cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis

• Published in: Frontiers in microbiology Vol. 10; p. 1687
• Main Authors: Liu, Yen-Yi, Lin, Ji-Wei, Chen, Chih-Chieh
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 24.07.2019
• Subjects: comparative genomic analysis; epidemiological investigation; feature selection; Microbiology; molecular typing; next generation sequencing; whole-genome multilocus sequence typing; whole-genome multilocus sequence typing; comparative genomic analysis; epidemiological investigation; next generation sequencing; feature selection; molecular typing
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2019.01687

With the decreasing cost of next-generation sequencing, whole-genome sequence-based bacterial genome comparisons are expected to become a mainstream process in the public health domain. Extended multilocus sequence typing (MLST) methods are becoming increasingly popular for use in comparing bacterial genetic relatedness in epidemiological investigations. Several extended MLST schemes based on biological signatures have been reported. Among them, whole-genome MLST (wgMLST) has gradually become one of the most widely used approaches for bacterial strain typing. In addition to using bacterial typing, many researchers aim to identify differences in the genes of compared strains. Because these differences might provide insights into critical bacterial functions, such as virulence and pathogenicity, researchers usually study these genes that differ between strains. Hence, we designed a web service tool based on wgMLST-constructed tree topology coupled with the feature selection method to create the "canonical wgMLST (cano-wgMLST) tree." The genes that differ between strains are shown at each split of the tree, thereby directly providing information for performing a comparative genomic analysis for each strain pair. We demonstrated that this web service tool could be operated efficiently on two datasets consisting of 22 isolates and 59 Heidelberg isolates, respectively. We imposed this tool on a designated web server, cano-wgMLST_BacCompare, to enable users to create a wgMLST tree and canonical wgMLST tree automatically from their uploaded bacterial genomes for not only epidemiological investigation but also comparative genomic analysis. Additionally, detailed information on how to use this service is provided. The cano-wgMLST_BacCompare is available at http://baccompare.imst.nsysu.edu.tw.