Source data & tools¶

Source Databases¶

Enterobase¶

Pathogenwatch¶

Salmonella Typhi: A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch, Argimón et al 2021
Neisseria gonorrhoeae: A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch, Sánchez-Busó et al 2021
Klebsiella pneumoniae: Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch, Argímon 2021
https://pathogen.watch/

Typing tools¶

AMRFinderPlus¶

Used for AMR typing in E. coli/Shigella and non-typhoidal Salmonella dashboards

AMRFinderPlus: https://github.com/ncbi/amr
AMRFinderPlus paper: AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence, Feldgarden 2021
Integration of AMRFinderPlus in Enterobase: EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens, Dyer et al 2025

Escherichia coli and Shigella¶

Genotype nomenclature¶

Achtman 7-locus MLST scheme: Developed by Enterobase
Core genome MLST scheme: The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity, Zhou et al 2020
Hierarchical clustering: HierCC: a multi-level clustering scheme for population assignments based on core genome MLST, Zhou et al 2020
MLST database: https://enterobase.warwick.ac.uk/species/index/ecoli/

Pathotype definition¶

The diarrheagenic E. coli (DEC) pathotypes are defined using Enterobase pathotyping logic
Shigella species identification : Hierarchical Clustering (HC)

Salmonella (non-typhoidal)¶

Genotype nomenclature¶

7-locus MLST scheme: Enterobase
Core genome MLST scheme: The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity, Zhou et al 2020
Hierarchical clustering: HierCC: a multi-level clustering scheme for population assignments based on core genome MLST, Zhou et al 2020

Serotyping¶

Serotypes: The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies, Yoshida et al 2016

Salmonella Typhi¶

Neisseria gonorrhoeae¶

7-locus MLST scheme: Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing, Bennett et al 2007
2-locus N. gonorrhoeae multi-antigen sequence typing (NG-MAST) scheme Rapid Sequence-Based Identification of Gonococcal Transmission Clusters in a Large Metropolitan Area, Martin et al 2004
MLST and NG-MAST databases: PubMLST
AMR prediction: A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch, Sánchez-Busó et al 2021

Klebsiella pneumoniae¶

Genotype nomenclature¶

7-locus MLST scheme: Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates, Diancourt 2005
Core genome MLST scheme: Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups, Bialek-Davenet et al 2014
Sublineages: A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains, Hennart et al 2022
MLST databases: BIGSdb Institut Pasteur

AMR typing¶

Kleborate v3: https://github.com/klebgenomics/Kleborate
Kleborate paper: A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex, Lam et al 2021