The University of Southampton
University of Southampton Institutional Repository

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
Gladstone, Rebecca
6a2011bf-2561-4956-9928-46e6b927ba6d
Clarke, Stuart
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Bentley, Stephen D
438443a4-8033-4a5d-a5a5-538dbd4e8d60
Lo, Stephanie W.
607ccad6-93b1-484c-ba8d-9821432fce90
Goater, Richard
f1fb5190-4843-4e3a-973f-531a36b2412e
Yeats, Corin
97d0b512-c306-4f0b-bcf0-ad7bcc540653
Hadfield, James
89f3f0a8-106c-4a42-8bcd-dff4306564d3
Lees, John A.
85c253a2-8b71-43ad-8f0f-61bfa71cdfd7
Croucher, Nicholas
3a14e93e-acdb-4886-8b6b-34bd18a41cf9
von Tonder, Andries J.
7dfe168f-41a0-4047-9189-f3eadbfe633b
J. Bentley, Leon
9719dab6-98c5-42b9-af93-3e3417e2ac10
Quah, Fu Xiang
6faebe6b-73b3-4f13-8653-bebb195a7d60
Blaschke, Anne J.
95453fb1-c1d1-46fe-9a6b-0062e636a3f1
Pershing, Nicole L.
d48bd829-df76-41c0-b3e1-9ee0ac74c4f9
Byington, Carrie L.
5e77d6fd-467e-494b-8ab8-3ca47fe6ecd2
Balaji, Verraraghavan
4bcefa44-8175-4412-bce3-9c4a9228e060
Hryniewicz, Waleria
4f00de8a-c891-4a59-b75a-a57568b0e375
Sigauque, Betuel
919d8bfe-1ed0-4a5f-b5fb-e5a952b8d11d
Ravikumar, K.L.
d236e657-3025-41a6-ba80-240a06f4a297
Grassi Almeida, Samantha Cristine
78d1464c-fd79-4f65-be8a-637c075709f3
Ochoa, Theresa J.
68452b6e-d133-473d-a41b-251e3c91476b
Leung Ho, Pak
3558b339-6813-4966-91b0-6905ce9821fb
du Plessis, Mignon
b142a817-ef0b-496f-ab57-7364e4b1af0c
Ndlangisa, Kedibone M.
96398c2e-a31d-4728-8316-c15f745ba558
Cornick, Jennifer E.
c2a8ddc9-8bc1-411e-8cdf-a3c2065544e9
Kwambana-Adams, Brenda
5e833382-867f-4ec3-9d39-6919093a5083
Benisty, Rachel
469c3044-cb3a-45a9-8f2f-15e437d5755b
Nzenze, Susan A.
ba3db123-d2fd-4d74-81d2-2d48a76a681c
Madhi, Shabir A.
718d4b02-7359-4b32-a593-ed06f6b80329
Hawkins, Paulina A.
1558c41f-1c25-4e5f-9550-5ce3fd666ed8
Pollard, Andrew J.
20fbb4c7-b607-487c-96c4-bff882cfec9f
Everett, Dean B.
526edf0b-c78b-4a2f-8005-38d48196c2bb
Antonio, Martin
99c279ee-55d3-4dd9-a95d-6c0f79289330
Dagan, Ron
f446d232-24bb-47c4-a28d-8be3ea50fe51
Klugman, Keith P.
8f3bec69-805f-4123-b15a-3fd8942ee8a0
von Gottberg, Anne
2f54203f-7e4a-4c46-ab28-c94e4a940b2b
Metcalf, Benjamin J.
83e531a3-e4e3-486d-873f-7c1c3c1bbb93
Li, Yuan
372966b7-8dd4-4fca-9664-46738f33f76a
Beall, Bernard W.
54b15c62-b75e-428b-a0d7-e9dd98a55ad7
McGee, Lesley
366f453d-f2ef-47d3-9dc0-6e9a0c418c15
Breiman, Robert F.
124111b9-17e3-478b-9b90-a9e7a4d0faea
Aanensen, David M.
9b35859b-0269-45a9-91b3-7952520ed28d
Bentley, Stephen D.
5122ce60-0055-471f-9a77-db0b650c5ee8
Gladstone, Rebecca
6a2011bf-2561-4956-9928-46e6b927ba6d
Clarke, Stuart
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Bentley, Stephen D
438443a4-8033-4a5d-a5a5-538dbd4e8d60
Lo, Stephanie W.
607ccad6-93b1-484c-ba8d-9821432fce90
