ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2021
Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers, 1 of them a synthesis that pooled it.
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Who cites it
134 citing papers in PubMed, 1 synthesis or guideline pooled it, 169 citations in OpenAlex.
- Pooled it
- Global Genomic Surveillance.Methods in molecular biology (Clifton, N.J.) · 2027Article
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- Tet-ON and Tet-OFF regulation in hypervirulentMicrobiology spectrum · 2026Article
- Genomic characterization of an ESBL-producingMicrobiology spectrum · 2026Article
- Application of FT-IR spectroscopy using the IR BiotyperEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Escalating burden and mortality of carbapenem-resistant Klebsiella pneumoniae species complex infections in Bangladeshi infants.npj antimicrobials and resistance · 2026Article
- Genomic characterization of multidrug-resistant Klebsiella pneumoniae clinical isolates from India.Scientific reports · 2026Article
- Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens.PLoS biology · 2026Article
- Pan-genome analysis and phylogenetic characterization ofFuture microbiology · 2026Article
- The Role of Neonatal Ward Environment as a Reservoir for the Dissemination of Multidrug-Resistant Klebsiella pneumoniae in Algeria.MicrobiologyOpen · 2026Article
- Article
- Evolutionary inference reveals global natural histories and predicted pathways of antimicrobial resistance in Klebsiella pneumoniae.PLoS biology · 2026Article
- Genetic clusteringof KPC-2-producing carbapenem-resistant Klebsiella pneumoniae ST5422-KL19 in Shanghai, China.BMC microbiology · 2026Article
- Mind the governance gap: a one health scoping review of national AMR performance indicators.npj antimicrobials and resistance · 2026Article
- Towards accurate genomic detection of fungal antimicrobial resistance: progress in fungal resistance databases and bioinformatic tools.Microbial genomics · 2026Review
74 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors at 8 institutions in 7 countries.
Funding
Abstract
backgroundKlebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting.
methodsWe developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR.
resultsUsing Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse.
conclusionsPathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
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