In May 2014, the FDA and collaborators established a publicly available database for Reference Grade microbial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species.
Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:
- Phase 1 entails collection of a previously identified microbe and nucleic acid extraction.
- Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS).
- Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.
The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.
How FDA-ARGOS Will Assist Medical Device Developers:
Manufacturers who develop sequence-based test to identify infectious agents and/or to detect resistance or virulence markers can use FDA-ARGOS to advance their development programs and to support the regulatory science review of such test. For example, FDA-ARGOS can be used as a tool for in-silico (computer simulation) data analysis.
Contributing Genomes to FDA-ARGOS:
Further population and curation of the database will support the success of FDA-ARGOS and promote adoption by the NGS community. The FDA-ARGOS team openly invites additional collaborators from the scientific community to assist in filling the gaps in this public resource. The FDA-ARGOS and collaborators are specifically searching for unique, hard to source microbes such as biothreat organisms, emerging pathogens, and clinically significant bacterial, viral, fungal, and parasitic genomes. The goal is to collect sequence information for a minimum of 5 isolates per species.
For more information about contributing samples for UMD-IGS sequencing as part of FDA-ARGOS efforts, or to qualify existing genomes by the FDA, please email FDA-ARGOS@fda.hhs.gov.