Researchers say horizontal gene transfer, especially plasmids, fuels AMR spread across microbiomes

Dr. Ilana Brito, a microbiome researcher introduced as from Cornell University, told the PACCARB panel that horizontal gene transfer (HGT) — not sporadic mutation — is the principal process by which bacteria acquire multiple antibiotic resistance traits. She explained that “plasmids, which carry antimicrobial resistance traits… are extrachromosomal pieces of DNA” and that conjugation, transduction and transformation enable these elements to move between bacteria.

Brito presented network and genomic analyses showing that bacteria within the same phylum exchange genes more readily but that transfers also occur between distantly related organisms, linking pathogens to human and environmental microbiomes. “Over half of these observable transfers include an antimicrobial resistance gene,” she said, and noted that many clinically relevant resistance genes sit on mobile plasmids that can cross taxonomic boundaries.

The practical challenge, Brito said, is that common DNA sequencing workflows fragment DNA and lose linkage between plasmids and their host genomes, making it hard to track where resistance genes originate and where they go. She described emerging laboratory and computational approaches — single-cell encapsulation, physical linkage methods, and methylation-mark patterning — that can re-associate plasmids with host genomes, but cautioned these techniques are currently difficult to scale.

Brito urged investment in robust, scalable surveillance tools that can associate mobile resistance elements with their bacterial hosts so public health systems can better detect and predict the emergence of multidrug-resistant pathogens.