Understanding pneumococcal serotype 1 biology through population genomic analysis

Details

• Alternative Title:
  BMC Infect Dis
• Personal Author:
  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.
• Corporate Authors:
  for the PAGe Consortium
• Description:
  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 (catpC194), 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.
  
  
• Subjects:
  Drug Resistance, Bacterial Genetic Variation Humans Nasopharynx Phylogeny Pneumococcal Infections Recombination, Genetic Selection, Genetic Serogroup Streptococcus Pneumoniae Tetracycline Resistance

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• Source:
  BMC Infect Dis. 16.
• Pubmed ID:
  27821148
• Pubmed Central ID:
  PMC5100261
• Document Type:
  Journal Article
• Place as Subject:
  Africa ; Asia
• Volume:
  16
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:53a58b04ae99a10b13c4da805f704a5f518e30427af63d89a8346e862af287be
• Download URL:
  https://stacks.cdc.gov/view/cdc/43051/cdc_43051_DS1.pdf
• File Type:
  [PDF - 1.85 MB ]