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BMC Genomics. 2015 Aug 27;16:641. doi: 10.1186/s12864-015-1857-x.

Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen.

Author information

1
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. erin.price@menzies.edu.au.
2
Menzies School of Health Research, PO Box 41096, Casuarina, NT, 0811, Australia. erin.price@menzies.edu.au.
3
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. derek.sarovich@menzies.edu.au.
4
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. elizabeth.nosworthy@menzies.edu.au.
5
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. jemima.beissbarth@menzies.edu.au.
6
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. robyn.marsh@menzies.edu.au.
7
University of Western Australia, Perth, WA, Australia. janessa.pickering@uwa.edu.au.
8
University of Western Australia, Perth, WA, Australia. lea-ann.kirkham@uwa.edu.au.
9
Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Perth, WA, Australia. anthony.keil@health.wa.gov.au.
10
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. anne.chang@menzies.edu.au.
11
Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. heidi.smith-vaughan@menzies.edu.au.

Abstract

BACKGROUND:

Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Despite its clinical significance, accurate identification of H. influenzae is a non-trivial endeavour. H. haemolyticus can be misidentified as H. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. On the molecular level, frequent genetic exchange amongst Haemophilus spp. has confounded accurate identification of H. influenzae, leading to both false-positive and false-negative results with existing speciation assays.

RESULTS:

Whole-genome single-nucleotide polymorphism data from 246 closely related global Haemophilus isolates, including 107 Australian isolate genomes generated in this study, were used to construct a whole-genome phylogeny. Based on this phylogeny, H. influenzae could be differentiated from closely related species. Next, a H. influenzae-specific locus, fucP, was identified, and a novel TaqMan real-time PCR assay targeting fucP was designed. PCR specificity screening across a panel of clinically relevant species, coupled with in silico analysis of all species within the order Pasteurellales, demonstrated that the fucP assay was 100 % specific for H. influenzae; all other examined species failed to amplify.

CONCLUSIONS:

This study is the first of its kind to use large-scale comparative genomic analysis of Haemophilus spp. to accurately delineate H. influenzae and to identify a species-specific molecular signature for this species. The fucP assay outperforms existing H. influenzae targets, most of which were identified prior to the next-generation genomics era and thus lack validation across a large number of Haemophilus spp. We recommend use of the fucP assay in clinical and research laboratories for the most accurate detection and diagnosis of H. influenzae infection and colonisation.

PMID:
26311542
PMCID:
PMC4551764
DOI:
10.1186/s12864-015-1857-x
[Indexed for MEDLINE]
Free PMC Article

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