NCBI’s Pathogen Detection resource collects, analyzes, and reports on bacterial and fungal isolate genome sequences for outbreak identification and tracking. Pathogen Detection is also central to the surveillance of anti-microbial resistance, virulence, and stress resistance for 97 pathogenic taxa covering 753 species, and now includes analysis results for over 2 million isolates!
How does Pathogen Detection work?
Pathogen Detection provides two major automated real-time analyses:
- It quickly clusters related pathogen genome sequences to identify potential transmission chains helping public health scientists investigate disease outbreaks.
- As part of the National Database of Antibiotic Resistant Organisms (NDARO), NCBI screens genomic sequences using AMRFinderPlus to identify the antimicrobial resistance, stress response, and virulence genes found in bacterial genomic sequences. This enables scientists to track the spread of resistance genes and to understand the relationships among antimicrobial resistance, stress response, and virulence.
To facilitate the use of this data by researchers and public health officials, Pathogen Detection provides the data in easy-to-use browsers on the web as well as in files on FTP and in Google Cloud for programmatic access.
This information and the analysis results generated by NCBI Pathogen Detection are used nationally and internationally to identify and investigate bacterial and fungal-related disease outbreaks in real-time. The central public deposition of this data maximizes the utility, allowing investigators to identify closely related isolates across the > 2,000,000 assemblies in the system.
Figure 1: Graph showing year-over-year increase of isolates in the Pathogen Detection Isolates Browser.
Pathogen Detection in Action
- Our collaborators at the FDA GenomeTrakr have used the system for over 1,229 regulatory actions estimated to save thousands of lives.
- The public and international nature of the data have enabled international investigation and notification of outbreaks and allowed the detection of outbreaks before they are large enough to be identified using more traditional methods.
- Hospitals used the system to identify cryptic MRSA outbreaks and characterize isolates.
- See our Success Stories page for other ways Pathogen Detection enables research and aids public health.
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Questions?
Please send any comments or questions to pd-help@ncbi.nlm.nih.gov.