PATRIC Antimicrobial Resistance (AMR) Gene Curation

PATRIC has undertaken an antimicrobial resistance (AMR) curation effort with the goal of providing PATRIC users with the ability to rapidly recognize and project known AMR related genome features to new genomes in an automated fashion and to use comparative genomics approaches for the discovery of new resistance mechanisms.

Specific Aims:

  • Catalog published AMR related genes in the 22 genera of infectious disease organisms, providing high quality detailed annotations of all AMR determinants
  • Enable rapid recognition and automated projection of known AMR related genome features to new genomes
  • Support classification of genomes as resistant or susceptible
  • Enable prediction and discovery of novel resistance mechanisms

The ongoing AMR curation enables this through the development and of a comprehensive up-to-date collection of AMR determinants and genomic variations.  These structured collections will be used in several ways including automated propagation of AMR-related annotations that will significantly enhance AMR analysis for PATRIC users.

Two approaches are currently under construction to project AMR gene annotations to a new genome. First, once a new AMR-related function has been entered into the database, it will be recognized by our k-mer-based projection software, and new genomes with the gene will be annotated with that function (1-3). Secondly, when a genome that is being annotated is very similar to one of the reference genomes in PATRIC, the AMR annotations from the reference genome will be directly applied to the new genome, when appropriate to do so.

The database that will drive this annotation module is currently under construction.  It is structured as a collection of dedicated AMR-related Subsystems that are being added to the genome annotation engine underlying the PATRIC database. Subsystems connect encoded AMR determinants to relevant literature, describe mechanisms of action (if available), and lay the basis for variation analysis.  Approximately half of new Subsystems required to encode known AMR-related genes and gene products are in place. An Excel spreadsheet with these data is available here.  Together they cover 265 unique Functional roles (isofunctional protein families), each corresponding to a specific AMR determinant encoded across a representative set of ~1000 diverse prokaryotic genomes.

Curation thus far has focused on encoding the following mechanisms of drug resistance (shown below): outer membrane porins, multidrug efflux mechanisms, and capsular and extracellular polysacchrides (as the balance of drug influx and efflux is the first line of microbial defense against antibiotics).  In addition, all types of tetracycline resistance have been captured and work on beta-lactamases has started.  The remaining AMR determinants will be encoded during the remainder the project.

Common mechanisms of drug resistance

  • Efflux pumps
    • Up-regulation, often via mutations in promotors, operators
  •  Outer membrane proteins/porins (influx)
    • Inactivation via loss of function mutations, deletions, truncations
  •  Drug modifying enzymes
    • Ribosome protection (TetR) proteins
    • β-lactamases
    • Aminoglycoside-modifying enzymes
    • RNA methyltransferases
  •  Target modifications
    • Gyrase modifications (gyrA/B, parC/E mutations)
    • Ribosomal subunit, rRNA mutations
    • mecA – PBP2a (MRSA)

References

  1. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365. PMID: 25666585. PMCID: PMC4322359.
  2. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. PMID: 24293654. PMCID: PMC3965101.
  3. Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H. PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. Front Microbiol. 2016 Feb 8;7:118. doi: 10.3389/fmicb.2016.00118. eCollection 2016. PMID: 26903996. PMCID: PMC4744870.