Antimicrobial Resistance and Other Clinical Metadata

Genome-Level Antimicrobial Resistance (AMR) Information

Genome-level AMR metadata are curated primarily from sequencing projects from the NIAID-funded Genomic Centers for Infectious Diseases. These data include panel data for antibiotics and chemicals. PATRIC support for AMR metadata includes:

Antimicrobial Resistance metadata field. This field shows genomes that have been specifically tested against certain antibiotics and the resulting phenotype from that test. Note that a genome can have multiple antibiotic phenotypes, such as being resistant to one drug and susceptible to another. The values included in this field are:

  • ‘Resistant’
  • ‘Susceptible’
  • ‘Intermediate’

Antimicrobial Resistance Evidence metadata field. Some of the genomes included in PATRIC have a specific phenotype that has been assigned, such as MRSA, and some of the genomes have been screened by broad, antimicrobial resistant panels (AMR panels). We have created a new field that identifies which metadata available on the PATRIC website contains the evidence supporting the resistance category assigned.

  • ‘Phenotype.’ Genomes in this category were assigned their resistance category based on phenotype information provided by the sequencing center, for instance MRSA or MSSA. This phenotype data is available at PATRIC as well.
  • ‘AMR Panel.’ Some genomes have been tested against a panel of antibiotics, with the results of the screening reported in a table using either a specific designation (such as ‘Susceptible,’ ‘Resistant,’ or ‘Intermediate’), or the minimum inhibitory concentration (MIC). For genomes in this category, the panel data is available for download. In future releases, this data will be more fully integrated on the PATRIC website.
  • ‘Comment.’ The basis for the resistance category for these genomes can be found in the comment metadata field. This information may have come from the comment field at GenBank, or in a comment field from data provided by the sequencing center or their sample provider. In some cases, the comment has been provided by literature-based curation by the PATRIC team; in these cases, a link to the corresponding publication is also available.

The Antimicrobial Resistance metadata field and the Antimicrobial Resistance Evidence metadata field are available as filterable facets on the Genome list pages, allowing sorting on the terms ‘Susceptible’, ‘Resistant’ or ‘Intermediate’ to locate the genomes tagged with that information. In addition, filters are available for the source of the information, which provides the ability, for example, to only include genomes that have complete AMR panel information and exclude genomes where there is only a comment.

Other Clinical Metadata

Some clinical metadata that is available for only a subset of the genomes available at PATRIC. This includes new typing methods that are specific to a small number of genomes (such as spa type or wzi type), but are still important to researchers. These data are stored as a key-value pairs so that the Global Search can find genomes that contain any data for that field (e.g., search for ‘wzi’) or for genomes with specific values for that field (e.g., search for ‘wzi:29’)

The Show/Hide capability on Genome lists to expose or hide the new metadata fields. The information is also available on each Genome Summary page by selecting clicking on the Summary information. When a list of genomes is downloaded, all of the new metadata fields are also included in the list of metadata available.