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Population genomics of disease-causing streptococcus pneumonia in Singapore

Population genomics of disease-causing streptococcus pneumonia in Singapore
Population genomics of disease-causing streptococcus pneumonia in Singapore
The World Health Organization (WHO) reports that approximately 500,000 deaths in children aged 0-59 months occur due to pneumococcal infections and that, in the developing world, pneumococcal pneumonia is the leading infectious cause of adult mortality. Pneumococcal diseases mainly affect the vulnerable populations: children under the age of five years (otitis media is very common), elderly and immunocompromised (most commonly pneumonia). Two thousand and one hundred fifty six pneumococcal isolates causing invasive and non-invasive diseases between 1997 and 2013 were collected from four hospitals in Singapore. The isolates were characterized using whole genome sequencing (WGS). Out of 67 serotypes found throughout the study period, the most common serotypes were 19F, 19A, 14, 23F and the recently reported serotype 6E. Estimated serotype coverage by the current pneumococcal vaccines (PCV-7, -10, -13 and PPV23) ranged from 50% to 74%. Further interrogation of the whole genome data classified isolates into 24 major clusters based on their core orthologous genes. As expected, the same serotypes and similar sequence types (STs) clustered together. Among the 512 STs found, the majority of novel STs were found in isolates from adults. Genetically diverse, rrgC genes (encoding pilin components) were more likely to be found in non-invasive disease-causing isolates while other genes previously associated with pneumococcal virulence, pspA, pspC and ply, were just as likely to be found among non-invasive and invasive disease causing isolates. This first large-scale pneumococcal study from Singapore includes analysis of WGS and clinical data from pneumococcal strains collected over the past 15 years. High genetic diversity identified among these strains may reflect the cosmopolitan nature of Singapore’s increasingly international population and might be a focus for the emergence of novel pneumococcal clones in the era of modern conjugate and protein-based pneumococcal vaccines.
University of Southampton
Jauneikaite, Elita
ed667cc2-1947-4234-816d-83c8fd58fb8e
Jauneikaite, Elita
ed667cc2-1947-4234-816d-83c8fd58fb8e
Clarke, Stuart
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17

Jauneikaite, Elita (2014) Population genomics of disease-causing streptococcus pneumonia in Singapore. University of Southampton, Doctoral Thesis, 376pp.

Record type: Thesis (Doctoral)

Abstract

The World Health Organization (WHO) reports that approximately 500,000 deaths in children aged 0-59 months occur due to pneumococcal infections and that, in the developing world, pneumococcal pneumonia is the leading infectious cause of adult mortality. Pneumococcal diseases mainly affect the vulnerable populations: children under the age of five years (otitis media is very common), elderly and immunocompromised (most commonly pneumonia). Two thousand and one hundred fifty six pneumococcal isolates causing invasive and non-invasive diseases between 1997 and 2013 were collected from four hospitals in Singapore. The isolates were characterized using whole genome sequencing (WGS). Out of 67 serotypes found throughout the study period, the most common serotypes were 19F, 19A, 14, 23F and the recently reported serotype 6E. Estimated serotype coverage by the current pneumococcal vaccines (PCV-7, -10, -13 and PPV23) ranged from 50% to 74%. Further interrogation of the whole genome data classified isolates into 24 major clusters based on their core orthologous genes. As expected, the same serotypes and similar sequence types (STs) clustered together. Among the 512 STs found, the majority of novel STs were found in isolates from adults. Genetically diverse, rrgC genes (encoding pilin components) were more likely to be found in non-invasive disease-causing isolates while other genes previously associated with pneumococcal virulence, pspA, pspC and ply, were just as likely to be found among non-invasive and invasive disease causing isolates. This first large-scale pneumococcal study from Singapore includes analysis of WGS and clinical data from pneumococcal strains collected over the past 15 years. High genetic diversity identified among these strains may reflect the cosmopolitan nature of Singapore’s increasingly international population and might be a focus for the emergence of novel pneumococcal clones in the era of modern conjugate and protein-based pneumococcal vaccines.

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Published date: September 2014

Identifiers

Local EPrints ID: 416902
URI: https://eprints.soton.ac.uk/id/eprint/416902
PURE UUID: f69093d0-5e62-4a45-beba-9f0f955575d9
ORCID for Stuart Clarke: ORCID iD orcid.org/0000-0002-7009-1548

Catalogue record

Date deposited: 12 Jan 2018 17:30
Last modified: 14 Mar 2019 01:41

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Contributors

Author: Elita Jauneikaite
Thesis advisor: Stuart Clarke ORCID iD

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