Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci
| العنوان: | Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci |
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| المؤلفون: | Jennifer E. Cornick, Robert F. Breiman, Benjamin J. Metcalf, Raymond Reid, Martin Antonio, Anna Skoczynska, Ewa Sadowy, Rebecca A. Gladstone, Katherine L O'Brien, Jennifer C. Moïsi, Lesley McGee, Claudette M. Thompson, Andrew J. Pollard, Amel Ghouila, Maria Georgieva, Waleria Hryniewicz, Bernard Beall, Pak-Leung Ho, Dean Everett, William P. Hanage, Brenda Kwambana-Adams, Mignon du Plessis, Stuart C. Clarke, Taj Azarian, Patrick K. Mitchell, Anne von Gottberg, Stephen D. Bentley |
| المساهمون: | Harvard University [Cambridge], Laboratoire de Transmission, Contrôle et Immunobiologie des Infections - Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Oxford Vaccine Group, University of Oxford [Oxford]-Oxford NIHR Biomedical Research Centre-The Churchill hospital, National Institute for Communicable Diseases [Johannesburg] (NICD), Medical Research Council Unit The Gambia (MRC), University of Southampton, University of Edinburgh, University of Liverpool, National Medicines Institute - Narodowy Instytut Leków [Warsaw] (NIL), Pfizer Ltd France, Pfizer, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Emory Global Health Institute [Atlanta] (EGHI), Emory University [Atlanta, GA], Department of Microbiology [HKU], The University of Hong Kong (HKU), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), The Wellcome Trust Sanger Institute [Cambridge], The study was funded in part by National Institute of Allergy and Infectious Disease award to WPH (R01 AI106786). The Global Pneumococcal Sequencing project is funded by The Bill and Melinda Gates Foundation (Grant OPP1034556). |
| المصدر: | PLoS Pathogens, Vol 14, Iss 11, p e1007438 (2018) Azarian, T, Mitchell, P K, Georgieva, M, Thompson, C M, Ghouila, A, Pollard, A J, von Gottberg, A, du Plessis, M, Antonio, M, Kwambana-Adams, B A, Clarke, S C, Everett, D, Cornick, J, Sadowy, E, Hryniewicz, W, Skoczynska, A, Moïsi, J C, McGee, L, Beall, B, Metcalf, B J, Breiman, R F, Ho, P L, Reid, R, O'Brien, K L, Gladstone, R A, Bentley, S D & Hanage, W P 2018, ' Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci ', PLoS Pathogens, vol. 14, no. 11, pp. e1007438 . https://doi.org/10.1371/journal.ppat.1007438Test PLoS Pathogens PLoS Pathogens, Public Library of Science, 2018, 14 (11), pp.e1007438. ⟨10.1371/journal.ppat.1007438⟩ PLOS PATHOGENS |
| بيانات النشر: | Public Library of Science (PLoS), 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | Serotype, MESH: Vaccines, Conjugate, Physiology, [SDV]Life Sciences [q-bio], Population Dynamics, Glycobiology, Biochemistry, Pneumococcal conjugate vaccine, Coalescent theory, Pneumococcal Vaccines, MESH: Pneumococcal Vaccines/immunology, Immune Physiology, Mobile Genetic Elements, MESH: Serotyping/methods, Genotype, Prevalence, Medicine and Health Sciences, MESH: Carrier State/epidemiology, MESH: Streptococcus pneumoniae/pathogenicity, Biology (General), MESH: Phylogeny, Clade, Phylogeny, MESH: Evolution, Molecular, Data Management, Genetics, Vaccines, 0303 health sciences, education.field_of_study, Immune System Proteins, Geography, MESH: Streptococcus pneumoniae/immunology, Genomics, Antigenic Variation, Recombinant Proteins, 3. Good health, Phylogenetics, Phylogeography, Streptococcus pneumoniae, Infectious Diseases, Biogeography, Carrier State, Research Article, medicine.drug, Computer and Information Sciences, Infectious Disease Control, Tetracycline, QH301-705.5, MESH: Bayes Theorem, Immunology, Population, Biology, Serogroup, Microbiology, Pneumococcal Infections, Evolution, Molecular, 03 medical and health sciences, Genetic Elements, MESH: Whole Genome Sequencing/methods, Polysaccharides, Microbial Control, MESH: Streptococcus pneumoniae/genetics, medicine, Humans, Evolutionary Systematics, MESH: Genetics, Population/methods, Serotyping, Antigens, education, MESH: Prevalence, Taxonomy, 030304 developmental biology, Pharmacology, Evolutionary Biology, Vaccines, Conjugate, MESH: Humans, Whole Genome Sequencing, Population Biology, 030306 microbiology, Ecology and Environmental Sciences, Transposable Elements, Biology and Life Sciences, Proteins, Bayes Theorem, MESH: Serogroup, MESH: Population Dynamics, RC581-607, MESH: Pneumococcal Infections/transmission, Genetics, Population, Carriage, Antibiotic Resistance, Earth Sciences, MESH: Pneumococcal Infections/immunology, Antimicrobial Resistance, Immunologic diseases. Allergy, Population Genetics |
