title: BacWGSTdb, a database for genotyping and source tracking bacterial pathogens.
abstract: Whole genome sequencing has become one of the routine methods in molecular epidemiological practice. In this study, we present BacWGSTdb (http://bacdb.org/BacWGSTdb), a bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. This database borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens.
authors.affiliation: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Ruan
authors.affiliation: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, 310029, China pandafengye@zju.edu.cn.
authors.forename: Ye
authors.initials: Y
authors.lastname: Feng
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D023281:Genomics; D060005:Genotyping Techniques / Q000379:methods*; D058885:Multilocus Sequence Typing