Culture-free discovery and host-affiliation of phages, plasmids, and AMR genes using proximity-ligation technology.

Studying antibiotic resistance dynamics in microbial communities is challenging because the purification of DNA from mixed samples disconnects mobile elements from their hosts. Thus it is very difficult to map the microbial hosts of plasmids, ARGs, and phages without culturing. Proximity ligation sequencing creates physical junctions between DNA molecules inside the same cells and allows the association of mobile elements with their hosts directly within microbiome samples. We will describe this technology and show published and unpublished data with a focus on microbiome discovery and tracking ARGs, plasmids, and phages in diverse microbial communities.