Metagenomics-based characterization using genomic and epidemiological comparisons

A method comprises obtaining results of metagenomics sequencing performed on biological samples from respective sample sources, identifying particular ones of the biological samples that are related to a disease, infection or contamination based at least in part on the results of metagenomics sequencing, generating a genomic comparison component comprising hit abundance score vectors for respective ones of the identified samples, generating an epidemiologic comparison component comprising a graph in which nodes corresponding to patients are connected in the graph based at least in part on patient comparative indexes, collectively processing portions of the genomic comparison component with portions of the epidemiologic comparison component to further characterize the disease, infection or contamination, and updating a profile of the disease, infection or contamination based at least in part on the further characterization.