FDA Tool Uses Genomics to Track Resistance Genes

The FDA this week launched a new interactive tool called “Resistome Tracker,” which will use genomic information to track antimicrobial resistance in pathogens. Initially, the system focuses on drug-resistance traits in Salmonella, but the genomic approach eventually will expand to include other food-borne pathogens such as E. coli and Campylobacter,

Since 2014, the National Antimicrobial Resistance Monitoring System (NARMS) has engaged in whole genome sequencing (WGS) on every Salmonella isolate collected in its surveillance program, and on over 4,500 historical Salmonella isolates collected from retail-meat sources since 2002. Whole genome sequencing allows detailed genetic comparison of strains from humans with those from other sources, and studies have shown the presence of known resistance determinants is highly correlated with clinical resistance. NARMS researchers used the WGS data to create a database at the National Center for Biotechnology Information (NCBI), which they say will evolve to incorporate temporal changes in the resistome along with the susceptibility information.

In its latest integrated report, NARMS notes plans to continue using whole genome DNA sequencing technology to develop prediction tools to reliably predict antibiotic resistance more quickly and at lower cost compared with other methods such as susceptibility testing.

The new Resistome Tracker system, designed primarily for researchers and public-health officials, “allows users to customize visualizations by antibiotic drug class, compare resistance genes across different sources, identify new resistance genes, and map selected resistance genes to geographic region.”

Currently, Salmonella genome sequences from the NCBI public databases are uploaded to Resistome Tracker on a weekly basis, allowing near real-time monitoring of antibiotic resistance. The system includes WGS data on 97,390 genomes from NCBI, 27,512 of which are U.S. isolates and 8,900 are isolates from the NARMS.