Prevalence

Antimicrobial resistance (AMR) molecular prevalence data was generated using the Resistance Gene Identifier (RGI), a tool for putative AMR gene detection from submitted sequence data using the AMR detection models available in CARD. To generate prevalence data, RGI was used to analyze molecular sequence data available in NCBI Genomes for the World Health Organization’s priority pathogens, the ESKAPE pathogens, and additional pathogens of interest. For each of these pathogens, complete chromosome sequences, complete plasmid sequences, and whole genome shotgun (WGS) assemblies were analyzed individually by RGI. RGI results were then aggregated to calculate percent occurrence. For example, if 50 WGS assemblies were analyzed and blaNDM-1 was predicted by RGI in 40, the calculated prevalence would be 80%. Results are further categorized using the Antibiotic Resistance Ontology (ARO), e.g. "beta-lactam resistance protein", "antibiotic inactivation enzyme", etc.

Prevalence data is available under both the Perfect and Strict paradigms of RGI, the former tracking perfect matches to the curated reference sequences and mutations in the CARD, while the latter detects previously unknown variants of known AMR genes, including secondary screen for key mutations, using detection models with curated similarity cut-offs to ensure the detected variant is likely a functional AMR gene. For more information, see the Resistance Gene Identifier.

The reported results are entirely dependant upon the curated AMR detection models in CARD, the algorithms available in RGI (currently only using protein homolog models and protein variant models), and the sequence data available at NCBI. Reported frequencies have not been corrected for unmeasured clonality or sampling bias of genomic data available at NCBI. Prevalence data will change over time as CARD curation, RGI software, and NCBI data evolve.

CARD Prevalence 1.0.2 is based on sequence data acquired from NCBI on August 28, 2017, analyzed using RGI 3.2.1 (DIAMOND homolog detection) and CARD 1.2.1.

Sampling

The number of completely sequenced genomes, completely sequenced plasmids, or whole-genome shotgun assemblies analyzed for each pathogen. All sequence data acquired from NCBI Genomes.

Species NCBI Chromosome NCBI Plasmid NCBI WGS
Phenotype

Prevalence of AMR genes and variants organized by Antibiotic Resistance Ontology phenotypic classification. Values reflect percentage of completely sequenced genomes, completely sequenced plasmids, or whole-genome shotgun assemblies that have at least one AMR determinant associated with the phenotypic class. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

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Genotype

Prevalence of AMR genes and variants organized by CARD detection model. Values reflect percentage of completely sequenced genomes, completely sequenced plasmids, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. The search box can be used to filter results by gene family names (e.g. TEM-), pathogens (e.g. Pseudomonas), or the ARO categories used in the Phenotype table above (e.g. macrolide). For more complex queries, please Download the full data set.

Gene Species Criteria NCBI Chromosome NCBI Plasmid NCBI WGS Category
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