Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis

Arif Mohammad Tanmoy; Esha Kazi; Naito Kanon; Hafizur Rahman; Harry C.H. Hung; Md Hasanuzzaman; Roly Malaker; Apurba Rajib Malaker; Deb Purna Keya; Sudipta Deb Nath; Belal Hossain; Shampa Saha; Mohammad Jamal Uddin; Lesley McGee; Stephen D. Bentley; Stephanie W. Lo; Yogesh Hooda; Samir K. Saha; Senjuti Saha

doi:10.1186/s12866-025-04484-5

Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis

Arif Mohammad Tanmoy, Esha Kazi, Naito Kanon, Hafizur Rahman, Harry C.H. Hung, Md Hasanuzzaman, Roly Malaker, Apurba Rajib Malaker, Deb Purna Keya, Sudipta Deb Nath, Belal Hossain, Shampa Saha, Mohammad Jamal Uddin, Lesley McGee, Stephen D. Bentley, Stephanie W. Lo, Yogesh Hooda, Samir K. Saha, Senjuti Saha

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

Abstract

Background: Invasive pneumococcal disease (IPD), caused by Streptococcus pneumoniae, remains a major global health concern, particularly for children. Among more than 100 pneumococcal serotypes, 19A is known for its multidrug resistance (MDR) and increased incidence following PCV7/PCV10 introduction in many countries. Bangladesh introduced PCV10 in 2015 considering the low burden of 19A in the country. Methods: Utilizing our IPD surveillance from 2004 to 2023, we investigated the hospital incidence of serotype 19A before and after PCV10 introduction among < 5 years old children in Bangladesh. Whole-genome sequencing was done for 153 serotype 19A isolates from IPD, otitis media, carriage, and urine samples. We used phylogenetic and BEAST analyses to investigate population structure, circulating subtypes, global pneumococcal sequence clusters (GPSCs), sequence types (STs), and antimicrobial resistance genes, and compared them with global 19A genomes. Results: Our findings indicate no increase in hospital IPD incidence due to serotype 19A following PCV10 introduction. The MDR 19A-ST320 lineage (GPSC1) remains absent in Bangladesh. ST12888 (GPSC84) became dominant in the post-PCV10 introduction (from 15% to 70%). GPSC84 carries the capsular locus of 19A subtype-I (19A-I), which emerged independently from the standard 19A locus. Macrolide resistance is increasing within the 19A-I/GPSC84 lineage and is estimated to have originated between 2007 and 2011. Conclusions: This study presents the first comprehensive genomic analysis of the serotype 19A population in Bangladesh, supporting the decision to introduce PCV10 in Bangladesh based on local pneumococcal serotype burden data. However, the rapid evolution within the local 19A population highlights the need for continuous epidemiological and genomic surveillance to support effective vaccination programs.

Original language	English
Article number	773
Number of pages	15
Journal	BMC Microbiology
Volume	25
Issue number	1
Early online date	24 Nov 2025
DOIs	https://doi.org/10.1186/s12866-025-04484-5
Publication status	E-pub ahead of print - 24 Nov 2025

Data Availability Statement

The raw reads (both Illumina and ONT) of 125 pneumococcal serotype 19A isolates from CHRF-PARSE and GPS2 projects supporting the conclusions of this article are available in the European Nucleotide Archive (ENA) under study accession ERP165169 (www.ebi.ac.uk/ena/browser/view/PRJEB81323). Raw reads of other 28 isolates from GPS project are available in ENA under study accession ERP001505 (www.ebi.ac.uk/ena/browser/view/PRJEB3084). All run accessions, isolate metadata, resistance genes/mutations, and inferred antimicrobial resistance of Bangladesh data supporting the conclusions of this article are available in Data S1 (Additional file 2). Details of the GPSC84 and global data are available in Data S2, and S3, respectively (Additional file 3, and 4). All R codes used to create the figures can be found in github folder (https://github.com/CHRF-Genomics/Spn19A).

Acknowledgements

We would like to thank Ms. Afroza Akter Tanni, Ms. Sharmistha Goswami, Ms.
Tasnim Jabin, Mr. Mobarok Hossain, Mr. Preonath Chandrow Dev, Mr. Neoyman
Nasir Shorkar, Ms. Hakka Naziat, and Mr. Dipu Chandra Das of the Child
Health Research Foundation (CHRF), Bangladesh for their help to culture the
pneumococcal isolates and generate sequence data.

