Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages
Background Streptococcus pneumoniae remains a major global health threat, causing diseases ranging from mild respiratory infections to severe conditions like pneumonia, sepsis, and meningitis. Although pneumococcal conjugate vaccines (PCVs), including PCV7, PCV10, and PCV13 have significantly reduce...
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Oxford University Press
2026
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| Online Access: | http://psasir.upm.edu.my/id/eprint/123764/1/123764.pdf http://psasir.upm.edu.my/id/eprint/123764/2/123764-accepted.pdf http://psasir.upm.edu.my/id/eprint/123764/ https://academic.oup.com/jambio/article/doi/10.1093/jambio/lxag040/8466407 |
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| author | Dzaraly, Nurul Diana Muthanna, Abdul Rahman John, James Masri, Siti Norbaya Suhaili, Zarizal Sulaiman, Nurshahira Rahman, Nor Iza A. Tuan Soh, Tuan Suhaila Abdullah, Fatimah Haslina Biswas, Sangita Al-Obaidi, Mazen M.Jamil Mohd Desa, Mohd Nasir |
| author_facet | Dzaraly, Nurul Diana Muthanna, Abdul Rahman John, James Masri, Siti Norbaya Suhaili, Zarizal Sulaiman, Nurshahira Rahman, Nor Iza A. Tuan Soh, Tuan Suhaila Abdullah, Fatimah Haslina Biswas, Sangita Al-Obaidi, Mazen M.Jamil Mohd Desa, Mohd Nasir |
| author_sort | Dzaraly, Nurul Diana |
| building | UPM Library |
| collection | Institutional Repository |
| content_provider | Universiti Putra Malaysia |
| content_source | UPM Institutional Repository |
| continent | Asia |
| country | Malaysia |
| description | Background Streptococcus pneumoniae remains a major global health threat, causing diseases ranging from mild respiratory infections to severe conditions like pneumonia, sepsis, and meningitis. Although pneumococcal conjugate vaccines (PCVs), including PCV7, PCV10, and PCV13 have significantly reduced disease burden, especially in children, S. pneumoniae continues to exhibit high serotype and genetic diversity. Whole-genome sequencing (WGS) analysis offers high-resolution insights into clonal lineages and multidrug-resistant strains. However, genomic data on Malaysian isolates remain limited. Methods This study characterized the whole genome features and comparative profiles of seven invasive S. pneumoniae isolates from two tertiary hospitals in Malaysia. WGS analyses described serotype, sequence type (ST), antimicrobial resistance determinant genes, pan-genome structure, and recombination events. Results The average genome size was ∼2.12 Mbp, with 1988–2205 coding sequences. WGS-based MLST identified five sequence types (ST236, ST320, ST386, ST671, ST695), with ST236 linked to serotypes 19A and 19F related to PMEN clones Taiwan19F-14 and CC271. Core genome analysis with 35 global reference strains revealed three major clades. Notably, isolates TSP95, SSP45, and SSP46 clustered closely with strains from South Korea, suggesting a long-term persistence of ST320 over a decade. Recombination analysis identified both shared and isolate-specific events, forming distinct phylogenetic clusters. Extensive shared recombination was observed in several isolates, while others displayed isolate-specific events, indicating ongoing genetic diversification. Conclusion These findings underscore the critical role of recombination in shaping pneumococcal population structure, evolution, and adaptation. |
| format | Article |
| id | my.upm.eprints-123764 |
| institution | Universiti Putra Malaysia |
| language | en en |
| publishDate | 2026 |
| publisher | Oxford University Press |
| record_format | eprints |
