Fig. 1

Genome-based differentiation of Haemophilus influenzae from closely-related species. A midpoint-rooted maximum parsimony phylogeny was constructed using genomic data from 246 global, closely related Haemophilus spp. isolates, 107 of which were Australian Haemophilus isolates sequenced in the present study. Phylogenetic reconstruction of 63,447 orthologous, core genome, bi-allelic single-nucleotide polymorphisms (SNPs) enabled differentiation of nontypeable and serotypeable H. influenzae (blue text) from H. haemolyticus (red text) and other “fuzzy” Haemophilus species (green text). ‘Clade I’ H. influenzae, which are genetically distinct from other H. influenzae [26], are denoted by purple text. NTHi strains encoding capsular loci that are not expressed (according to [26]) are denoted by an asterisk. The H. haemolyticus and “fuzzy” strains share the same ecological niches as H. influenzae and are indistinguishable from H. influenzae based on morphological characteristics including X and V factor dependency. Bootstrap values are shown for major branches. Consistency index = 0.14. NB. More distantly related Haemophilus species (H. haemoglobinophilus, H. parahaemolyticus, H. parainfluenzae and H. paraphrohaemolyticus) were excluded to maximise core genome size