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Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations.

The rapid spread of antibiotic resistance is a global health threat. A range of environments have been identified as reservoirs of the antibiotic resistance genes (ARGs) found in pathogens, but we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to an inability to identify the bacterial hosts of ARGs and the mobile genetic elements that mediate horizontal gene transfer due to the loss of intra-cellular contiguity upon DNA extraction. In two recent studies we describe the application of proximity-ligation methods for the determination of the in situ host range of numerous ARGs, viruses, plasmids, and integrons within complex microbiome samples. This method forms physical junctions between sequences present within the same cell prior to DNA extraction. Subsequent sequencing generates a dataset that robustly connects mobile elements to their hosts and can assemble de novo genomes from mixed communities. Our application of this technology to complex wastewater and rumen samples yielded hundreds of novel ARG-, virus-, and plasmid-host interactions, as well as over a thousand new microbial genomes. These studies highlight the power of the proximity-ligation approach to deconvolving microbiome samples and foreshadow the development of rapid culture-free strategies for tracking and managing the spread of antimicrobial resistance. References: Linking the Resistome and Plasmidome to the Microbiome; Thibault Stalder et al., Dec. 2018, bioRxiv. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation; Derek Bickhart et. al., Dec. 2018, bioRxiv.