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. The following Brite files summarize various datasets stored in the GENOME, GENES, PATHWAY, DISEASE and DRUG databases.
Category Brite file
Disease classification 08401 Infectious diseases (with pathogen genomes)
Drug classification 08307 Antimicrobials (with target information)
Disease pathway map 08901 Infectious disease: viral
08901 Infectious disease: bacterial
08901 Infectious disease: parasitic
AMR pathway map 08901 Drug resistance: antimicrobial
Drug development 08901 Chronology: Antiinfectives (KEGG DRUG structure maps)
Toxin 08009 Natural toxins (Compound dataset)
02024 Bacterial toxins (KO dataset)

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.
Category Brite file
KO data 01504 Antimicrobial resistance genes
01600 KEGG signatures (signature KOs and signature modules)
Sequence data 01553 beta-Lactamases
01554 Aminoglycoside resistance genes
01556 Tetracyclin resistance genes
01555 Macrolide resistance genes
01557 Other resistance genes

See more details in KEGG Sequence Data Collection

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.

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

Last updated: August 12, 2022