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BMC Infectious Diseases
Published in: BMC Infectious Diseases 1/2016

Open Access 01-12-2016 | Research article

Understanding pneumococcal serotype 1 biology through population genomic analysis

Authors: Chrispin Chaguza, Jennifer E. Cornick, Simon R. Harris, Cheryl P. Andam, Laura Bricio-Moreno, Marie Yang, Feyruz Yalcin, Sani Ousmane, Shanil Govindpersad, Madikay Senghore, Chinelo Ebruke, Mignon Du Plessis, Anmol M. Kiran, Gerd Pluschke, Betuel Sigauque, Lesley McGee, Keith P. Klugman, Paul Turner, Jukka Corander, Julian Parkhill, Jean-Marc Collard, Martin Antonio, Anne von Gottberg, Robert S. Heyderman, Neil French, Aras Kadioglu, William P. Hanage, Dean B. Everett, Stephen D. Bentley, for the PAGe Consortium

Published in: BMC Infectious Diseases | Issue 1/2016

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Abstract

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.
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Metadata
Title
Understanding pneumococcal serotype 1 biology through population genomic analysis
Authors
Chrispin Chaguza
Jennifer E. Cornick
Simon R. Harris
Cheryl P. Andam
Laura Bricio-Moreno
Marie Yang
Feyruz Yalcin
Sani Ousmane
Shanil Govindpersad
Madikay Senghore
Chinelo Ebruke
Mignon Du Plessis
Anmol M. Kiran
Gerd Pluschke
Betuel Sigauque
Lesley McGee
Keith P. Klugman
Paul Turner
Jukka Corander
Julian Parkhill
Jean-Marc Collard
Martin Antonio
Anne von Gottberg
Robert S. Heyderman
Neil French
Aras Kadioglu
William P. Hanage
Dean B. Everett
Stephen D. Bentley
for the PAGe Consortium
Publication date
01-12-2016
Publisher
BioMed Central
Published in
BMC Infectious Diseases / Issue 1/2016
Electronic ISSN: 1471-2334
DOI
https://doi.org/10.1186/s12879-016-1987-z

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