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International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease
International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

BACKGROUND: Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them.

METHODS: Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating.

RESULTS: Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017.

CONCLUSION: The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

Molecular epidemiology, Outbreak, PCVs, PPV23, Pneumococcal, ST801, Serotype 4, Streptococcus pneumoniae, Whole genome sequencing
0264-410X
1054-1060
Gladstone, R A
dc46a4be-7958-4f35-b3df-d5c3f8ae55ab
Siira, L
233e1755-b927-4c43-a11a-2169da414523
Brynildsrud, O B
bb071d58-221f-4283-a655-2216b86354c0
Vestrheim, D F
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Turner, P
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Clarke, S C
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Srifuengfung, S
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Ford, R
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Lehmann, D
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Egorova, E
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Voropaeva, E
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Haraldsson, G
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Kristinsson, K G
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McGee, L
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Breiman, R F
38ff5868-bb32-43c3-97c4-d52ceba325d0
Bentley, S D
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Sheppard, C L
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Fry, N K
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Corander, J
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Toropainen, M
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Steens, A
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Global Pneumococcal Sequencing Consortium
Gladstone, R A
dc46a4be-7958-4f35-b3df-d5c3f8ae55ab
Siira, L
233e1755-b927-4c43-a11a-2169da414523
Brynildsrud, O B
bb071d58-221f-4283-a655-2216b86354c0
Vestrheim, D F
61431855-6413-4afe-a9f5-a04b0667db15
Turner, P
9df85f52-ad0b-4927-888e-256dfbbae8ab
Clarke, S C
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Srifuengfung, S
4da3faa8-6482-4f33-b4b7-c0eb9db44d67
Ford, R
fa8e259d-f9ae-476d-850f-82dae331deaf
Lehmann, D
567ada0b-ab0a-45d8-a036-a29d27b37d78
Egorova, E
ee7f9360-c0d4-4b88-9b62-2bf77e227c51
Voropaeva, E
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Haraldsson, G
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Kristinsson, K G
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McGee, L
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Breiman, R F
38ff5868-bb32-43c3-97c4-d52ceba325d0
Bentley, S D
01538685-1303-4e58-9c31-f005d90a0ae3
Sheppard, C L
70baaadd-57e7-4847-be4e-6b23faf6b5e5
Fry, N K
011d8ebf-ff1e-4055-bff8-6f3cad7a5dc5
Corander, J
36c9769f-9e9d-4252-a37c-c0549974a4c2
Toropainen, M
c5163369-b339-47a8-89e7-30a65537194f
Steens, A
178c5501-2dea-470f-9ca2-d2de995be2e0

Gladstone, R A, Siira, L and Brynildsrud, O B , Global Pneumococcal Sequencing Consortium (2022) International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease. Vaccine, 40 (7), 1054-1060. (doi:10.1016/j.vaccine.2021.10.046).

Record type: Article

Abstract

BACKGROUND: Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them.

METHODS: Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating.

RESULTS: Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017.

CONCLUSION: The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

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Accepted/In Press date: 20 October 2021
e-pub ahead of print date: 5 January 2022
Published date: 11 February 2022
Additional Information: Funding Information: We would like to acknowledge the Global Pneumococcal Sequencing project (GPS) and other pneumococcal sequencing projects performed at the Wellcome Sanger Institute whose genomes were screened to identify isolates that could provide context for this analysis, and the Wellcome Sanger Institute Pathogen Informatics Team. The GPS data was supported by the Wellcome Trust, grant number 206194/Z/17/Z, and by the Bill and Melinda Gates Foundation, Investment ID INV-003570. Furthermore, we acknowledge Lene Kolstad, Martha Bjørnstad and Nadia Debech of the Norwegian Institute of Public Health for the analysis of the Norwegian isolates, Brita A Winje for the Norwegian IPD surveillance data and the rest of the outbreak team for their work during the outbreak. We would like to acknowledge Anni Vainio, Milla Hietikko, Elina Yamazaki and Riitta Pulkkinen for laboratory and sequencing work of the Finnish isolates and the outbreak investigation team for their work to control the outbreak. The findings and conclusions in this manuscript are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. Sequencing of outbreak and contemporary IPD surveillance isolates were funded internally in the respective public health institutes. The Global Pneumococcal Sequencing project was funded by Wellcome Trust, grant number 206194/Z/17/Z, and by the Bill and Melinda Gates Foundation, Investment ID INV-003570. J.C. was funded by the European Research Council grant no. 742158. PT is funded by the Wellcome Trust (Thailand-Laos AAP core award, grant no. 220211). Funding Information: We would like to acknowledge the Global Pneumococcal Sequencing project (GPS) and other pneumococcal sequencing projects performed at the Wellcome Sanger Institute whose genomes were screened to identify isolates that could provide context for this analysis, and the Wellcome Sanger Institute Pathogen Informatics Team. The GPS data was supported by the Wellcome Trust, grant number 206194/Z/17/Z, and by the Bill and Melinda Gates Foundation, Investment ID INV-003570. Furthermore, we acknowledge Lene Kolstad, Martha Bjørnstad and Nadia Debech of the Norwegian Institute of Public Health for the analysis of the Norwegian isolates, Brita A Winje for the Norwegian IPD surveillance data and the rest of the outbreak team for their work during the outbreak. Funding Information: Sequencing of outbreak and contemporary IPD surveillance isolates were funded internally in the respective public health institutes. The Global Pneumococcal Sequencing project was funded by Wellcome Trust, grant number 206194/Z/17/Z, and by the Bill and Melinda Gates Foundation, Investment ID INV-003570. J.C. was funded by the European Research Council grant no. 742158. PT is funded by the Wellcome Trust (Thailand-Laos AAP core award, grant no. 220211). Publisher Copyright: © 2021 The Author(s)
Keywords: Molecular epidemiology, Outbreak, PCVs, PPV23, Pneumococcal, ST801, Serotype 4, Streptococcus pneumoniae, Whole genome sequencing

Identifiers

Local EPrints ID: 454389
URI: http://eprints.soton.ac.uk/id/eprint/454389
ISSN: 0264-410X
PURE UUID: 83aae3f4-d37e-4342-8808-baacac5fcc06
ORCID for S C Clarke: ORCID iD orcid.org/0000-0002-7009-1548

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Date deposited: 08 Feb 2022 17:47
Last modified: 17 Mar 2024 07:04

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Contributors

Author: R A Gladstone
Author: L Siira
Author: O B Brynildsrud
Author: D F Vestrheim
Author: P Turner
Author: S C Clarke ORCID iD
Author: S Srifuengfung
Author: R Ford
Author: D Lehmann
Author: E Egorova
Author: E Voropaeva
Author: G Haraldsson
Author: K G Kristinsson
Author: L McGee
Author: R F Breiman
Author: S D Bentley
Author: C L Sheppard
Author: N K Fry
Author: J Corander
Author: M Toropainen
Author: A Steens
Corporate Author: Global Pneumococcal Sequencing Consortium

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