BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking

Abstract

An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.

Figure 1.

Overview of the content and function modules of BacWGSTdb 2.0. ‘Infrastructure’ lists the public database and tools integrated in BacWGSTdb 2.0. ‘Browse’ functions to visualize and compare the genetic relationships among isolates deposited in BacWGSTdb 2.0. ‘Tools’ functions for whole genome sequence typing and source tracking based on user uploaded sequence(s). ‘Species’ represents 20 bacterial species currently supported by BacWGSTdb 2.0.

Figure 2.

Screenshots of the updated web interface of the Single Genome Analysis module and the detailed outputs using a Salmonella enterica isolate as an example. After uploading the preassembled genomic sequence and setting the appropriate parameters, the analytical results return and can subsequently be classified into three sections: conventional seven-locus MLST, identification of AMR and virulence genes, and source tracking of plasmids and bacteria. In particular, the phylogenetic analysis revealed that the query isolate shows high degree of genetic relatedness in the database, suggesting that these isolates might have originated from the same source. The entire analysis process takes 3–5 min.

Figure 3.

Screenshots of the updated web interface of the Multiple Genome Analysis module and the detailed outputs using nine S. enterica isolates as an example. The Results page lists for each of the uploaded genomes the conventional seven-locus MLST results and the predictions of AMR and virulence genes. In addition, the phylogenetic trees based on the SNP and cgMLST approaches both reveal that the query isolates did not involve an outbreak event, since they differ from one another by over 100 SNPs or cgMLST loci. The entire analysis process takes 5–8 min.

Figure 4.

Screenshots of the updated Browse interface. Users can sort and select isolates based on their various attributes. For the selected isolates, phylogenetic trees following both the SNP and cgMLST approaches are provided.