title: Construction of a Pan-Genome Allele Database ofSalmonella entericaSerovar Enteritidis for Molecular Subtyping and Disease Cluster Identification.
abstract: We built a pan-genome allele database with 395 genomes ofSalmonella entericaserovar Enteritidis and developed computer tools for analysis of whole genome sequencing (WGS) data of bacterial isolates for disease cluster identification. A web server (http://wgmlst.imst.nsysu.edu.tw) was set up with the database and the tools, allowing users to upload WGS data to generate whole genome multilocus sequence typing (wgMLST) profiles and to perform cluster analysis of wgMLST profiles. The usefulness of the database in disease cluster identification was demonstrated by analyzing a panel of genomes from 55 epidemiologically well-definedS.Enteritidis isolates provided by the Minnesota Department of Health. The wgMLST-based cluster analysis revealed distinct clades that were concordant with the epidemiologically defined outbreaks. Thus, using a common pan-genome allele database, wgMLST can be a promising WGS-based subtyping approach for disease surveillance and outbreak investigation across laboratories.
authors.affiliation: Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control Taichung, Taiwan.
authors.forename: Yen-Yi
authors.initials: YY
authors.lastname: Liu
authors.affiliation: Institute of Medical Science and Technology, National Sun Yat-sen UniversityKaohsiung, Taiwan; Medical Science and Technology Center, National Sun Yat-sen UniversityKaohsiung, Taiwan.
authors.forename: Chih-Chieh
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control Taichung, Taiwan.
authors.forename: Chien-Shun
authors.initials: CS
authors.lastname: Chiou
keywords: molecular epidemiology; next generation sequencing (NGS); pan-genome allele database; typing; whole genome multilocus sequence typing (wgMLST)