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Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch
BACKGROUND: Klebsiella 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 bioinformati...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634497/ https://www.ncbi.nlm.nih.gov/pubmed/34850838 http://dx.doi.org/10.1093/cid/ciab784 |
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author | Argimón, Silvia David, Sophia Underwood, Anthony Abrudan, Monica Wheeler, Nicole E Kekre, Mihir Abudahab, Khalil Yeats, Corin A Goater, Richard Taylor, Ben Harste, Harry Muddyman, Dawn Feil, Edward J Brisse, Sylvain Holt, Kathryn Donado-Godoy, Pilar Ravikumar, K L Okeke, Iruka N Carlos, Celia Aanensen, David M |
author_facet | Argimón, Silvia David, Sophia Underwood, Anthony Abrudan, Monica Wheeler, Nicole E Kekre, Mihir Abudahab, Khalil Yeats, Corin A Goater, Richard Taylor, Ben Harste, Harry Muddyman, Dawn Feil, Edward J Brisse, Sylvain Holt, Kathryn Donado-Godoy, Pilar Ravikumar, K L Okeke, Iruka N Carlos, Celia Aanensen, David M |
author_sort | Argimón, Silvia |
collection | PubMed |
description | BACKGROUND: Klebsiella 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. METHODS: We 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. RESULTS: Using 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. CONCLUSIONS: Pathogenwatch 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. |
format | Online Article Text |
id | pubmed-8634497 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-86344972021-12-02 Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch Argimón, Silvia David, Sophia Underwood, Anthony Abrudan, Monica Wheeler, Nicole E Kekre, Mihir Abudahab, Khalil Yeats, Corin A Goater, Richard Taylor, Ben Harste, Harry Muddyman, Dawn Feil, Edward J Brisse, Sylvain Holt, Kathryn Donado-Godoy, Pilar Ravikumar, K L Okeke, Iruka N Carlos, Celia Aanensen, David M Clin Infect Dis Supplement Articles BACKGROUND: Klebsiella 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. METHODS: We 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. RESULTS: Using 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. CONCLUSIONS: Pathogenwatch 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. Oxford University Press 2021-12-01 /pmc/articles/PMC8634497/ /pubmed/34850838 http://dx.doi.org/10.1093/cid/ciab784 Text en © The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Supplement Articles Argimón, Silvia David, Sophia Underwood, Anthony Abrudan, Monica Wheeler, Nicole E Kekre, Mihir Abudahab, Khalil Yeats, Corin A Goater, Richard Taylor, Ben Harste, Harry Muddyman, Dawn Feil, Edward J Brisse, Sylvain Holt, Kathryn Donado-Godoy, Pilar Ravikumar, K L Okeke, Iruka N Carlos, Celia Aanensen, David M Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch |
title | Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch |
title_full | Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch |
title_fullStr | Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch |
title_full_unstemmed | Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch |
title_short | Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch |
title_sort | rapid genomic characterization and global surveillance of klebsiella using pathogenwatch |
topic | Supplement Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8634497/ https://www.ncbi.nlm.nih.gov/pubmed/34850838 http://dx.doi.org/10.1093/cid/ciab784 |
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