Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13

Sophie Belman; Sona Soeng; Chansovannara Soputhy; Rebecca Gladstone; Paulina A Hawkins; Robert F Breiman; Lesley McGee; Stephen D Bentley; Stephanie W Lo; Paul Turner

doi:10.1099/mgen.0.000837

Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13

Sophie Belman, Sona Soeng, Chansovannara Soputhy, Rebecca Gladstone, Paulina A Hawkins, Robert F Breiman, Lesley McGee, Stephen D Bentley, Stephanie W Lo, Paul Turner

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

2 Citations (SciVal)

Abstract

Streptococcus pneumoniae (the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns. We sought to elucidate the genetic background (global pneumococcal sequence clusters; GPSCs) of pneumococci carried by Cambodian children following perturbation by pneumococcal conjugate vaccine (PCV) 13. We sequenced pre-PCV13 (01/2013-12/2015, N=258) and post-PCV13 carriage isolates (01/2016-02/2017, N=428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. Following PCV13 implementation in Cambodia, we saw expansions of non-vaccine type (NVT) serotypes 23A (GPSC626), 34 (GPSC45) and 6D (GPSC16). We predicted antimicrobial susceptibility using the CDC-AMR pipeline and determined concordance with phenotypic data. The CDC-AMR pipeline had >90 % concordance with the phenotypic antimicrobial-susceptibility testing. We detected a high prevalence of AMR in both expanding non-vaccine serotypes and residual vaccine serotype 6B. Persistently high levels of AMR, specifically persisting multidrug-resistant lineages, warrant concern. The implementation of PCV13 in Cambodia has resulted in NVT serotype expansion reflected in the carriage population and driven by specific genetic backgrounds. Continued monitoring of these GPSCs during the ongoing collection of additional carriage isolates in this population is necessary.

Original language	English
Journal	Microbial Genomics
Volume	8
Issue number	6
DOIs	https://doi.org/10.1099/mgen.0.000837
Publication status	Published - 28 Jun 2022

Bibliographical note

Data statement: All supporting data, code and protocols have been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article.

Funding information
This study was co-funded by the Bill and Melinda Gates Foundation (grant code OPP1034556), the Wellcome Sanger Institute (core Wellcome grants 098051 and 206194), and the US Centres for Disease Control and Prevention. P.T. and Cambodia Oxford Medical Research Unit (COMRU) are supported by core funding from Wellcome (grant 220211). The funding sources had no role in isolate selection, analysis nor data interpretation. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centres for Disease Control and Prevention. The corresponding author had full access to the data and is responsible for the final decision to submit for publication.

Keywords

Anti-Infective Agents
Asian People
Child
Genetic Background
Humans
Pneumococcal Vaccines
Streptococcus pneumoniae/genetics
Vaccines, Conjugate

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1099/mgen.0.000837Licence: CC BY-NC

Cite this

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title = "Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13",

abstract = "Streptococcus pneumoniae (the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns. We sought to elucidate the genetic background (global pneumococcal sequence clusters; GPSCs) of pneumococci carried by Cambodian children following perturbation by pneumococcal conjugate vaccine (PCV) 13. We sequenced pre-PCV13 (01/2013-12/2015, N=258) and post-PCV13 carriage isolates (01/2016-02/2017, N=428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. Following PCV13 implementation in Cambodia, we saw expansions of non-vaccine type (NVT) serotypes 23A (GPSC626), 34 (GPSC45) and 6D (GPSC16). We predicted antimicrobial susceptibility using the CDC-AMR pipeline and determined concordance with phenotypic data. The CDC-AMR pipeline had >90 % concordance with the phenotypic antimicrobial-susceptibility testing. We detected a high prevalence of AMR in both expanding non-vaccine serotypes and residual vaccine serotype 6B. Persistently high levels of AMR, specifically persisting multidrug-resistant lineages, warrant concern. The implementation of PCV13 in Cambodia has resulted in NVT serotype expansion reflected in the carriage population and driven by specific genetic backgrounds. Continued monitoring of these GPSCs during the ongoing collection of additional carriage isolates in this population is necessary.",

keywords = "Anti-Infective Agents, Asian People, Child, Genetic Background, Humans, Pneumococcal Vaccines, Streptococcus pneumoniae/genetics, Vaccines, Conjugate",

author = "Sophie Belman and Sona Soeng and Chansovannara Soputhy and Rebecca Gladstone and Hawkins, {Paulina A} and Breiman, {Robert F} and Lesley McGee and Bentley, {Stephen D} and Lo, {Stephanie W} and Paul Turner",

note = "Data statement: All supporting data, code and protocols have been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article. Funding information This study was co-funded by the Bill and Melinda Gates Foundation (grant code OPP1034556), the Wellcome Sanger Institute (core Wellcome grants 098051 and 206194), and the US Centres for Disease Control and Prevention. P.T. and Cambodia Oxford Medical Research Unit (COMRU) are supported by core funding from Wellcome (grant 220211). The funding sources had no role in isolate selection, analysis nor data interpretation. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centres for Disease Control and Prevention. The corresponding author had full access to the data and is responsible for the final decision to submit for publication.",

year = "2022",

month = jun,

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doi = "10.1099/mgen.0.000837",

language = "English",

volume = "8",

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T1 - Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13

