Abstract
We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/
Highlights
There are a number of computation tools for visualizing pathogen surveillance data on world atlases
We present the Geogenomic Mutational Atlas of Pathogens (GoMAP)-Human Immunodeficiency Virus (HIV) open-access web application, which provides a visual mining tool to help scientists better understand the global distribution of HIV drug resistance mutations (DRMs)
GoMAP-HIV User Interface The main interface is composed of two primary sections, the
Summary
There are a number of computation tools for visualizing pathogen surveillance data on world atlases. This, and similar applications are useful in managing responses to pathogen outbreaks. There are several examples of pathogens that have acquired mutations that make them resistant to one or more drugs. This is a serious concern for treatment of patients infected with Staphylococcus aureus, Clostridium difficile, Streptococcus pyogenes, Mycobacterium tuberculosis, Salmonella, Escherichia coli, Influenza viruses, Human Immunodeficiency Virus (HIV), and several other viral infections. Examining the geographic distribution of mutations that are associated with drug resistance has the potential to contribute to the management of pathogen treatments.
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