Funding

The work presented here was partially supported by Gavi, the Vaccine Alliance, through the World Health Organization-supported Invasive Bacterial Vaccine Preventable Diseases study (grant numbers: 201588766, 201233523, 201022732, and 200749550) to S.K.S., and leveraging the Pneumococcal Vaccines Accelerated Development and Introduction Plan (PneumoADIP) to S.K.S. Pfizer Inc funded the project “Impact of Pneumococcal Conjugate Vaccine (PCV) on Otitis Media in Bangladesh” (grant number: WI209075) to S.K.S. The pneumococcal carrige studies were supported by multiple funding sources, all awarded to S.K.S.: The Sanofi Pasteur (Nasopharyngeal pneumococcal carriage study in South Asian infants; grant number: EPN00014), the Bill and Melinda Gates Foundation, BMGF (Vaccination & the pediatric Microbiome; grant number OPP1024654), and Gavi, the Vaccine Alliance (NP Carriage Study activities in Bangladesh). The whole-genome sequencing of pneumococcal isolates was partially supported by BMGF through the Global Pneumococcal Sequence (GPS) surveillance and GPS-2 projects (grant numbers: OPP1034556 and INV-003570) awarded to L.M., S.D.B., S.K.S., and S.S. The funding bodies had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Keywords

Bangladesh
Evolution
Genomics
Invasive pneumococcal disease
PCV10
Serotype 19A
Streptococcus pneumoniae

ASJC Scopus subject areas

Microbiology
Microbiology (medical)

UN SDGs

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

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10.1186/s12866-025-04484-5Licence: CC BY-NC-ND

Cite this

Tanmoy, A. M., Kazi, E., Kanon, N., Rahman, H., Hung, H. C. H., Hasanuzzaman, M., Malaker, R., Malaker, A. R., Keya, D. P., Nath, S. D., Hossain, B., Saha, S., Uddin, M. J., McGee, L., Bentley, S. D., Lo, S. W., Hooda, Y., Saha, S. K., & Saha, S. (2025). Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis. BMC Microbiology, 25(1), Article 773. Advance online publication. https://doi.org/10.1186/s12866-025-04484-5

Tanmoy, AM, Kazi, E, Kanon, N, Rahman, H, Hung, HCH, Hasanuzzaman, M, Malaker, R, Malaker, AR, Keya, DP, Nath, SD, Hossain, B, Saha, S, Uddin, MJ, McGee, L, Bentley, SD, Lo, SW, Hooda, Y, Saha, SK & Saha, S 2025, 'Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis', BMC Microbiology, vol. 25, no. 1, 773. https://doi.org/10.1186/s12866-025-04484-5

@article{cd39e58b52764e2091b354b10a737949,

title = "Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis",

abstract = "Background: Invasive pneumococcal disease (IPD), caused by Streptococcus pneumoniae, remains a major global health concern, particularly for children. Among more than 100 pneumococcal serotypes, 19A is known for its multidrug resistance (MDR) and increased incidence following PCV7/PCV10 introduction in many countries. Bangladesh introduced PCV10 in 2015 considering the low burden of 19A in the country. Methods: Utilizing our IPD surveillance from 2004 to 2023, we investigated the hospital incidence of serotype 19A before and after PCV10 introduction among < 5 years old children in Bangladesh. Whole-genome sequencing was done for 153 serotype 19A isolates from IPD, otitis media, carriage, and urine samples. We used phylogenetic and BEAST analyses to investigate population structure, circulating subtypes, global pneumococcal sequence clusters (GPSCs), sequence types (STs), and antimicrobial resistance genes, and compared them with global 19A genomes. Results: Our findings indicate no increase in hospital IPD incidence due to serotype 19A following PCV10 introduction. The MDR 19A-ST320 lineage (GPSC1) remains absent in Bangladesh. ST12888 (GPSC84) became dominant in the post-PCV10 introduction (from 15\% to 70\%). GPSC84 carries the capsular locus of 19A subtype-I (19A-I), which emerged independently from the standard 19A locus. Macrolide resistance is increasing within the 19A-I/GPSC84 lineage and is estimated to have originated between 2007 and 2011. Conclusions: This study presents the first comprehensive genomic analysis of the serotype 19A population in Bangladesh, supporting the decision to introduce PCV10 in Bangladesh based on local pneumococcal serotype burden data. However, the rapid evolution within the local 19A population highlights the need for continuous epidemiological and genomic surveillance to support effective vaccination programs.",

keywords = "Bangladesh, Evolution, Genomics, Invasive pneumococcal disease, PCV10, Serotype 19A, Streptococcus pneumoniae",

author = "Tanmoy, \{Arif Mohammad\} and Esha Kazi and Naito Kanon and Hafizur Rahman and Hung, \{Harry C.H.\} and Md Hasanuzzaman and Roly Malaker and Malaker, \{Apurba Rajib\} and Keya, \{Deb Purna\} and Nath, \{Sudipta Deb\} and Belal Hossain and Shampa Saha and Uddin, \{Mohammad Jamal\} and Lesley McGee and Bentley, \{Stephen D.\} and Lo, \{Stephanie W.\} and Yogesh Hooda and Saha, \{Samir K.\} and Senjuti Saha",

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month = nov,

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doi = "10.1186/s12866-025-04484-5",

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TY - JOUR

T1 - Evolution of pneumococcal serotype 19A in children in Bangladesh

T2 - insights from genomic analysis

AU - Tanmoy, Arif Mohammad

AU - Kazi, Esha

AU - Kanon, Naito

AU - Rahman, Hafizur

AU - Hung, Harry C.H.

