Who’s got the plasmid? Tracking the spread of antimicrobial resistance genes in the human gut microbiome at the single-cell level

Purpose and aims: Bulk shotgun metagenomic sequencing (bulk metaG) methods, which sequence all DNA present in a sample, are being used globally for antimicrobial resistance (AMR) surveillance and diagnostics.

However, state-of-the-art bulk metaG methods are incapable of accurately detecting horizontal gene transfer (HGT) of AMR genes between strains.

To address this critical gap, this project will facilitate the development of a (i) single-cell metagenomic sequencing (scMetaG) method (Aim 1) and (ii) bioinformatic toolkit (Aim 2), which can be used to link AMR genes to individual bacterial cells in a microbial community; the methods developed here will be used to monitor single-cell AMR dynamics (AMR gene gain, loss, and HGT) in the human gut microbiome over the course of antibiotic treatment.Project organization: This three-year project will be undertaken by myself (single-cell methods development), Dr.

Laura Carroll (bioinformatician), Dr. Johan Normark (clinician), and three postdocs (one hired through this grant).

Scientific methods used include single-cell droplet encapsulation, genomic sequencing, and bioinformatics.Importance: This project will result in a complete, end-to-end scMetaG data generation and analysis pipeline, which can be used freely by laboratories around the world.

Beyond AMR, scMetaG methods developed here have the potential to transform microbiome research, as they can query microbial communities at unprecedented resolution.