Understanding pneumococcal serotype 1 biology through population genomic analysis. Chaguza Chrispin et al. BMC infectious diseases 2016 Nov (1) 649 || Public Health Genomics Knowledge Base (v1.2)

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Citation Understanding pneumococcal serotype 1 biology through population genomic analysis.
Chaguza Chrispin et al. BMC infectious diseases 2016 Nov (1) 649
Authors: Chaguza Chrispin, Cornick Jennifer E, Harris Simon R, Andam Cheryl P, Bricio-Moreno Laura, Yang Marie, Yalcin Feyruz, Ousmane Sani, Govindpersad Shanil, Senghore Madikay, Ebruke Chinelo, Du Plessis Mignon, Kiran Anmol M, Pluschke Gerd, Sigauque Betuel, McGee Lesley, Klugman Keith P, Turner Paul, Corander Jukka, Parkhill Julian, Collard Jean-Marc, Antonio Martin, von Gottberg Anne, Heyderman Robert S, French Neil, Kadioglu Aras, Hanage William P, Everett Dean B, Bentley Stephen D,
Title: Understanding pneumococcal serotype 1 biology through population genomic analysis.
Journal: BMC infectious diseases
PubMed ID: 27821148
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.
Type: CDC-Authored Publication
Category:
Database Source: CDC-Authored Genomics Publication Database