Table 1.
Commonly used web-based systems, and MGTdb, incorporating genomic-based methods for surveillance of pathogenic bacteria.
| Tool | Availability | Nomenclature method | Resolution | Browse, search and additional features | Application species |
|---|---|---|---|---|---|
| Enterobase (16) | Publicly available online (https://enterobase.warwick.ac.uk) | MLST, cgMLST, HierCC | Multiple levels | Searched isolates browsable as table, and downloadable. API provided for programmatic data access and download | Eight organisms |
| SnapperDB (19) | Code available online (https://github.com/phe-bioinformatics/snapperdb) | SNPs calculated w.r.t. a reference, linkage clustering at seven thresholds | Multiple levels | – | Used by Public Health England for Salmonella |
| SeqSphere+ | Commercial (https://www.ridom.de/seqsphere/) | MLST, cgMLST, linkage clustering and more | – | – | 54 organisms |
| BacWGSTdb (31) | Publicly available online (http://bacdb.cn/BacWGSTdb/) | MLST, cgMLST, SNP phylogenetic trees and minimal-spanning tree | Low, high | All public isolates (or searched isolates) as table. AMR and virulence genes. Can upload single or multiple genomes and perform various analyses (e.g. phenotype prediction, or MST) | 20 organisms |
| PathogenWatch (32) | Publicly available online (https://pathogen.watch) | MLST, cgMLST, single linkage clustering and coreSNP phylogenetic trees | Low, high | All public isolates (or searched isolates) as table. Report for each isolate with various isolate characteristics, e.g. plasmids, virulence or AMR Graphical view of related strains, where relatedness determined by cgMLST clusters | 13 organisms |
| PubMLST (33) | Publicly available online (https://pubmlst.org) | MLST-based schemes, linkage clustering | Low, high | Interactive graphic summaries of public isolates and searched isolate; searched isolates can be browsed as table. All data exportable. Multiple analysis tools integrated | 130 organisms |
| 5NosoAE (34) | Publicly available online (https://nosoae.imst.nsysu.edu.tw) | Antibiogram and cgMLST | High | Interactive graphic summaries. Database browsable for closely related isolates to a user submitted isolate | Five organisms |
| MGTdb | Publicly available online (https://mgtdb.unsw.edu.au) | MGT, CC and ODC | Multiple levels; stable and standardized nomenclature | All public isolates (or searched isolates) as table or interactive graphics. Summary of trends by country. Data export for Microreact and GrapeTree. Download of all public isolate assignments and all alleles | Four organisms (1 unpublished) |