Genetic population structure of Haemophilus influenzae at local and global scales

MacAlasdair, N; Pontinen, AK; Ling, C; Mallawaarachchi, S; Thaipadungpanit, J; Nosten, FH; Turner, C; Bentley, SD; Croucher, NJ; Turner, P; Corander, J

Author(s): MacAlasdair, N; Pontinen, AK; Ling, C; Mallawaarachchi, S; Thaipadungpanit, J; Nosten, FH; Turner, C; Bentley, SD; Croucher, NJ; Turner, P; Corander, J;
Details: Publication Year 2025-12,Volume 10,Issue #12,Page 3136-3147
Journal Title: Nature Microbiology
Publication Type: Research article
Abstract: 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.
Keywords: *Haemophilus influenzae/genetics/classification/isolation & purification/drug; effects; Humans; *Haemophilus Infections/microbiology/epidemiology; Genome, Bacterial; Thailand/epidemiology; Genetic Variation; Whole Genome Sequencing; Child, Preschool; Child; Infant; Carrier State/microbiology/epidemiology; Phylogeny; Serogroup; Drug Resistance, Multiple, Bacterial/genetics
Department(s): Laboratory Research
Publisher's Version: https://doi.org/10.1038/s41564-025-02171-9
Open Access at Publisher's Site: https://doi.org/10.1038/s41564-025-02171-9
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-12-05 02:49:45

Last Modified: 2025-12-05 02:55:47