Inference of bacterial pathogen load in US rivers from landscape-scale shotgun metagenomic sequencing

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Presenter(s)

Alyssa Cruz

Abstract or Description

Surface waters contain possible human pathogens, but their sources and distribution remain understudied with modern methods. Using high-throughput DNA sequencing methods like metagenomics, large-scale microorganism identification can be completed. Using hundreds of surface water samples from the Genome Resolved Open Watersheds project, we are characterizing the pathogenic potential of samples from freshwater ecosystems. The samples are highly varied and come from diverse locations, ranging from relatively pristine, to polluted by anthropogenic input. As a proxy for pathogenic potential, these samples are being used for broadly characterizing virulence factor diversity and distribution. Using 2093 Metagenome Assembled Genomes, candidate virulence-associated proteins were identified using homology searches against the Virulence Factor Database (VFDB). We identified 27,177 unique candidate virulence factor proteins using specific homology search criterion (e-value <= 1e-10, similarity >= 60%, bit score >=60). Genomic and taxonomic context can be used to further classify these candidate proteins into virulence factor confidence groups.

Mentor

Chris Miller