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Understanding pneumococcal serotype 1 biology through population genomic analysis

Chaguza, Chrispin and Cornick, Jennifer E. and Harris, Simon R. and Andam, Cheryl P. and Bricio-Moreno, Laura and Yang, Marie and Yalcin, Feyruz and Ousmane, Sani and Govindpersad, Shanil and Senghore, Madikay and Ebruke, Chinelo and Du Plessis, Mignon and Kiran, Anmol M. and Pluschke, Gerd and Sigauque, Betuel and McGee, Lesley and Klugman, Keith P. and Turner, Paul and Corander, Jukka and Parkhill, Julian and Collard, Jean-Marc and Antonio, Martin and von Gottberg, Anne and Heyderman, Robert S. and French, Neil and Kadioglu, Aras and Hanage, William P. and Everett, Dean B. and Bentley, Stephen D. and PAGe Consortium, . (2016) Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC infectious diseases, 16. p. 649.

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Abstract

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.; 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.; 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.; 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.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology > Molecular Immunology (Pluschke)
UniBasel Contributors:Pluschke, Gerd
Item Type:Article, refereed
Publisher:BioMed Central
ISSN:1471-2334
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:13 Dec 2016 14:13
Deposited On:08 Dec 2016 10:14

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