Genetic population structure of Haemophilus influenzae at local and global scales
Haemophilus influenzae is an opportunistic bacterial pathogen that causes both non-invasive and invasive disease in humans. Although the H. influenzae type b vaccine can reduce invasive disease, it is not effective against non-b serotypes or unencapsulated non-typeable H. influenzae (NTHi). The genetic population structure of H. influenzae, especially NTHi, which is typically prevalent in lower- and middle-income countries, is unclear. Here we whole-genome sequenced 4,474 isolates of H. influenzae from an unvaccinated paediatric carriage and pneumonia cohort from the Maela camp for displaced persons in northwestern Thailand. Despite no H. influenzae type b immunization, serotype b was uncommon, whereas 92.4% of the isolates were NTHi. Most multidrug-resistant lineages were NTHi, and there were no lineages enriched among disease samples. Incorporating 5,976 published genomes revealed a highly admixed population structure, low core genome nucleotide diversity and evidence of pervasive negative selection. Our findings expand our understanding of this major pathogen in lower- and middle-income countries and at a global scale.
Authors
- Anna Kaarina Pöntinen (ORCID: https://orcid.org/0000-0002-3160-2042)
- Sudaraka Mallawaarachchi (ORCID: https://orcid.org/0000-0001-8899-3323)
- Paul Turner (ORCID: https://orcid.org/0000-0002-1013-7815)
- Jukka Corander (ORCID: https://orcid.org/0000-0002-7752-1942)
- Nicholas J. Croucher (ORCID: https://orcid.org/0000-0001-6303-8768)
- Clare Ling (ORCID: https://orcid.org/0000-0002-5188-0349)
- Janjira Thaipadungpanit (ORCID: https://orcid.org/0000-0002-6184-3381)
- Neil MacAlasdair (ORCID: https://orcid.org/0000-0002-4033-6970)
- Stephen D. Bentley (ORCID: https://orcid.org/0000-0001-8094-3751)
- Claudia Turner
- François Henry Nosten (ORCID: https://orcid.org/0000-0002-7951-0745)
Institutions
- Statistics Finland (FI)
- University of Helsinki (FI)
- The University of Melbourne (AU)
- University of Oslo (NO)
- Mahidol University (TH)
- Angkor Hospital for Children (KH)
- Peter MacCallum Cancer Centre (AU)
- Wellcome Sanger Institute (GB)
- University of Oxford (GB)
- Shoklo Malaria Research Unit (TH)
- Cambodia-Oxford Medical Research Unit (KH)
- Mahidol Oxford Tropical Medicine Research Unit (TH)
- London Centre for Neglected Tropical Disease Research (GB)
- Imperial College London (GB)
Publication Details
- Journal
- Nature Microbiology
- Published
- 2025-10-31
- DOI
- https://doi.org/10.1038/s41564-025-02171-9
- Primary Topic
- Bacterial Infections and Vaccines
- Type
- article
- Field-Weighted Citation Impact
- 0.00