AU - Belman, Sophie

AU - Soeng, Sona

AU - Soputhy, Chansovannara

AU - Gladstone, Rebecca

AU - Hawkins, Paulina A

AU - Breiman, Robert F

AU - McGee, Lesley

AU - Bentley, Stephen D

AU - Lo, Stephanie W

AU - Turner, Paul

N1 - Data statement: All supporting data, code and protocols have been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article. Funding information This study was co-funded by the Bill and Melinda Gates Foundation (grant code OPP1034556), the Wellcome Sanger Institute (core Wellcome grants 098051 and 206194), and the US Centres for Disease Control and Prevention. P.T. and Cambodia Oxford Medical Research Unit (COMRU) are supported by core funding from Wellcome (grant 220211). The funding sources had no role in isolate selection, analysis nor data interpretation. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centres for Disease Control and Prevention. The corresponding author had full access to the data and is responsible for the final decision to submit for publication.

PY - 2022/6/28

Y1 - 2022/6/28

N2 - Streptococcus pneumoniae (the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns. We sought to elucidate the genetic background (global pneumococcal sequence clusters; GPSCs) of pneumococci carried by Cambodian children following perturbation by pneumococcal conjugate vaccine (PCV) 13. We sequenced pre-PCV13 (01/2013-12/2015, N=258) and post-PCV13 carriage isolates (01/2016-02/2017, N=428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. Following PCV13 implementation in Cambodia, we saw expansions of non-vaccine type (NVT) serotypes 23A (GPSC626), 34 (GPSC45) and 6D (GPSC16). We predicted antimicrobial susceptibility using the CDC-AMR pipeline and determined concordance with phenotypic data. The CDC-AMR pipeline had >90 % concordance with the phenotypic antimicrobial-susceptibility testing. We detected a high prevalence of AMR in both expanding non-vaccine serotypes and residual vaccine serotype 6B. Persistently high levels of AMR, specifically persisting multidrug-resistant lineages, warrant concern. The implementation of PCV13 in Cambodia has resulted in NVT serotype expansion reflected in the carriage population and driven by specific genetic backgrounds. Continued monitoring of these GPSCs during the ongoing collection of additional carriage isolates in this population is necessary.

AB - Streptococcus pneumoniae (the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns. We sought to elucidate the genetic background (global pneumococcal sequence clusters; GPSCs) of pneumococci carried by Cambodian children following perturbation by pneumococcal conjugate vaccine (PCV) 13. We sequenced pre-PCV13 (01/2013-12/2015, N=258) and post-PCV13 carriage isolates (01/2016-02/2017, N=428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. Following PCV13 implementation in Cambodia, we saw expansions of non-vaccine type (NVT) serotypes 23A (GPSC626), 34 (GPSC45) and 6D (GPSC16). We predicted antimicrobial susceptibility using the CDC-AMR pipeline and determined concordance with phenotypic data. The CDC-AMR pipeline had >90 % concordance with the phenotypic antimicrobial-susceptibility testing. We detected a high prevalence of AMR in both expanding non-vaccine serotypes and residual vaccine serotype 6B. Persistently high levels of AMR, specifically persisting multidrug-resistant lineages, warrant concern. The implementation of PCV13 in Cambodia has resulted in NVT serotype expansion reflected in the carriage population and driven by specific genetic backgrounds. Continued monitoring of these GPSCs during the ongoing collection of additional carriage isolates in this population is necessary.

KW - Anti-Infective Agents

KW - Asian People

KW - Child

KW - Genetic Background

KW - Humans

KW - Pneumococcal Vaccines

KW - Streptococcus pneumoniae/genetics

KW - Vaccines, Conjugate

U2 - 10.1099/mgen.0.000837

DO - 10.1099/mgen.0.000837

M3 - Article

C2 - 35763412

SN - 2057-5858

VL - 8

JO - Microbial Genomics

JF - Microbial Genomics

IS - 6

ER -

Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13

Abstract

Bibliographical note

Keywords

UN SDGs

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