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

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dc.contributor.author Gladstone, Rebecca A.
dc.contributor.author Lo, Stephanie W.
dc.contributor.author Goater, Richard
dc.contributor.author Yeats, Corin
dc.contributor.author Taylor, Ben
dc.contributor.author Hadfield, James
dc.contributor.author Lees, John A.
dc.contributor.author Croucher, Nicholas J.
dc.contributor.author van Tonder, Andries J.
dc.contributor.author Bentley, Leon J.
dc.contributor.author Quah, Fu Xiang
dc.contributor.author Blaschke, Anne J.
dc.contributor.author Pershing, Nicole L.
dc.contributor.author Byington, Carrie L.
dc.contributor.author Balaji, Veeraraghavan
dc.contributor.author Hryniewicz, Waleria
dc.contributor.author Sigauque, Betuel
dc.contributor.author Ravikumar, K. L.
dc.contributor.author Grassi Almeida, Samanta Cristine
dc.contributor.author Ochoa, Theresa J.
dc.contributor.author Ho, Pak Leung
dc.contributor.author du Plessis, Mignon
dc.contributor.author Ndlangisa, Kedibone M.
dc.contributor.author Cornick, Jennifer E.
dc.contributor.author Kwambana-Adams, Brenda
dc.contributor.author Benisty, Rachel
dc.contributor.author Nzenze, Susan A.
dc.contributor.author Madhi, Shabir A.
dc.contributor.author Hawkins, Paulina A.
dc.contributor.author Pollard, Andrew J.
dc.contributor.author Everett, Dean B.
dc.contributor.author Antonio, Martin
dc.contributor.author Dagan, Ron
dc.contributor.author Klugman, Keith P.
dc.contributor.author von Gottberg, Anne
dc.contributor.author Metcalf, Benjamin J.
dc.contributor.author Li, Yuan
dc.contributor.author Beall, Bernard W.
dc.contributor.author McGee, Lesley
dc.contributor.author Breiman, Robert F.
dc.contributor.author Aanensen, David M.
dc.contributor.author Bentley, Stephen D.
dc.contributor.author The Global Pneumococcal Sequencing Consortium
dc.date.accessioned 2020-07-14T00:01:12Z
dc.date.available 2020-07-14T00:01:12Z
dc.date.issued 2020
dc.identifier.uri https://hdl.handle.net/20.500.12866/8295
dc.description.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 dissemi-nation 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 20 kb 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. en_US
dc.language.iso eng
dc.publisher Microbiology Society
dc.relation.ispartof urn:issn:2057-5858
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Streptococcus pneumoniae en_US
dc.subject whole genome sequencing en_US
dc.subject population structure en_US
dc.subject antibiotic resistance en_US
dc.subject pangenome en_US
dc.subject phylogenetic dating en_US
dc.subject pneumococcal en_US
dc.subject recombination en_US
dc.title Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1099/mgen.0.000357
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#3.02.00 es_PE

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