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Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.
2057-5858
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Dagan, Ron
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Li, Yuan
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Beall, Bernard W.
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McGee, Lesley
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Hryniewicz, Waleria
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Ochoa, Theresa J.
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Kwambana-Adams, Brenda
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Benisty, Rachel
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Pollard, Andrew J.
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Antonio, Martin
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Dagan, Ron
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Klugman, Keith P.
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von Gottberg, Anne
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Metcalf, Benjamin J.
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Li, Yuan
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Beall, Bernard W.
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McGee, Lesley
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Breiman, Robert F.
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Aanensen, David M.
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Bentley, Stephen D.
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Gladstone, Rebecca, Clarke, Stuart, Bentley, Stephen D, Lo, Stephanie W., Goater, Richard, Yeats, Corin, Hadfield, James, Lees, John A., Croucher, Nicholas, von Tonder, Andries J., J. Bentley, Leon, Quah, Fu Xiang, Blaschke, Anne J., Pershing, Nicole L., Byington, Carrie L., Balaji, Verraraghavan, Hryniewicz, Waleria, Sigauque, Betuel, Ravikumar, K.L., Grassi Almeida, Samantha Cristine, Ochoa, Theresa J., Leung Ho, Pak, du Plessis, Mignon, Ndlangisa, Kedibone M., Cornick, Jennifer E., Kwambana-Adams, Brenda, Benisty, Rachel, Nzenze, Susan A., Madhi, Shabir A., Hawkins, Paulina A., Pollard, Andrew J., Everett, Dean B., Antonio, Martin, Dagan, Ron, Klugman, Keith P., von Gottberg, Anne, Metcalf, Benjamin J., Li, Yuan, Beall, Bernard W., McGee, Lesley, Breiman, Robert F., Aanensen, David M. and Bentley, Stephen D. (2020) Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. Microbial Genomics. (doi:10.1099/mgen.0.000357).

Record type: Article

Abstract

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.

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e-pub ahead of print date: 30 April 2020

Identifiers

Local EPrints ID: 447444
URI: http://eprints.soton.ac.uk/id/eprint/447444
ISSN: 2057-5858
PURE UUID: a26c6ed5-4b32-4266-b194-97cefd1021e8
ORCID for Stuart Clarke: ORCID iD orcid.org/0000-0002-7009-1548

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Date deposited: 11 Mar 2021 17:36
Last modified: 15 Sep 2021 01:51

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Contributors

Author: Rebecca Gladstone
Author: Stuart Clarke ORCID iD
Author: Stephen D Bentley
Author: Stephanie W. Lo
Author: Richard Goater
Author: Corin Yeats
Author: James Hadfield
Author: John A. Lees
Author: Nicholas Croucher
Author: Andries J. von Tonder
Author: Leon J. Bentley
Author: Fu Xiang Quah
Author: Anne J. Blaschke
Author: Nicole L. Pershing
Author: Carrie L. Byington
Author: Verraraghavan Balaji
Author: Waleria Hryniewicz
Author: Betuel Sigauque
Author: K.L. Ravikumar
Author: Samantha Cristine Grassi Almeida
Author: Theresa J. Ochoa
Author: Pak Leung Ho
Author: Mignon du Plessis
Author: Kedibone M. Ndlangisa
Author: Jennifer E. Cornick
Author: Brenda Kwambana-Adams
Author: Rachel Benisty
Author: Susan A. Nzenze
Author: Shabir A. Madhi
Author: Paulina A. Hawkins
Author: Andrew J. Pollard
Author: Dean B. Everett
Author: Martin Antonio
Author: Ron Dagan
Author: Keith P. Klugman
Author: Anne von Gottberg
Author: Benjamin J. Metcalf
Author: Yuan Li
Author: Bernard W. Beall
Author: Lesley McGee
Author: Robert F. Breiman
Author: David M. Aanensen
Author: Stephen D. Bentley

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