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Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK

Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK
Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK

Serotype replacement has been reported in carriage and disease after pneumococcal conjugate vaccine (PCV) introductions in the UK and globally. We previously described concurrent expansion and decline of sequence types associated with serotype replacement over 5 years following PCV introductions in the UK. Here we use whole-genome sequencing to fully characterise the population structure of pneumococcal isolates collected over seven winters encompassing PCV7 and PCV13 introductions in the UK, investigating the importance of lineages in serotype replacement. We analysed 672 pneumococcal genomes from colonised children of 4 years old or less. The temporal prevalence of 20 lineages, defined by hierarchical Bayesian analysis of population structure (BAPS), was assessed in the context of serotype replacement. Multiple serotypes were detected in the primary winter of sampling within three vaccine-type (VT) lineages BAPS4, BAPS10 and BAPS11, in which serotype replacement were observed. In contrast, serotype replacement was not seen in the remaining three VT lineages (BAPS1, BAPS13 and BAPS14), that expressed a single serotype (6B, 6A and 3, respectively) in the primary winter. One lineage, BAPS1 serotype 6B was undetectable in the population towards the end of the study period. The dynamics of serotype replacement, in this UK population, was preceded by the presence or absence of multiple serotypes within VT lineages, in the pre-PCV population. This observation could help predict which non-vaccine types (NVTs) may be involved in replacement in future PCV introductions here and elsewhere. It could further indicate whether any antibiotic resistance associated with the lineages is likely to be affected by replacement.

Journal Article
2057-5858
3
Gladstone, Rebecca A.
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Devine, Vanessa
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Jones, Jessica
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Cleary, David
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Jefferies, Johanna M.
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Bentley, Stephen D.
438443a4-8033-4a5d-a5a5-538dbd4e8d60
Faust, Saul N.
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Clarke, Stuart C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Gladstone, Rebecca A.
6a2011bf-2561-4956-9928-46e6b927ba6d
Devine, Vanessa
1fbacb99-1e47-4e8a-be56-6db4c956bb62
Jones, Jessica
69dbdb74-21d8-4d10-9ac4-3539f2b54142
Cleary, David
f4079c6d-d54b-4108-b346-b0069035bec0
Jefferies, Johanna M.
d3c7f86b-c08e-4c8f-9ce1-c2ac5a511746
Bentley, Stephen D.
438443a4-8033-4a5d-a5a5-538dbd4e8d60
Faust, Saul N.
f97df780-9f9b-418e-b349-7adf63e150c1
Clarke, Stuart C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17

Gladstone, Rebecca A., Devine, Vanessa, Jones, Jessica, Cleary, David, Jefferies, Johanna M., Bentley, Stephen D., Faust, Saul N. and Clarke, Stuart C. (2017) Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK. Microbial Genomics, 3 (6), 3. (doi:10.1099/mgen.0.000119).

Record type: Article

Abstract

Serotype replacement has been reported in carriage and disease after pneumococcal conjugate vaccine (PCV) introductions in the UK and globally. We previously described concurrent expansion and decline of sequence types associated with serotype replacement over 5 years following PCV introductions in the UK. Here we use whole-genome sequencing to fully characterise the population structure of pneumococcal isolates collected over seven winters encompassing PCV7 and PCV13 introductions in the UK, investigating the importance of lineages in serotype replacement. We analysed 672 pneumococcal genomes from colonised children of 4 years old or less. The temporal prevalence of 20 lineages, defined by hierarchical Bayesian analysis of population structure (BAPS), was assessed in the context of serotype replacement. Multiple serotypes were detected in the primary winter of sampling within three vaccine-type (VT) lineages BAPS4, BAPS10 and BAPS11, in which serotype replacement were observed. In contrast, serotype replacement was not seen in the remaining three VT lineages (BAPS1, BAPS13 and BAPS14), that expressed a single serotype (6B, 6A and 3, respectively) in the primary winter. One lineage, BAPS1 serotype 6B was undetectable in the population towards the end of the study period. The dynamics of serotype replacement, in this UK population, was preceded by the presence or absence of multiple serotypes within VT lineages, in the pre-PCV population. This observation could help predict which non-vaccine types (NVTs) may be involved in replacement in future PCV introductions here and elsewhere. It could further indicate whether any antibiotic resistance associated with the lineages is likely to be affected by replacement.

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Accepted/In Press date: 8 May 2017
e-pub ahead of print date: 9 June 2017
Published date: June 2017
Keywords: Journal Article

Identifiers

Local EPrints ID: 422585
URI: https://eprints.soton.ac.uk/id/eprint/422585
ISSN: 2057-5858
PURE UUID: 45972be5-e3e2-48b9-8cae-5aa837602120
ORCID for David Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for Saul N. Faust: ORCID iD orcid.org/0000-0003-3410-7642
ORCID for Stuart C. Clarke: ORCID iD orcid.org/0000-0002-7009-1548

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Date deposited: 25 Jul 2018 16:30
Last modified: 03 Dec 2019 01:46

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Contributors

Author: Rebecca A. Gladstone
Author: Vanessa Devine
Author: Jessica Jones
Author: David Cleary ORCID iD
Author: Johanna M. Jefferies
Author: Stephen D. Bentley
Author: Saul N. Faust ORCID iD

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