Automated Klebsiella Genome Analysis

Genome assemblies were uploaded to Pathogenwatch v2.3.1 [46 (link)] where Kleborate v2.2 [47 (link)] and Kaptive v2.0 [17 (link)] were automatically deployed to call multi-locus sequence types (STs) using the seven-locus scheme [65 (link)], capsular polysaccharide (K) and lipopolysaccharide O locus types, and serotype predictions, acquired virulence traits including the siderophores aerobactin (iuc), yersiniabactin (ybt) and salmochelin (iro), the genotoxin colibactin (clb) and the hypermucoidy locus (rmpADC). Pathogenwatch also deploys Kleborate to identify established AMR determinants (acquired genes and chromosomal mutations) [47 (link)] for the following antimicrobial classes: aminoglycosides, carbapenems, third-generation cephalosporins, third-generation cephalosporins plus β-lactamase inhibitors, colistin, fluoroquinolones, fosfomycin, penicillins, penicillins + β-lactamase inhibitors, phenicols, sulfonamides, tetracyclines, tigecycline and trimethoprim.

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Foster-Nyarko E., Cottingham H., Wick R.R., Judd L.M., Lam M.M., Wyres K.L., Stanton T.D., Tsang K.K., David S., Aanensen D.M., Brisse S, & Holt K.E. (2023). Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. Microbial Genomics, 9(2), mgen000936.

Publication 2023

Aerobactin Aminoglycosides Antimicrobial Capsular Carbapenems Cephalosporins Chromosomal Colibactin Colistin Fluoroquinolones Fosfomycin Genes Genome Genotoxin Lipopolysaccharide Mutations Penicillins Polysaccharide Salmochelin Siderophores Sulfonamides Tetracyclines Tigecycline Trimethoprim Virulence Yersiniabactin β lactamase inhibitors

Corresponding Organization :

Other organizations : London School of Hygiene & Tropical Medicine, Monash University, University of Oxford, Université Paris Cité, Institut Pasteur

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Variable analysis

independent variables

Genome assemblies uploaded to Pathogenwatch v2.3.1

dependent variables

Multi-locus sequence types (STs) using the seven-locus scheme
Capsular polysaccharide (K) and lipopolysaccharide O locus types
Serotype predictions
Acquired virulence traits including the siderophores aerobactin (iuc), yersiniabactin (ybt) and salmochelin (iro), the genotoxin colibactin (clb) and the hypermucoidy locus (rmpADC)
Established AMR determinants (acquired genes and chromosomal mutations) for the following antimicrobial classes: aminoglycosides, carbapenems, third-generation cephalosporins, third-generation cephalosporins plus β-lactamase inhibitors, colistin, fluoroquinolones, fosfomycin, penicillins, penicillins + β-lactamase inhibitors, phenicols, sulfonamides, tetracyclines, tigecycline and trimethoprim

control variables

Genome assemblies

Annotations

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