PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing.
With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon's study used for discerning among epidemiologically related and non-related isolates.
Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
Yen-Yi
YY
Liu
Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
Chien-Shun
CS
Chiou
Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.|Medical Science and Technology Center, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.
Chih-Chieh
CC
Chen
D000483:Alleles; D015373:Bacterial Typing Techniques / Q000379:methods; D030541:Databases, Genetic; D016680:Genome, Bacterial; D020407:Internet; D058885:Multilocus Sequence Typing / Q000379:methods*; D012486:Salmonella typhimurium / Q000235:genetics*; D000073336:Whole Genome Sequencing / Q000379:methods*