Understanding pneumococcal serotype 1 biology through population genomic analysis

Autor: Chaguza, Chrispin, Cornick, Jennifer, Harris, Simon, Andam, Cheryl, Bricio-Moreno, Laura, Yang, Marie, Yalcin, Feyruz, Ousmane, Sani, Govindpersad, Shanil, Senghore, Madikay, Ebruke, Chinelo, du Plessis, Mignon, Kiran, Anmol, Pluschke, Gerd, Sigauque, Betuel, McGee, Lesley, Klugman, Keith, Turner, Paul, Corander, Jukka, Parkhill, Julian, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, Heyderman, Robert, French, Neil, Kadioglu, Aras, Hanage, William, Everett, Dean, Bentley, Stephen, Consortium, the PAGe
Přispěvatelé: University of Liverpool, Malawi Liverpool Wellcome Trust Clinical Research Programme (MLW), Liverpool School of Tropical Medicine (LSTM)-University of Liverpool-Wellcome Trust-University of Malawi, The Wellcome Trust Sanger Institute [Cambridge], Harvard T.H. Chan School of Public Health, Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), National Institute for Communicable Diseases [Johannesburg] (NICD), Medical Research Council Unit The Gambia (MRC), University of Warwick [Coventry], London School of Hygiene and Tropical Medicine (LSHTM), Swiss Tropical and Public Health Institute [Basel], Centro de Investigação em Saúde de Manhiça [Maputo, Mozambique] (CISM), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Emory University [Atlanta, GA], Bill & Melinda Gates Foundation [Seattle], Angkor Hospital for Children (AHC), University of Oxford [Oxford], University of Helsinki, University of the Witwatersrand [Johannesburg] (WITS), University College of London [London] (UCL), This work was supported by funds from the Bill and Melinda Gates Foundation (BMGF) (grant number: OPP1023440 awarded to DBE [http://www.pagegenomes.org/page/consortium]) and The Wellcome Trust Major Overseas programme core award (Award number: 084679/Z/08/Z). CC acknowledges support in form of a PhD scholarship from the Commonwealth Scholarship Commission, UK., Department of Mathematics and Statistics, Jukka Corander / Principal Investigator, Biostatistics Helsinki, Chaguza, Chrispin [0000-0002-2108-1757], Apollo - University of Cambridge Repository
Jazyk: angličtina
Rok vydání: 2016
Předmět:
MESH: Tetracycline Resistance
Antibiotic resistance
MESH: Selection
Genetic
MENINGITIS
STREPTOCOCCUS-PNEUMONIAE
RECOMBINATION
ST217
MESH: Africa
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Nasopharynx
MESH: Pneumococcal Infections
MESH: Genetic Variation
MESH: Phylogeny
112 Statistics and probability
Phylogeny
1183 Plant biology
microbiology
virology
Recombination
Genetic
MESH: Asia
Research Support
Non-U.S. Gov't
Tetracycline Resistance
Phylogeography
Streptococcus pneumoniae
Infectious Diseases
MESH: Recombination
Genetic
VIRULENCE FACTORS
CONJUGATE VACCINE
MESH: Streptococcus pneumoniae
Research Article
Asia
Evolution
Serogroup
Pneumococcal Infections
lcsh:Infectious and parasitic diseases
INVASIVE-DISEASE
Pneumococcal serotype 1
Drug Resistance
Bacterial
MESH: Drug Resistance
Bacterial
Journal Article
Humans
lcsh:RC109-216
Selection
Genetic
MESH: Humans
Genetic Variation
MESH: Serogroup
[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
DNA-SEQUENCES
MESH: Nasopharynx
DISCOVERY
Africa
[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
SEROLOGICAL CHARACTERIZATION
GENERATION
Zdroj: BMC Infectious Diseases
BMC Infectious Diseases, BioMed Central, 2016, 16 (1), pp.649. ⟨10.1186/s12879-016-1987-z⟩
BMC Infectious Diseases, Vol 16, Iss 1, Pp 1-14 (2016)
Chaguza, C, Cornick, J E, Harris, S R, Andam, C P, Bricio-Moreno, L, Yang, M, Yalcin, F, Ousmane, S, Govindpersad, S, Senghore, M, Ebruke, C, Du Plessis, M, Kiran, A M, Pluschke, G, Sigauque, B, McGee, L, Klugman, K P, Turner, P, Corander, J, Parkhill, J, Collard, J-M, Antonio, M, von Gottberg, A, Heyderman, R S, French, N, Kadioglu, A, Hanage, W P & Everett, D B & Bentley, S D 2016, ' Understanding pneumococcal serotype 1 biology through population genomic analysis ', BMC Infectious Diseases, vol. 16, no. 1, pp. 649 . https://doi.org/10.1186/s12879-016-1987-z
ISSN: 1471-2334
DOI: 10.1186/s12879-016-1987-z⟩
Popis: Background Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. Methods We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. Results Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1’s rarity in carriage and consequently its lower recombination rates. Conclusions The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1987-z) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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