GEAR-base

GEAR-base integrates whole-genome sequence data and culture-based antibiotic susceptibility profiles to support analysis of genetic determinants of bacterial antibiotic resistance.

Key Features:

• Extensive data collection: Contains 11,087 newly sequenced whole genomes from clinical isolates across 18 main bacterial species sampled over a 30-year period.
• Comprehensive resistance profiling: Includes culture-based resistance profiles for 10,991 isolates tested against a panel of 22 antibiotics.
• Pan-genome construction: Builds species-level pan-genomes that capture conserved essential genes and known resistance factors for each bacterial species.
• Genotype–phenotype integration: Links whole-genome sequence data with antibiotic susceptibility profiles to enable joint analyses of genetic and phenotypic resistance determinants.
• Species-specific resistance trends: Enables analysis of species- and drug-specific resistance patterns, including increased resistance in Acinetobacter baumannii to carbapenems and in Escherichia coli to fluoroquinolones.

Scientific Applications:

• Molecular diagnostics: Identifying genetic markers associated with antibiotic resistance to inform diagnostic assay development.
• Drug development: Characterizing resistance determinants and genetic contexts to guide antimicrobial discovery and optimization.
• Evolutionary studies: Investigating the evolution and dissemination of resistance determinants across species and time.
• Surveillance and epidemiology: Monitoring species- and drug-specific resistance trends, such as carbapenem resistance in A. baumannii and fluoroquinolone resistance in E. coli.

Methodology:

Integration of whole-genome sequence data with culture-based antibiotic susceptibility profiles, construction of species-level pan-genomes, and statistical testing to infer gene–drug resistance associations.