# Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations

## TL;DR

The study reveals that plasmids like pGut1, found in healthy human guts, can spread antibiotic resistance genes across diverse bacteria, posing a risk for multidrug-resistant pathogens.

## Contribution

The discovery of a hidden reservoir of multi-host plasmids, including pGut1, that silently propagate antibiotic resistance genes in healthy human populations.

## Key findings

- A global plasmid pGut1 was found in over 50% of individuals and across diverse bacterial species.
- pGut1 contains a conserved backbone and a variable region with antibiotic resistance genes like cfr(C), erm(B), and aphA.
- pGut1 was detected in 93 bacterial strains across 49 genera, suggesting cross-species transmission.

## Abstract

Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a “plug-and-play” module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.