Characterisation of colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.

is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including , , spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain . Individuals who have not yet acquired have a higher abundance of (particularly ) than individuals who never acquire , suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, , was successfully isolated and sequenced.