GeneMates

GeneMates identifies horizontal gene co-transfer (HGcoT) between bacteria from whole-genome sequencing (WGS) data to detect co-transferred genes, including antimicrobial resistance (AMR) determinants and mobile genetic elements (MGEs), while controlling for population structure.

Key Features:

• Network approach: Implements a network-based analysis using WGS data to detect co-transfer relationships among genes.
• Univariate linear mixed models: Uses univariate linear mixed models to test associations between presence/absence of bacterial genes while accounting for core-genome variation and population structure.
• Distance consistency evaluation: Evaluates distance consistency using measured physical distances between genes to support inference of horizontal co-transfer.
• AMR and MGE recovery: Demonstrates capability to identify co-transferred antimicrobial resistance (AMR) genes and recover known mobile genetic elements (MGEs) from Escherichia coli and Salmonella Typhimurium WGS data.

Scientific Applications:

• Detection of co-transferred AMR genes: Identification of horizontally co-transferred antimicrobial resistance determinants in bacterial populations.
• Characterization of MGEs: Recovery and characterization of mobile genetic elements from WGS data.
• Disentangling associations from population structure: Distinguishing genuine gene-gene associations from spurious correlations caused by clonal population structure.
• Investigating spread of antimicrobial resistance: Studying mechanisms underlying the emergence and dissemination of AMR across bacterial populations.

Methodology:

Uses whole-genome sequencing data with a network approach, applies univariate linear mixed models to test presence/absence gene associations while accounting for core-genome variation, and evaluates physical distance consistency between genes when distances can be measured.