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AST Browser Documentation Main documentation page

Beta Release

What is the AST Browser AST_Browser TOC Main documentation page

For many isolates, NCBI has collected antibiotic susceptibility testing data (AST), which currently are stored in each isolate's BioSample record. To allow easier examination of these AST data and to allow users to access other NCBI resources for those isolates which have interesting AST data, we have developed the AST Browser, which presents these data in a searchable, tabular format. These data can be downloaded for further analysis as well. The entire collection of AST data also can be viewed in BioSample by using the Entrez search prompt "antibiogram[filter]].

Each row in this browser is an individual AST result, and usually multiple AST results are provided for an individual isolate. See Cross-browser selection below for information on how to view more information on the isolates and geneotype for those isolates.

The context of the AST Browser data AST_Browser TOC Main documentation page

These data are submitted by users, and thus we do not verify relationships between fields: for example, if someone stated they used a certain concentration of a beta-lactamase inhibitor, even though that is not CLSI standard, the AST Browser still displays those data. Note these data are not computed from genomic data—these data are the results of phenotypic testing by the submitter. In addition, the AST Browser currently does not support AST data generated for Mycobacterium sp., as these data use a different format.

Relationship between the Pathogen Detection AST Browser, Isolates Browser, and MicroBIGG-E AST_Browser TOC Main documentation page

The Pathogen Detection AST Browser has AST data for isolates that are also in the Isolates Browser and have genome sequences that have been analyzed by the Pathogen Detection system. Using the Cross-browser selection tool you can link out to identify the isolates and the genetic elements for the isolates associated with each AST result.

Where to access the Pathogen Detection AST Browser AST_Browser TOC Main documentation page

The Pathogen Detection AST Browser is accessible from a link on the right margin of the Pathogen Detection Project home page, from the AMR landing page, the AMR Resources page, and directly from the URL https://www.ncbi.nlm.nih.gov/pathogens/ast/.

Using the AST Browser AST_Browser TOC Main documentation page

Search terms AST_Browser TOC Main documentation page

The AST Browser can be searched by the terms that appear in any of the fields and filters described below. Information on how to use the filter panels is described here.

Filters AST_Browser TOC Main documentation page

The "Filters" options in the Pathogen Detection AST Browser enable you to subset the data in a variety of ways, and therefore can be used to refine your results, whether you have done a basic search or an advanced search. The numbers along side the filters display the number of rows for that option once selected.

  • By default, each filter displays the top 100 terms (based on the number of items retrieved by a term) listed by count of value within that set of top 100.
  • A Boolean "OR" is applied if multiple items are checked in the same filter field. This way you can choose multiple values in the same filter. For example: A Boolean "OR" is applied if multiple items are checked in the same filter field. This way you can choose multiple values in the same filter. For example:
  • Click the "Filters" bar of the AST Browser, then click the "Antibiotic" filter. In the new panel select "carbapenems" to filter the list for ASTs for carbapenem drugs.
  • A Boolean "AND" is applied if you select items in several different filter panels (Type, Scope, etc). For example:
  • As explained in the Isolates Browser Help, Filters are generated on the fly. As a result, the terms that are listed under each filter will depend on the data your are currently displaying in the browser.

Data fields in the AST Browser AST_Browser TOC Main documentation page

The data fields listed below have been indexed by the Pathogen Detection project, and can be searched using the advanced search techniques that are described in the Isolates Browser help, because both use the SOLR query language. Note that the data field names and values are case sensitive, as described in the Isolates Browser help.