| الوصف: | Streptococcus pneumoniae serotype 3 remains a significant cause of morbidity and mortality worldwide, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13). Serotype 3 increased in carriage since the implementation of PCV13 in the USA, while invasive disease rates remain unchanged. We investigated the persistence of serotype 3 in carriage and disease, through genomic analyses of a global sample of 301 serotype 3 isolates of the Netherlands3–31 (PMEN31) clone CC180, combined with associated patient data and PCV utilization among countries of isolate collection. We assessed phenotypic variation between dominant clades in capsule charge (zeta potential), capsular polysaccharide shedding, and susceptibility to opsonophagocytic killing, which have previously been associated with carriage duration, invasiveness, and vaccine escape. We identified a recent shift in the CC180 population attributed to a lineage termed Clade II, which was estimated by Bayesian coalescent analysis to have first appeared in 1968 [95% HPD: 1939–1989] and increased in prevalence and effective population size thereafter. Clade II isolates are divergent from the pre-PCV13 serotype 3 population in non-capsular antigenic composition, competence, and antibiotic susceptibility, the last of which resulting from the acquisition of a Tn916-like conjugative transposon. Differences in recombination rates among clades correlated with variations in the ATP-binding subunit of Clp protease, as well as amino acid substitutions in the comCDE operon. Opsonophagocytic killing assays elucidated the low observed efficacy of PCV13 against serotype 3. Variation in PCV13 use among sampled countries was not independently correlated with the CC180 population shift; therefore, genotypic and phenotypic differences in protein antigens and, in particular, antibiotic resistance may have contributed to the increase of Clade II. Our analysis emphasizes the need for routine, representative sampling of isolates from disperse geographic regions, including historically under-sampled areas. We also highlight the value of genomics in resolving antigenic and epidemiological variations within a serotype, which may have implications for future vaccine development. Author summary Streptococcus pneumoniae is a leading cause of bacterial pneumoniae, meningitis, and otitis media. Despite its inclusion in the most recent pneumococcal conjugate vaccine, PCV13, serotype 3 remains epidemiologically important globally. We investigated the persistence of serotype 3 using whole-genome sequencing data from 301 isolates collected among 24 countries from 1993–2014. Through phylogenetic analysis, we identified three distinct lineages within a single clonal complex, CC180, and found one that has recently emerged and grown in prevalence. We then compared genomic difference among lineages as well as variations in pneumococcal vaccine use among sampled countries. We found that the recently emerged lineage, termed Clade II, has a higher prevalence of antibiotic resistance compared to other lineages, diverse surface protein antigens, and a higher rate of recombination, a process by which bacteria can uptake and incorporate genetic material from its surroundings. Differences in vaccine use among sampled countries did not appear to be associated with the emergence of Clade II. We highlight the need for routine, representative sampling of bacterial isolates from diverse geographic areas and show the utility of genomic data in resolving epidemiological differences within a pathogen population. |
| وصف الملف: | application/pdf; text |
| اللغة: | English |
| تدمد: | 1553-7366 1553-7374 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::559995c4f95d92e583bdecd77c2f78baTest https://researchonline.lshtm.ac.uk/id/eprint/4653379/1/Azarian-etal-2018-Global-emergence-and-population-dynamics.pdfTest |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....559995c4f95d92e583bdecd77c2f78ba |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15537366 15537374 |
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