MetaCompare

MetaCompare ranks resistome risks across metagenomic sequencing data, differentiating between human health and ecological risks by projecting samples into a hazard space and calculating risk scores based on antibiotic resistance gene (ARG) mobility.

Key Features:

• Differential Risk Ranking: MetaCompare 2.0 differentiates human health resistome risk (potential for human pathogens of acute resistance concern to acquire ARGs) from ecological resistome risk (overall mobility of ARGs and potential for pathogen acquisition).
• Robustness to Technical Variation: Risk scores remain consistent despite variations in sequence assembly methods, sequencing depth, contig count, and metagenomic library coverage bias.
• Multi-Environment Analysis: The pipeline analyzes diverse metagenomes from wastewater, surface water, soil, sediment, human gut, and synthetic microbial communities.
• Hazard Space Projection: Samples are projected into a hazard space to calculate resistome risk scores based on ARG mobility.

Scientific Applications:

• Environmental Risk Assessment: Quantifying relative contributions of environmental factors to the spread of antibiotic resistance genes across different ecosystems.
• Anthropogenic Impact Detection: Identifying elevated resistome risks in environments influenced by human activity or other stressors.
• ARG Surveillance: Monitoring antibiotic resistance gene mobility and potential pathogen acquisition in environmental and clinical metagenomic samples.

Methodology:

MetaCompare 2.0 improves upon the original MetaCompare pipeline by differentiating indicators of human health resistome risk from ecological resistome risk, with risk scores calculated based on ARG mobility after projecting samples into a hazard space.