CoxBase

CoxBase provides centralized storage, in silico genotyping, and geospatial analysis of Coxiella burnetii genomic data and metadata to support epidemiological surveillance and research into Q fever.

Key Features:

• Database Repository: Hosts genotyping information for over 400 Coxiella burnetii isolates with associated metadata annotations.
• In Silico Genotyping: Performs in silico genotyping on complete or minimally assembled C. burnetii sequences using five distinct typing methods.
• Query Functionality: Enables querying and retrieval of isolates and their genotypic metadata for comparative analysis.
• Geospatial Visualization: Aggregates isolate geodata onto a world map to visualize geographic distribution and spread patterns.
• Submission Portal: Accepts submission of new isolates and metadata to expand the repository.
• Genomic Analysis Tools: Applied to 50 RefSeq C. burnetii genomes (genotyping all except those with poor sequence quality) and employs MST to identify new spacer sequences, assign adaA gene phenotypes, and determine plasmid types.

Scientific Applications:

• Epidemiological surveillance: Supports surveillance of Q fever by integrating genotyping and geospatial data for population-level monitoring.
• Outbreak investigation: Enables rapid typing and comparison of isolates to assist outbreak detection and response.
• Genetic diversity assessment: Facilitates analysis of C. burnetii genetic diversity using multiple typing methods including MST.
• Transmission tracing: Supports tracing of transmission pathways through comparative genotyping combined with geolocation data.
• Reference-based comparative analysis: Integrates RefSeq genomes for benchmarking and comparative genotyping analyses.

Methodology:

Implements database management and bioinformatics analysis; performs in silico genotyping on complete or minimally assembled sequences using five typing methods including MST to identify spacer sequences, establish adaA gene phenotypes, and determine plasmid types; leverages RefSeq genomes for testing and comparison.