CARD:Live

Pilot Phase Started April 2020: Data for 1293 isolates collected

The CARD:Live project collects pathogen identification, MLST, AMR gene list (RGI Perfect & Strict hits only), date, and geographical region for genome sequences submitted to RGI online, providing a dynamic view of antibiotic resistant isolates being analyzed around the world. All information collected is based on consent and no sequence information is retained. We ask RGI users to please consider sharing their AMR metadata so we can build and share a dynamic data set of antibiotic resistance pathogens from around the globe.

Currently, CARD:Live is running as a pilot project to assess community engagement and as a software test. As data accumulates, we will pilot geotemporal plots of AMR gene frequencies across the globe, including downloadable summary data.

Example data collected from a single RGI submission:
Pathogen ID Citrobacter freundii
MLST 88
Region Latin America and the Caribbean
Timestamp 2020-03-31 09:01:01.318835

Results:
Hit Criteria CARD Bitscore Cut Off Hit Bitscore AMR Gene ARO Accession Percent Identity Percentage Length of Reference Sequence Model ID Model Type SNPs in Best Hit ARO Other SNPs Drug Class Resistance Mechanism AMR Gene Family CARD Kmer Prediction
Strict 400 459.9 QnrB10 3002724 98.67 100 139 protein homolog model n/a n/a fluoroquinolone antibiotic antibiotic target protection quinolone resistance protein (qnr) Citrobacter freundii (plasmid)
Perfect 500 544.3 NDM-1 3000589 100 100 783 protein homolog model n/a n/a carbapenem; cephalosporin; cephamycin; penam antibiotic inactivation NDM beta-lactamase Citrobacter freundii (chromosome or plasmid)
Strict 1500 1538.5 Escherichia coli gyrA conferring resistance to fluoroquinolones 3003294 91.09 100.34 1545 protein variant model S83I n/a fluoroquinolone antibiotic antibiotic target alteration fluoroquinolone resistant gyrA Citrobacter freundii (chromosome)

Resistome and CARD Kmer predictions produced by the Resistome Gene Identifier, Pathogen Identification predicted by LMAT, MLST predicted by PubMLST, Geographical region supplied by User (following United Nations, Department of Economic and Social Affairs, Statistics Division).