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With the advance of next generation sequencing (NGS) techniques, whole genome sequencing (WGS) is expected to be the “ultimate” molecular method in subtyping of bacterial isolates for disease outbreak investigation and disease surveillance. To make WGS as a common subtyping tool for epidemiological studies, the layout of genetic fingerprints (genotypes) generated from WGS data needs to be comparable among laboratories. However, it is still a big challenge in using WGS data for fine typing purpose. Single nucleotide polymorphism (SNP) is the most used method and has been demonstrated in many evolutionary studies and outbreak investigation. However, nucleotides are slow-evolving markers with a mutation rate of 10-10 mutations per generation, and are more suitable in establishing “long-term” evolutionary relationships among strains. For the application in short-term epidemiological studies, ones need to develop an analytical approach to generate fine genotypes from WGS data for discriminating very close-related strains. Whole genome multilocus sequence typing, wgMLST, an extended concept of the traditional MLST, is considered to be a solution. To apply wgMLST as a standard subtyping tool, a supragenome allele database that consists of “all” the genes present in a bacterial population has to be first established. In a supragenome database, genes (loci) and their sequence variants (alleles) are numbered in alphabetical order. A wgMLST profile of a strain is presented by a bunch of alphabetical numbers in order. wgMLST profiles generated from a common supragenome allele database can therefore be compared across laboratories. In this study, we present the first free wgMLST web-service-wgMLSTdb-builder (, which provide users to build their own bacterial supragenome allele databases and to generate wgMLST profiles of bacterial strains for epidemiological studies.

Copyright © 2016 Centers for Disease Control, Taiwan (Taiwan CDC) and Institute of Medical Science and Technology, National Sun Yat-sen University, Taiwan. Contact
Liu YY, Chiou CS & Chen CC. PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing. Sci. Rep. 6, 36213; doi: 10.1038/srep36213 (2016).