Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity

Arash Iranzadeh; Arghavan Alisoltani; Anmol M. Kiran; Robert F. Breiman; Chrispin Chaguza; Chikondi Peno; Jennifer E. Cornick; Dean B. Everett; Nicola Mulder

doi:10.1099/mgen.0.001370

Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity

Arash Iranzadeh¹, Arghavan Alisoltani^2,3,4, Anmol M. Kiran^5,6, Robert F. Breiman^7,8, Chrispin Chaguza^9,10,11, Chikondi Peno^5,6,10, Jennifer E. Cornick^5,12, Dean B. Everett^13,14 and Nicola Mulder¹
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¹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Western Cape, South Africa ² Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA ³ Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA ⁴ Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA ⁵ Malawi-Liverpool-Wellcome Trust, Queen Elizabeth Central Hospital, College of Medicine, Blantyre, Malawi ⁶ Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK ⁷ Rollins School of Public Health, Emory University, Atlanta, Georgia, USA ⁸ Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa ⁹ Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK ¹⁰ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA ¹¹ Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA ¹² Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK ¹³ Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE ¹⁴ Infection Research Unit, Khalifa University, Abu Dhabi, UAE
*Correspondence: Arash Iranzadeh, [email protected] *Correspondence: Nicola Mulder, [email protected] *Correspondence: Dean B. Everett, [email protected] *Correspondence: Jennifer E. Cornick, [email protected]
Published: 15 April 2025 https://doi.org/10.1099/mgen.0.001370

Abstract

Streptococcus pneumoniae is a significant cause of bacterial infections, including pneumonia, meningitis and septicemia, primarily affecting children, the elderly and immunocompromised individuals. This study aimed to elucidate the serotype and lineage distribution and molecular mechanisms underlying pneumococcal invasiveness through a comprehensive pangenomic analysis of 1416 isolates from Malawi. Our analysis comprised 810 isolates from asymptomatic carriers and 606 isolates from patients with bacteraemia or meningitis. We identified 58 serotypes, with serotypes 1, 5 and 12F exhibiting significantly higher prevalence among patients. These serotypes likely exhibit reduced nasopharyngeal colonization and demonstrate rapid dissemination to sterile sites. Notably, these serotypes form a distinct lineage with distinct genomic characteristics, including the absence of V-type ATP synthase. The pangenome analysis revealed two highly conserved surface protein complexes, F-type ATP synthase and SecA1-SecY, which deserve further investigation as potential targets for novel therapeutic interventions.

Received: 14/11/2023
Accepted: 23/01/2025
Published Online: 15/04/2025

Keyword(s): F-type ATP synthase , pangenomics , serotype 1 , serotype 12F , serotype 5 , Streptococcus pneumoniae and V-type ATP synthase

Funding

This study was supported by the:

Wellcome Trust (Award 079828)
- Principal Award Recipient: NotApplicable

This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

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/content/journal/mgen/10.1099/mgen.0.001370

Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity

M Gen 11, 001370 (2025); https://doi.org/10.1099/mgen.0.001370

/content/journal/mgen/10.1099/mgen.0.001370

Microbial Genomics

Volume 11, Issue 4

Research Article

Open Access

Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity

Abstract

Funding

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Data summary

Supplementary material 1

Supplementary material 2

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