Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch

Silvia Argimon; Sophia David; Anthony Underwood; Monica Abrudan; Nicole Wheeler; Mihir Kekre; Khalil Abudahab; Corin A. Yeats; Richard Goater; Ben Taylor; Harry Harste; Dawn Muddyman; Edward J. Feil; Sylvain Brisse; Kathryn Holt; Pilar Donado-Godoy; K. L. Ravikumar; Iruka N. Okeke; Celia C. Carlos; David Aanensen

doi:10.1101/2021.06.22.448967

Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch

Silvia Argimon, Sophia David, Anthony Underwood, Monica Abrudan, Nicole Wheeler, Mihir Kekre, Khalil Abudahab, Corin A. Yeats, Richard Goater, Ben Taylor, Harry Harste, Dawn Muddyman, Edward J. Feil, Sylvain Brisse, Kathryn Holt, Pilar Donado-Godoy, K. L. Ravikumar, Iruka N. Okeke, Celia C. Carlos, David Aanensen

Microbes, Infections and Microbiomes

Research output: Working paper/Preprint › Preprint

Abstract

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 1,636 genomes from four 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 (e.g. 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 three 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.

Original language	English
Publisher	bioRxiv
DOIs	https://doi.org/10.1101/2021.06.22.448967
Publication status	Published - 22 Jun 2021

Keywords

genomics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Argimon, S., David, S., Underwood, A., Abrudan, M., Wheeler, N., Kekre, M., Abudahab, K., Yeats, C. A., Goater, R., Taylor, B., Harste, H., Muddyman, D., Feil, E. J., Brisse, S., Holt, K., Donado-Godoy, P., Ravikumar, K. L., Okeke, I. N., Carlos, C. C., & Aanensen, D. (2021). Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch. bioRxiv. https://doi.org/10.1101/2021.06.22.448967

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title = "Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch",

abstract = "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 1,636 genomes from four 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 (e.g. 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 three 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.",

keywords = "genomics",

author = "Silvia Argimon and Sophia David and Anthony Underwood and Monica Abrudan and Nicole Wheeler and Mihir Kekre and Khalil Abudahab and Yeats, {Corin A.} and Richard Goater and Ben Taylor and Harry Harste and Dawn Muddyman and Feil, {Edward J.} and Sylvain Brisse and Kathryn Holt and Pilar Donado-Godoy and Ravikumar, {K. L.} and Okeke, {Iruka N.} and Carlos, {Celia C.} and David Aanensen",

year = "2021",

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Argimon, S, David, S, Underwood, A, Abrudan, M, Wheeler, N, Kekre, M, Abudahab, K, Yeats, CA, Goater, R, Taylor, B, Harste, H, Muddyman, D, Feil, EJ, Brisse, S, Holt, K, Donado-Godoy, P, Ravikumar, KL, Okeke, IN, Carlos, CC & Aanensen, D 2021 'Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch' bioRxiv. https://doi.org/10.1101/2021.06.22.448967

TY - UNPB

T1 - Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch

AU - Argimon, Silvia

AU - David, Sophia

AU - Underwood, Anthony

AU - Abrudan, Monica

AU - Wheeler, Nicole

AU - Kekre, Mihir

AU - Abudahab, Khalil

AU - Yeats, Corin A.

AU - Goater, Richard

AU - Taylor, Ben

AU - Harste, Harry

AU - Muddyman, Dawn

AU - Feil, Edward J.

AU - Brisse, Sylvain

AU - Holt, Kathryn

AU - Donado-Godoy, Pilar

AU - Ravikumar, K. L.

AU - Okeke, Iruka N.

AU - Carlos, Celia C.

AU - Aanensen, David

PY - 2021/6/22

Y1 - 2021/6/22

N2 - 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 1,636 genomes from four 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 (e.g. 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 three 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.

AB - 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 1,636 genomes from four 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 (e.g. 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 three 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.

KW - genomics

U2 - 10.1101/2021.06.22.448967

DO - 10.1101/2021.06.22.448967

M3 - Preprint

BT - Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch

PB - bioRxiv

ER -

Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch

Abstract

Keywords

UN SDGs

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