Goater, Richard
f1fb5190-4843-4e3a-973f-531a36b2412e
Yeats, Corin
97d0b512-c306-4f0b-bcf0-ad7bcc540653
Hadfield, James
89f3f0a8-106c-4a42-8bcd-dff4306564d3
Lees, John A.
85c253a2-8b71-43ad-8f0f-61bfa71cdfd7
Croucher, Nicholas
3a14e93e-acdb-4886-8b6b-34bd18a41cf9
von Tonder, Andries J.
7dfe168f-41a0-4047-9189-f3eadbfe633b
J. Bentley, Leon
9719dab6-98c5-42b9-af93-3e3417e2ac10
Quah, Fu Xiang
6faebe6b-73b3-4f13-8653-bebb195a7d60
Blaschke, Anne J.
95453fb1-c1d1-46fe-9a6b-0062e636a3f1
Pershing, Nicole L.
d48bd829-df76-41c0-b3e1-9ee0ac74c4f9
Byington, Carrie L.
5e77d6fd-467e-494b-8ab8-3ca47fe6ecd2
Balaji, Verraraghavan
4bcefa44-8175-4412-bce3-9c4a9228e060
Hryniewicz, Waleria
4f00de8a-c891-4a59-b75a-a57568b0e375
Sigauque, Betuel
919d8bfe-1ed0-4a5f-b5fb-e5a952b8d11d
Ravikumar, K.L.
d236e657-3025-41a6-ba80-240a06f4a297
Grassi Almeida, Samantha Cristine
78d1464c-fd79-4f65-be8a-637c075709f3
Ochoa, Theresa J.
68452b6e-d133-473d-a41b-251e3c91476b
Leung Ho, Pak
3558b339-6813-4966-91b0-6905ce9821fb
du Plessis, Mignon
b142a817-ef0b-496f-ab57-7364e4b1af0c
Ndlangisa, Kedibone M.
96398c2e-a31d-4728-8316-c15f745ba558
Cornick, Jennifer E.
c2a8ddc9-8bc1-411e-8cdf-a3c2065544e9
Kwambana-Adams, Brenda
5e833382-867f-4ec3-9d39-6919093a5083
Benisty, Rachel
469c3044-cb3a-45a9-8f2f-15e437d5755b
Nzenze, Susan A.
ba3db123-d2fd-4d74-81d2-2d48a76a681c
Madhi, Shabir A.
718d4b02-7359-4b32-a593-ed06f6b80329
Hawkins, Paulina A.
1558c41f-1c25-4e5f-9550-5ce3fd666ed8
Pollard, Andrew J.
20fbb4c7-b607-487c-96c4-bff882cfec9f
Everett, Dean B.
526edf0b-c78b-4a2f-8005-38d48196c2bb
Antonio, Martin
99c279ee-55d3-4dd9-a95d-6c0f79289330
Dagan, Ron
f446d232-24bb-47c4-a28d-8be3ea50fe51
Klugman, Keith P.
8f3bec69-805f-4123-b15a-3fd8942ee8a0
von Gottberg, Anne
2f54203f-7e4a-4c46-ab28-c94e4a940b2b
Metcalf, Benjamin J.
83e531a3-e4e3-486d-873f-7c1c3c1bbb93
Li, Yuan
372966b7-8dd4-4fca-9664-46738f33f76a
Beall, Bernard W.
54b15c62-b75e-428b-a0d7-e9dd98a55ad7
McGee, Lesley
366f453d-f2ef-47d3-9dc0-6e9a0c418c15
Breiman, Robert F.
124111b9-17e3-478b-9b90-a9e7a4d0faea
Aanensen, David M.
9b35859b-0269-45a9-91b3-7952520ed28d
Bentley, Stephen D.
5122ce60-0055-471f-9a77-db0b650c5ee8

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.

Text
mgen000357 - Version of Record
Available under License Creative Commons Attribution.
Download (1MB)
Text
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates - PubMed
Restricted to Repository staff only
Request a copy

More information

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

Catalogue record

Date deposited: 11 Mar 2021 17:36
Last modified: 17 Mar 2024 03:07

Export record

Altmetrics

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

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×