The Geogenomic Mutational Atlas of Pathogens (GoMAP) Web System

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/

Pathogen metadata platform: software for accessing and analyzing pathogen strain information

“…Second, the platform integrates mapping of geographical locations for genomes from a large database. Available software for mapping geolocations of pathogen genomes includes Supramap, which superimposes phylogenies onto a map [ 16 ], and GoMap, which is currently implemented to map HIV strains with drug resistance mutation information [ 17 ]. Unlike these, the Pathogen Metadata Platform links mapping with all samples from BioSample, though without a DNA analysis component.…”

Geogenomics: Toward synthesis

“…In the meantime, we re‐focus briefly on geogenomics' origins in Baker et al (2014) and the counterpoint of Sargeant et al (2014) as food for thought. Whereas Sargeant et al (2014) appeared largely an extension of existing practice, Baker et al (2014) joined a chorus for updating and extending phylogeography sensu lato (Dawson, 2014; Hickerson et al, 2010; Knowles & Maddison, 2002; Marske et al, 2013; Papadopoulou & Knowles, 2016), and perhaps because Baker et al (2014) expounded a new core idea and identified a specific audience, it had greater impact. Yet, many papers in the special issue include components that are not encapsulated by the original definition of geogenomics ( sensu Baker et al, 2014), as they do not test or constrain specific geological hypotheses, but use geological data to build predictions about biological processes (e.g.…”

“…Intriguingly, Sargeant et al (2014) also coined the term ‘geogenomics’ but from a very different perspective, specifically the geography of pathogens, and emphasizing finer spatial and temporal scales. Sargeant et al (2014) defined geogenomics as the ‘examin[ation of] the geographic distribution of … genomes … with a particular emphasis on those mutations that give rise to [adaptations]’; their vision of geogenomics was an extension of evolutionary biology, historical and phylogenetic biogeography, and phylogeography. The differences between these two visions—one explicitly hypothesis driven (Baker et al, 2014), and the other largely descriptive (Sargeant et al, 2014)—and their fates are perhaps illuminating: Baker et al (2014) has been well cited (Figure 1), whereas Sargeant et al (2014) has been cited only once.…”

“…What these contributions imply for the future of geogenomics is something to consider again when all the papers in the collection are available. In the meantime, we re‐focus briefly on geogenomics' origins in Baker et al (2014) and the counterpoint of Sargeant et al (2014) as food for thought. Whereas Sargeant et al (2014) appeared largely an extension of existing practice, Baker et al (2014) joined a chorus for updating and extending phylogeography sensu lato (Dawson, 2014; Hickerson et al, 2010; Knowles & Maddison, 2002; Marske et al, 2013; Papadopoulou & Knowles, 2016), and perhaps because Baker et al (2014) expounded a new core idea and identified a specific audience, it had greater impact.…”

“…Intriguingly, Sargeant et al (2014) also coined the term ‘geogenomics’ but from a very different perspective, specifically the geography of pathogens, and emphasizing finer spatial and temporal scales. Sargeant et al (2014) defined geogenomics as the ‘examin[ation of] the geographic distribution of … genomes … with a particular emphasis on those mutations that give rise to [adaptations]’; their vision of geogenomics was an extension of evolutionary biology, historical and phylogenetic biogeography, and phylogeography.…”