| spelling | my.upm.eprints-1237642026-04-08T09:40:32Z http://psasir.upm.edu.my/id/eprint/123764/ Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages Dzaraly, Nurul Diana Muthanna, Abdul Rahman John, James Masri, Siti Norbaya Suhaili, Zarizal Sulaiman, Nurshahira Rahman, Nor Iza A. Tuan Soh, Tuan Suhaila Abdullah, Fatimah Haslina Biswas, Sangita Al-Obaidi, Mazen M.Jamil Mohd Desa, Mohd Nasir Background Streptococcus pneumoniae remains a major global health threat, causing diseases ranging from mild respiratory infections to severe conditions like pneumonia, sepsis, and meningitis. Although pneumococcal conjugate vaccines (PCVs), including PCV7, PCV10, and PCV13 have significantly reduced disease burden, especially in children, S. pneumoniae continues to exhibit high serotype and genetic diversity. Whole-genome sequencing (WGS) analysis offers high-resolution insights into clonal lineages and multidrug-resistant strains. However, genomic data on Malaysian isolates remain limited. Methods This study characterized the whole genome features and comparative profiles of seven invasive S. pneumoniae isolates from two tertiary hospitals in Malaysia. WGS analyses described serotype, sequence type (ST), antimicrobial resistance determinant genes, pan-genome structure, and recombination events. Results The average genome size was ∼2.12 Mbp, with 1988–2205 coding sequences. WGS-based MLST identified five sequence types (ST236, ST320, ST386, ST671, ST695), with ST236 linked to serotypes 19A and 19F related to PMEN clones Taiwan19F-14 and CC271. Core genome analysis with 35 global reference strains revealed three major clades. Notably, isolates TSP95, SSP45, and SSP46 clustered closely with strains from South Korea, suggesting a long-term persistence of ST320 over a decade. Recombination analysis identified both shared and isolate-specific events, forming distinct phylogenetic clusters. Extensive shared recombination was observed in several isolates, while others displayed isolate-specific events, indicating ongoing genetic diversification. Conclusion These findings underscore the critical role of recombination in shaping pneumococcal population structure, evolution, and adaptation. Oxford University Press 2026-02-06 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/123764/1/123764.pdf text en http://psasir.upm.edu.my/id/eprint/123764/2/123764-accepted.pdf Dzaraly, Nurul Diana and Muthanna, Abdul Rahman and John, James and Masri, Siti Norbaya and Suhaili, Zarizal and Sulaiman, Nurshahira and Rahman, Nor Iza A. and Tuan Soh, Tuan Suhaila and Abdullah, Fatimah Haslina and Biswas, Sangita and Al-Obaidi, Mazen M.Jamil and Mohd Desa, Mohd Nasir (2026) Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages. Journal of Applied Microbiology, 137 (2). art. no. lxag040. pp. 1-12. ISSN 1364-5072; eISSN: 1365-2672 https://academic.oup.com/jambio/article/doi/10.1093/jambio/lxag040/8466407 Biotechnology Applied Microbiology and Biotechnology 10.1093/jambio/lxag040 |
| spellingShingle | Biotechnology Applied Microbiology and Biotechnology Dzaraly, Nurul Diana Muthanna, Abdul Rahman John, James Masri, Siti Norbaya Suhaili, Zarizal Sulaiman, Nurshahira Rahman, Nor Iza A. Tuan Soh, Tuan Suhaila Abdullah, Fatimah Haslina Biswas, Sangita Al-Obaidi, Mazen M.Jamil Mohd Desa, Mohd Nasir Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| title | Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| title_full | Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| title_fullStr | Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| title_full_unstemmed | Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| title_short | Comparative whole-genome sequencing of seven invasive Streptococcus pneumoniae isolates from Malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| title_sort | comparative whole-genome sequencing of seven invasive streptococcus pneumoniae isolates from malaysia reveals genetic diversity, recombination events, and global lineage linkages |
| topic | Biotechnology Applied Microbiology and Biotechnology |
| url | http://psasir.upm.edu.my/id/eprint/123764/1/123764.pdf http://psasir.upm.edu.my/id/eprint/123764/2/123764-accepted.pdf http://psasir.upm.edu.my/id/eprint/123764/ https://academic.oup.com/jambio/article/doi/10.1093/jambio/lxag040/8466407 |
| url_provider | http://psasir.upm.edu.my/ |