Visualizing variation within global pneumococcal sequence clusters (GPSCS) and country population snapshots to contextualize pneumococcal isolates

• Autores: Gladstone, Rebecca A.; Lo, Stephanie W.; Goater, Richard; Yeats, Corin; Taylor, Ben; Hadfield, James; Lees, John A.; Croucher, Nicholas J.; van Tonder, Andries; Bentley, Leon J.; Quah, Fu Xiang; Blaschke, Anne J.; Pershing, Nicole L.; Byington, Carrie L.; Balaji, Veeraraghavan; Hryniewicz, Waleria; Sigauque, Betuel; Ravikumar, K. L.; Grassi Almeida, Samanta Cristine; Ochoa, Theresa J.; Ho, Pak Leung; du Plessis, Mignon; Ndlangisa, Kedibone M.; Cornick, Jennifer; Kwambana Adams, Brenda; Benisty, Rachel; Nzenze, Susan A.; Madhi, Shabir A.; Hawkins, Paulina A.; Faccone, Diego Francisco
• Año de publicación: 2020
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: ANTIBIOTIC RESISTANCE; PANGENOME; PHYLOGENETIC DATING; PNEUMOCOCCAL; POPULATION STRUCTURE; RECOMBINATION; STREPTOCOCCUS PNEUMONIAE; WHOLE GENOME SEQUENCING
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

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.
Fil: Gladstone, Rebecca A.. Wellcome Sanger Institute; Reino Unido
Fil: Lo, Stephanie W.. Wellcome Sanger Institute; Reino Unido
Fil: Goater, Richard. Wellcome Sanger Institute; Reino Unido. University of Oxford; Reino Unido
Fil: Yeats, Corin. Wellcome Sanger Institute; Reino Unido. University of Oxford; Reino Unido
Fil: Taylor, Ben. Wellcome Sanger Institute; Reino Unido. University of Oxford; Reino Unido
Fil: Hadfield, James. Fred Hutchinson Cancer Research Center; Estados Unidos
Fil: Lees, John A.. Imperial College London; Reino Unido
Fil: Croucher, Nicholas J.. Imperial College London; Reino Unido
Fil: van Tonder, Andries. Wellcome Sanger Institute; Reino Unido. University of Cambridge; Estados Unidos
Fil: Bentley, Leon J.. Wellcome Sanger Institute; Reino Unido
Fil: Quah, Fu Xiang. Wellcome Sanger Institute; Reino Unido
Fil: Blaschke, Anne J.. University of Utah; Estados Unidos
Fil: Pershing, Nicole L.. University of Utah; Estados Unidos
Fil: Byington, Carrie L.. University of California; Estados Unidos
Fil: Balaji, Veeraraghavan. Christian Medical College; India
Fil: Hryniewicz, Waleria. National Medicines Institute; Polonia
Fil: Sigauque, Betuel. Instituto Nacional de Saude Maputo; Mozambique
Fil: Ravikumar, K. L.. Kempegowda Institute Of Medical Sciences; India
Fil: Grassi Almeida, Samanta Cristine. Adolfo Lutz Institute; Brasil
Fil: Ochoa, Theresa J.. Universidad Peruana Cayetano Heredia; Perú
Fil: Ho, Pak Leung. The University Of Hong Kong; Hong Kong
Fil: du Plessis, Mignon. National Institute for Communicable Diseases; Sudáfrica
Fil: Ndlangisa, Kedibone M.. National Institute for Communicable Diseases; Sudáfrica
Fil: Cornick, Jennifer. Malawi liverpool wellcome Trust Clinical Research Programme; Malaui
Fil: Kwambana Adams, Brenda. Colegio Universitario de Londres; Reino Unido. Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine; Gambia
Fil: Benisty, Rachel. Ben Gurion University of the Negev; Israel
Fil: Nzenze, Susan A.. University of the Witwatersrand; Sudáfrica
Fil: Madhi, Shabir A.. University of the Witwatersrand; Sudáfrica
Fil: Hawkins, Paulina A.. Emory University; Estados Unidos
Fil: Faccone, Diego Francisco. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas. Área de Antimicrobianos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina