Enteric Diseases Laboratory Branch
Centers for Disease Control and Prevention (CDC)
Atlanta, GA, USA
Whole Genome Sequencing (WGS) and Bioinformatics of Escherichia
Shiga toxin-producing Escherichia coli (STEC) strains are important foodborne pathogens. Current methods for the characterization of STEC are time consuming and expensive. We therefore began work to replace traditional methods with whole genome sequence (WGS) using an allele database of individual Escherichia genes in BioNumerics. This will allow characterization and subtyping of Escherichia in a single workflow using a multi-locus sequence typing (MLST) approach.
To build the BioNumerics database, 314 reference genomes from CDC, the USDA and NCBI were included in the BioNumerics allele database as well as genes from databases developed by Danish scientists to represent genes encoding known virulence factors, antimicrobial resistance and O and H antigens. The annotated reference genomes represented 50 E. coli serogroups, Shigella species and other Escherichia species. Multiple subschema are being built within the database to perform identification, characterization and scalable, hierarchical subtyping that will include classical, extended, core and whole genome MLST. To test the epidemiologic clustering ability of the subtyping algorithms and increase the allelic diversity of the database, an additional 500 strains from outbreak related and sporadic infections were sequenced and will be analyzed. A pilot version of the BioNumerics software will be available to states and collaborators in the fall of 2015.
The Escherichia BioNumerics database provides a single, cost effective approach for accurate species identification, serotyping, virulence characterization and subtyping for the surveillance of both outbreak-related and sporadic E. coli infections. The end-users in the public health labs will be able to analyze their own data with little training, making the system equally efficient for local and central investigations. The system will be refined through continued collaboration with domestic and international partners.