AU - Hasanuzzaman, Md

AU - Malaker, Roly

AU - Malaker, Apurba Rajib

AU - Keya, Deb Purna

AU - Nath, Sudipta Deb

AU - Hossain, Belal

AU - Saha, Shampa

AU - Uddin, Mohammad Jamal

AU - McGee, Lesley

AU - Bentley, Stephen D.

AU - Lo, Stephanie W.

AU - Hooda, Yogesh

AU - Saha, Samir K.

AU - Saha, Senjuti

PY - 2025/11/24

Y1 - 2025/11/24

N2 - Background: Invasive pneumococcal disease (IPD), caused by Streptococcus pneumoniae, remains a major global health concern, particularly for children. Among more than 100 pneumococcal serotypes, 19A is known for its multidrug resistance (MDR) and increased incidence following PCV7/PCV10 introduction in many countries. Bangladesh introduced PCV10 in 2015 considering the low burden of 19A in the country. Methods: Utilizing our IPD surveillance from 2004 to 2023, we investigated the hospital incidence of serotype 19A before and after PCV10 introduction among < 5 years old children in Bangladesh. Whole-genome sequencing was done for 153 serotype 19A isolates from IPD, otitis media, carriage, and urine samples. We used phylogenetic and BEAST analyses to investigate population structure, circulating subtypes, global pneumococcal sequence clusters (GPSCs), sequence types (STs), and antimicrobial resistance genes, and compared them with global 19A genomes. Results: Our findings indicate no increase in hospital IPD incidence due to serotype 19A following PCV10 introduction. The MDR 19A-ST320 lineage (GPSC1) remains absent in Bangladesh. ST12888 (GPSC84) became dominant in the post-PCV10 introduction (from 15% to 70%). GPSC84 carries the capsular locus of 19A subtype-I (19A-I), which emerged independently from the standard 19A locus. Macrolide resistance is increasing within the 19A-I/GPSC84 lineage and is estimated to have originated between 2007 and 2011. Conclusions: This study presents the first comprehensive genomic analysis of the serotype 19A population in Bangladesh, supporting the decision to introduce PCV10 in Bangladesh based on local pneumococcal serotype burden data. However, the rapid evolution within the local 19A population highlights the need for continuous epidemiological and genomic surveillance to support effective vaccination programs.

AB - Background: Invasive pneumococcal disease (IPD), caused by Streptococcus pneumoniae, remains a major global health concern, particularly for children. Among more than 100 pneumococcal serotypes, 19A is known for its multidrug resistance (MDR) and increased incidence following PCV7/PCV10 introduction in many countries. Bangladesh introduced PCV10 in 2015 considering the low burden of 19A in the country. Methods: Utilizing our IPD surveillance from 2004 to 2023, we investigated the hospital incidence of serotype 19A before and after PCV10 introduction among < 5 years old children in Bangladesh. Whole-genome sequencing was done for 153 serotype 19A isolates from IPD, otitis media, carriage, and urine samples. We used phylogenetic and BEAST analyses to investigate population structure, circulating subtypes, global pneumococcal sequence clusters (GPSCs), sequence types (STs), and antimicrobial resistance genes, and compared them with global 19A genomes. Results: Our findings indicate no increase in hospital IPD incidence due to serotype 19A following PCV10 introduction. The MDR 19A-ST320 lineage (GPSC1) remains absent in Bangladesh. ST12888 (GPSC84) became dominant in the post-PCV10 introduction (from 15% to 70%). GPSC84 carries the capsular locus of 19A subtype-I (19A-I), which emerged independently from the standard 19A locus. Macrolide resistance is increasing within the 19A-I/GPSC84 lineage and is estimated to have originated between 2007 and 2011. Conclusions: This study presents the first comprehensive genomic analysis of the serotype 19A population in Bangladesh, supporting the decision to introduce PCV10 in Bangladesh based on local pneumococcal serotype burden data. However, the rapid evolution within the local 19A population highlights the need for continuous epidemiological and genomic surveillance to support effective vaccination programs.

KW - Bangladesh

KW - Evolution

KW - Genomics

KW - Invasive pneumococcal disease

KW - PCV10

KW - Serotype 19A

KW - Streptococcus pneumoniae

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DO - 10.1186/s12866-025-04484-5

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AN - SCOPUS:105022727527

SN - 1471-2180

VL - 25

JO - BMC Microbiology

JF - BMC Microbiology

IS - 1

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ER -

Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis

Abstract

Data Availability Statement

Acknowledgements

Funding

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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