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

Price, Erin P., Sarovich, Derek S., Nosworthy, Elizabeth, Beissbarth, Jemima, Marsh, Robyn L., Pickering, Janessa, Kirkham, Lea-Ann S., Keil, Anthony D., Chang, Anne B. and Smith-Vaughan, Heidi C. (2015). Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen. BMC Genomics,16(1 - Article No. 641).

Document type: Journal Article
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ARC Grant No. 1023781
IRMA ID 11381xPUB141
NHMRC Grant No. 1024175
1061428
1034703
Title Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen
Author Price, Erin P.
Sarovich, Derek S.
Nosworthy, Elizabeth
Beissbarth, Jemima
Marsh, Robyn L.
Pickering, Janessa
Kirkham, Lea-Ann S.
Keil, Anthony D.
Chang, Anne B.
Smith-Vaughan, Heidi C.
Journal Name BMC Genomics
Publication Date 2015
Volume Number 16
Issue Number 1 - Article No. 641
ISSN 1471-2164   (check CDU catalogue  open catalogue search in new window)
Scopus ID 2-s2.0-84940192316
Total Pages 10
Place of Publication United Kingdom
Publisher BioMed Central Ltd.
HERDC Category C1 - Journal Article (DIISR)
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.

Keywords Haemophilus influenzae
aemophilus haemolyticus
NTHi
Genomics
fucP
PCR
Real-time PCR
Species
TaqMan
Assay
DOI http://dx.doi.org/10.1186/s12864-015-1857-x   (check subscription with CDU E-Gateway service for CDU Staff and Students  check subscription with CDU E-Gateway in new window)
Additional Notes This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Description for Link Link to CC Attribution 4.0 License
URL https://creativecommons.org/licenses/by/4.0/au


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