from pathogen genomes. Note that the Pathogen Checker tool has been discontinued and merged into BlastKOALA. Upload a set of amino acid sequences of a pathogen genome to the BlastKOALA server, which automatically assigns KOs and creates KEGG Mapper links in the result page. The Reconstruct Brite option of KEGG Mapper will show the mapping results against Brite hierarchy files (such as Antimicrobial resistance genes) and Brite table files (such as KEGG signatures), which may be used for interpretation of AMR.
BlastKOALA Query Data Input

  1. Kanehisa, M.; Inferring antimicrobial resistance from pathogen genomes in KEGG. Methods Mol. Biol. 1807, 225-239 (2018). [pubmed]

Last updated: August 14, 2018