Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus : a formal re-classification of ' Haemophilus intermedius '

• Published in: Microbial genomics 2020-01, Vol.6 (1)
• Main Authors: Harris, Tegan M, Price, Erin P, Sarovich, Derek S, Nørskov-Lauritsen, Niels, Beissbarth, Jemima, Chang, Anne B, Smith-Vaughan, Heidi C
• Format: Article
• Language: English
• ISSN: 2057-5858; 2057-5858
• DOI: 10.1099/mgen.0.000303

The heterogeneous and highly recombinogenic genus comprises several species, some of which are pathogenic to humans. All share an absolute requirement for blood-derived factors during growth. Certain species, such as the pathogen and the commensal , are thought to require both haemin (X-factor) and nicotinamide adenine dinucleotide (NAD, V-factor), whereas others, such as the informally classified ' subsp. ', and , only require V-factor. These differing growth requirements are commonly used for species differentiation, although a number of studies are now revealing issues with this approach. Here, we perform large-scale phylogenomics of 240 spp. genomes, including five ' ' genomes generated in the current study, to reveal that strains of the ' ' group are in fact haemin-independent (hi ). Closer examination of these hi strains revealed that they encode an intact haemin biosynthesis pathway, unlike haemin-dependent and , which lack most haemin biosynthesis genes. Our results suggest that the common ancestor of modern-day and lost key haemin biosynthesis loci, likely as a consequence of specialized adaptation to otorhinolaryngeal and respiratory niches during their divergence from . Genetic similarity analysis demonstrated that the haemin biosynthesis loci acquired in the hi lineage were likely laterally transferred from a ancestor, and that this event probably occurred only once in hi . This study further challenges the validity of phenotypic methods for differentiating among species, and highlights the need for whole-genome sequencing for accurate characterization of species within this taxonomically challenging genus.