Intrahost Genomic Variation of Haemophilus influenzae Isolates from Asymptomatic Nasopharyngeal Carriers Involves Genes Encoding Proteins with Diverse Inferred Functions

Haemophilus influenzae is a human-specific pathogen that causes infections, ranging in severity from otitis media to potentially fatal meningitis. It also asymptomatically colonizes the upper respiratory tract. Although intrahost genomic variation of H. influenzae has been investigated in some anatomic sites, the genes most frequently acquiring nonsynonymous (amino acid–changing) or nonsense (protein-truncating) single-nucleotide polymorphisms (SNPs) during human carriage remain largely unidentified. To study intrahost genomic variation of H. influenzae during human asymptomatic carriage in the nasopharynx, the genomes of 805 isolates recovered from 24 healthy Icelandic children were sequenced. Most children were colonized with isolates with a single multilocus sequence type, although some were concurrently colonized with isolates with multiple multilocus sequence types. Intrahost genomic variation was discovered, with 120 genes acquiring SNPs in at least one isolate. Among them, 69 genes were recurrently polymorphic in isolates recovered from multiple children, and 72 SNPs occurred in multiple isolates recovered from the same child. The polymorphic genes encode proteins with diverse inferred functions, including transcription regulators and putative virulence factors. Many of the proteins likely play roles in bacterial fitness, virulence, and host-pathogen molecular interactions. This intrahost variation study provides a model for understanding the genomic diversity acquired by H. influenzae during human asymptomatic carriage in the nasopharynx.