Showing papers by "Carrie L. Byington published in 2020"
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University of Oxford1, Fred Hutchinson Cancer Research Center2, Imperial College London3, University of Cambridge4, University of Utah5, University of California, Berkeley6, Christian Medical College & Hospital7, International Military Sports Council8, Kempegowda Institute of Medical Sciences9, Instituto Adolfo Lutz10, Cayetano Heredia University11, University of Hong Kong12, Wellcome Trust13, University of London14, University College London15, Ben-Gurion University of the Negev16, University of the Witwatersrand17, Emory University18, University of Edinburgh19, Centers for Disease Control and Prevention20
TL;DR: This work prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshot of 73 common Global Pneumococcal Sequence Clusters previously defined using PopPUNK, and presents them in Microreact, to increase dissemination of genomic insights to the wider community, without the need for specialist training.
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 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.
28 citations
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University of California, Irvine1, George Washington University2, University of Minnesota3, California State University, Los Angeles4, University of California, Berkeley5, Case Western Reserve University6, University of California, Davis7, Children's Memorial Hospital8, University of Arkansas for Medical Sciences9, University of Washington10, MacLean Center for Clinical Medical Ethics11, University of Colorado Denver12, Icahn School of Medicine at Mount Sinai13
TL;DR: Author(s): Cooper, Dan M; Guay-Woodford, Lisa; Blazar, Bruce R; Bowman, Scott; Byington, Carrie L; Dome, Jeffrey; Forthal, Donald; Konstan, Michael W; Kuppermann, Nathan; Liem, Robert I; Ochoa, Eduardo R; Pollock, Brad H; Price, Olga Acosta; Ramsey, Bonnie W; Ross, Lainie Friedman; Sokol, Ronald
16 citations