HAM-ART

HAM-ART links extrachromosomal antimicrobial resistance (AMR) genes to their host bacterial genomes using Hi-C assisted metagenomics to enable comprehensive detection and tracking of AMR in complex microbial communities.

Key Features:

• Hi-C integration: Utilizes Hi-C sequencing data to associate extrachromosomal DNA, including plasmids, with host bacterial genomes.
• Addressing shotgun metagenomics limitation: Links plasmid-borne resistance genes to bacterial chromosomes, overcoming the inability of traditional shotgun metagenomics to assign extrachromosomal elements to hosts.
• Metagenome-assembled genomes (MAGs): Optimized to generate high-quality MAGs that include both chromosomal and extrachromosomal AMR genes.
• Integrated laboratory and computational pipeline: Combines laboratory Hi-C protocols with bioinformatics analysis to assemble genomes and identify AMR genes within their genomic context.

Scientific Applications:

• Comparative farm microbiome analysis: Applied to 100 pig faecal microbiomes from organic (low-use) and conventional (high-use) farms to compare AMR gene distribution between environments.
• Plasmid-borne resistance discovery: Enabled identification of a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial-use farms found within three species of Lactobacilli.

Methodology:

Hi-C assisted metagenomic sequencing data are processed through the HAM-ART pipeline to assemble genomes (including MAGs), identify AMR genes, and link extrachromosomal elements such as plasmids to their bacterial hosts.