Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure

Abstract

Significance Several human pathogens exploit genomic variability to adapt to the host environment. Genome sequencing of collections of isolates and classification of strains according to their genomic content are pivotal to the formulation of vaccines able to elicit broad protection. We sequenced a collection of carriage and disease isolates of nontypeable Haemophilus influenzae , a component of the microbial flora of the upper respiratory tract that can cause a spectrum of diseases, including otitis media and meningitis. We identified distinct evolutionary clades that correlate with the presence of selected surface-associated proteins and virulence determinants. The high-resolution definition of the population structure of nontypeable Haemophilus influenzae allowed by whole-genome sequencing will be key for the development of efficacious containment strategies for this important human pathogen.

Microbiology: Ditch the term pathogen

“…This hunt for microbial genes or mutations associated with disease continues to this day. For example, researchers are applying genomics to try to discern signatures of virulence among S. aureus, Haemophilus influenzae and Enterococcus faecium strains, to name a few [2][3][4] .…”

Simultaneous Identification of Haemophilus Influenzae and Haemophilus Haemolyticus using Real-Time PCR

“…This genomic dissimilarity between fucP-negative and conventional fucP-positive strains previously led us to also propose that fucP-negative strains, while closely related to H. influenzae, might comprise a novel 'fuzzy' Haemophilus species [6]. However, this distance RESEaRch aRticlE Price [18], at the time the largest comparative genomic analysis of H. influenzae. We have since shown that Clade I H. influenzae and fucP-negative strains share a node [6], implying that they have shared ancestry.…”

“…genomes were available for this study: 316 H. influenzae (145 generated in the current study, 19 unpublished and 152 published elsewhere [6,[18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]), 59 H. haemolyticus (44 generated in the current study, one unpublished and 14 published elsewhere [6,26,28,[35][36] Table 1). The hypD assay differentiates H. haemolyticus (red) from all other species and the siaT assay differentiates H. influenzae (blue), 'Clade I' H. influenzae (purple) and fucose operon-negative H. influenzae strains (green) from all other species.…”

“…The hypD assay differentiates H. haemolyticus (red) from all other species and the siaT assay differentiates H. influenzae (blue), 'Clade I' H. influenzae (purple) and fucose operon-negative H. influenzae strains (green) from all other species. The fucP assay [6] was designed to differentiate fucose operonpositive H. influenzae (blue) and 'Clade I' H. influenzae (purple) [18] from all other species. However, we uncovered three isolates in the 'conventional' H. influenzae clade (grey shading) that are fucP-negative by PCR and in silico.…”

“…strains showed high nucleotide similarity of strains both harboring and lacking the fucK locus, suggesting that these strains are genetically related and are in fact the same species [16]. On a phylogenomic level, these 'fuzzy' fucosenegative isolates share a node with 'Clade I' H. influenzae [6], a genetically distinct cluster of H. influenzae that is nonetheless considered to belong to this species [18].…”