  • Biosample: The BioSample accession of the isolate. For more information, see here.
  • Organism group: Name of the organism group. For more information about organism groups, see here.
  • Scientific name: Scientific name (in NCBI Taxonomy) of the isolate from the submitter. To search for specific taxa, you can enter the genus name (or the full genus and species name) of the pathogen, with the first letter of the genus capitalized.
  • Isolation type: Isolation type of an isolate: clinical OR environmental/other OR NULL. Note, this field is derived from the attribute package selected by the isolate's submitter using one of the Pathogen templates in BioSample.
    • If attribute_package=Pathogen.cl.1.0 then isolation type is clinical.
    • If attribute_package=Pathogen.env.1.0 then isolation type is environmental/other, unless host or isolation_source indicates that it was isolated from a human subject in which case isolation type is clinical.
    • If neither of these packages is used then isolation type is NULL. Additional information can be found here.
  • Location: The geographical location where the sample was collected, if provided by the submitter. This matches the /country qualifier of GenBank records. For more information, see here.
  • Isolate: Pathogen Detection accession of the isolate. The accession begins with the prefix "PDT," which stands for Pathogen Detection Target. This database is the primary resource issuing PDT accessions. Additional information can be found here.
  • Antibiotic: The antibiotic used for testing. The values for antibiotics are derived directly from the values in BioSample. In the filter, antibiotics in this field are arranged in a hierarchy based on how antibiotics are related to each other, and selecting a higher node will automatically select the lower nodes, even without specifically selecting the lower nodes. For example, selecting “streptogramins” in the Antibiotic filter panel will select all lower nodes, including “quinupristin-dalfopristin” and “synercid”. To search this field for specific antibiotics directly, enter a query such as "antibiotic:ciprofloxacin". To mimic the filter operation, users can entry a query such as “MESH:streptogramins”. The complete list of antibiotics and additional information can be found here. The complete list of antibiotics and additional information can be found here.
  • Resistance phenotype: The resistance phenotype as determined by phenotypic testing, not derived from genomic or genotypic data. This determination is made by the submitter. To search this field directly, enter a query such as "phenotype:resistant". Additional information can be found here.
  • MIC (mg/L): The concentration of the antibiotic used. For combination drugs, the concentrations of the two drugs are expressed as “X/Y”. For example, a value of 32/4 for the drug combination piperacillin-tazobactam means that piperacillin and tazobactam were tested simultaneously at concentrations of 32 and 4 mg/L respectively. To search this field directly, enter a query such as "mic:4". Additional information can be found here.
  • Disk diffusion (mm): The size of the zone of inhibition surrounding the disk in mm. Note that the minimal value is 6mm. To search this field directly, enter a query such as "disk_diffusion:14". Additional information can be found here.
  • Laboratory typing platform: The name of the testing platform. This is an optional field. To search this field directly, enter a query such as "platform:Vitek". Additional information can be found here.
  • Vendor: The name of the test manufacturer. This is an optional field. To search this field directly, enter a query such as "vendor:Siemens". Additional information can be found here.
  • Laboratory typing method version or reagent: The specific version or test used. This is an optional field. To search this field directly, enter a query such as "reagent:GM-NEG". Additional information can be found here.
  • Testing standard: The testing standard used for the determination of resistance cutoffs and testing methods (e.g., CLSI). To search this field directly, enter a query such as "standard:CLSI". A list of acceptable values can be found here.
  • BioProject: The BioProject accession of the BioProject to which the isolate belongs.
  • Collection date: Date sample was collected, in the format the submitter supplied. This may differ from the type the data was submitted to INSDC and also different than the time the data was added to the Pathogen Detection project. For real-time submissions of pathogen surveillance data, these dates will be in close proximity. For legacy data, or research projects, these dates may differ wildly and be separated by years. Importantly, for some isolates these data are missing, unlike Create date, where every isolate has a first date of uptake into the Pathogen Detection system.
  • Create date: The date on which this isolate was first seen by the Pathogen Detection system, in the format: YYYY-MM-DD. Note, these dates are in ISO format.
  • Host: The host species, if provided by the submitter. This field contains values exactly as they were entered by the data submitters. Some submitters might have entered a scientific name while others might have entered a common name; therefore, search for synonyms if you would like to retrieve more comprehensive results. Data field names and values are case sensitive.
  • Isolation source: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived, if provided by the submitter. This field contains values exactly as they were entered by the data submitters. Data field names and values are case sensitive. Additional information can be found here.
  • Isolation type: Isolation type of an isolate: clinical OR environmental/other OR NULL. Note, this field is derived from the attribute package selected by the isolate's submitter using one of the Pathogen templates in BioSample.
    • If attribute_package=Pathogen.cl.1.0 then isolation type is clinical.
    • If attribute_package=Pathogen.env.1.0 then isolation type is environmental/other, unless host or isolation_source indicates that it was isolated from a human subject in which case isolation type is clinical.
    • If neither of these packages is used then isolation type is NULL. Additional information can be found here.

Output AST_Browser TOC Main documentation page

Users have two options for output. One is to download the data as a table, and the other is to use the search results to interogate other NCBI resources.

Tabular List of AST Data AST_Browser TOC Main documentation page

To download the data in a tabular format, click the "Download" button in the header of the AST Browser table to download data. You can either download a tab-delimited or csv formatted representation of the table view. Downloads are limited to 100,000 rows.

Cross-Browser Selection: Interactions with other NCBI tools AST_Browser TOC Main documentation page

Having selected a set of AST data using the filters (and the MicroBIGG-E International Map Panel, if desired), users can view those isolates with those AST data either in the Isolates Browser or MicroBIGG-E. To use these features users must be logged in to MyNCBI, see the login button in the upper right of the screen to log in or set up an account if you don't have one already.

To view isolates with the selected AST data in the Isolates Browser, select the buttons adjacent to “View selected isolates in…” in the blue bar at the top. This cross browser selection will display the isolates containing the selected AST data in the Isolates Browser, but for the MicroBIGG-E selection, the subset of rows will be for all all elements.

Update Frequency AST_Browser TOC Main documentation page

The database behind the AST browser is updated daily as new taxgroup processing is complete. Because AST data submitted to BioSample may take some time to be transmitted to the Pathogen Detection System the delay for updates for AST data can sometimes be longer.

Submitting AST Data AST_Browser TOC Main documentation page

AST data can be supplied as a separate table at submission time along with the isolate metadata via the Submission Portal. There are two templates, one for standard MIC-based antibiograms for most bacteria, and one specifically for mycobacteria without MICs.

Specifications for the antibiogram submission format, along with controlled vocabularies for various fields can be found at: