Mosaic genome structure of Haemophilus influenzae revealed by horizontal gene transfer of functional loci

Haemophilus influenzae (Hi) exhibits high clinical and genetic diversity, but the extent to which horizontal gene transfer (HGT) shapes its functional genome remains unclear. We analyzed a 1,037-locus core-genome scheme across 6,555 Hi isolates from the global PubMLST collection, characterizing locus-level divergence and phylogenetic relationships between specific Hi loci and their non-Hi homologues. For each core locus we computed pairwise nucleotide and protein distances and constructed maximum-likelihood phylogenetic trees. The divergent allele clusters were compared with NCBI nt database using BLASTn algorithm. A subset of loci displayed discrete, multi-cluster distance distributions patterns indicative of whole-allele replacement. Representative loci, including ftsI , for which altered alleles are known to contribute to β-lactam resistance, and dmsC and sapB , which belong to systems previously implicated in non-typeable Hi (NTHi) host fitness, as well as several additional loci of unknown phenotypic consequence, contained divergent alleles that clustered with non-Hi sequences, consistent with homologous introgression. Analysis of cap locus also revealed mosaic structure. Regions I and III were found to be highly conserved across capsule strains, whereas the serotype-specific region II exhibited taxonomically mixed homology to other representatives of the Pasteurellaceae family. Like several core genes, cap locus has been repeatedly reshaped by HGT and recombination, consistent with mechanisms that could facilitate capsule switching. These results demonstrated that Hi genomes are mosaic: recurrent interspecific recombination had imported functional foreign alleles into core genome loci. This reticulate evolutionary mechanism challenges standard typing methods and surveillance approaches, and may have public health implications for vaccine escape and antimicrobial resistance. Presented results argue for locus-aware genomic surveillance and experimental work to determine the functional impacts of acquired alleles.