Phylogenomic and Molecular Demarcation of the Core Members of the PolyphyleticPasteurellaceaeGeneraActinobacillus,Haemophilus, andPasteurella

Abstract

The generaActinobacillus, Haemophilus,andPasteurellaexhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters ofActinobacillus, Haemophilus,andPasteurellaspecies which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared bysensu strictomembers ofActinobacillus, Haemophilus,andPasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing generaAggregatibacterandMannheimia, respectively. It is now possible to demarcate the generaActinobacillus sensu stricto, Haemophilus sensu stricto,andPasteurella sensu strictoon the basis of discrete molecular signatures. The other members of the generaActinobacillus, Haemophilus,andPasteurellathat do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.