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

Erin P Price; Derek S Sarovich; E Nosworthy; J Beissbarth; R L Marsh; J Pickering; L A S Kirkham; A D Keil; A B Chang; H C Smith-Vaughan

doi:10.1186/s12864-015-1857-x

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

Journal article

Open access

Peer reviewed

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

Erin P Price, Derek S Sarovich, E Nosworthy, J Beissbarth, R L Marsh, J Pickering, L A S Kirkham, A D Keil, A B Chang and H C Smith-Vaughan

BMC Genomics, Vol.16(1), 641

2015

DOI: https://doi.org/10.1186/s12864-015-1857-x

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Abstract

haemophilus influenzae

haemophilus haemolyticus

NTHi

genomics

fucP

PCR

real-time PCR

species

TaqMan

assay

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. © 2015 Price et al.

Details

Title: Haemophilus influenzae: Using comparative genomics to accurately identify a highly recombinogenic human pathogen
Authors: Erin P Price (Author) - Menzies School of Health Research
Derek S Sarovich (Author) - Menzies School of Health Research
E Nosworthy (Author) - Menzies School of Health Research
J Beissbarth (Author) - Menzies School of Health Research
R L Marsh (Author) - Menzies School of Health Research
J Pickering (Author) - University of Western Australia
L A S Kirkham (Author) - University of Western Australia
A D Keil (Author) - Princess Margaret Hospital for Children
A B Chang (Author) - Menzies School of Health Research
H C Smith-Vaughan (Author) - Menzies School of Health Research
Publication details: BMC Genomics, Vol.16(1), 641; 10
Publisher: BioMed Central Ltd.
Date published: 2015
DOI: 10.1186/s12864-015-1857-x
ISSN: 1471-2164
Copyright note: Copyright © 2015 Price et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99451171402621
Output Type: Journal article

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