Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes

Jake Jervis Bardy, Derek S. Sarovich, Erin P. Price, Eike Steinig, Steven Tong, Amanda Drilling, Judy Ou, Sarah Vreugde, Peter John Wormald, Alkis J. Psaltis

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    Abstract

    Background: Staphylococcus aureus has a high prevalence in chronic rhinosinusitis (CRS) patients and is suggested to play a more etiopathogenic role in CRS patients with nasal polyps (CRSwNP), a severe form of the CRS spectrum with poorer surgical outcomes. We performed a microbial genome-wide association study (mGWAS) to investigate whether S. aureus isolates from CRS patients have particular genetic markers associated with CRS with nasal polyps (CRSwNP) or CRS without nasal polyps (CRSsNP).

    Methods: Whole genome sequencing was performed on S. aureus isolates collected from 28 CRSsNP and 30 CRSwNP patients. A mGWAS approach was employed using large-scale comparative genomics to identify genetic variation within our dataset.

    Results: Considerable genetic variation was observed, with > 90,000 single nucleotide polymorphisms (SNPs) sites identified. There was little correlation with CRS subtype based on SNPs and Insertion/Delection (Indels). One indel was found to significantly correlate with CRSwNP and occurred in the promoter region of a bacitracin transport system ATP-binding protein. Additionally, two variants of the highly variable superantigen-like (SSL) proteins were found to significantly correlate with each CRS phenotype. No significant association with other virulence or antibiotic resistance genes were observed, consistent with previous studies.

    Conclusion: To our knowledge this study is the first to use mGWAS to investigate the contribution of microbial genetic variation to CRS presentations. Utilising the most comprehensive genome-wide analysis methods available, our results suggest that CRS phenotype may be influenced by genetic factors other than specific virulence mechanisms within the S. aureus genome.

    Original languageEnglish
    Article number16
    Pages (from-to)1-8
    Number of pages8
    JournalBMC Ear, Nose and Throat Disorders
    Volume18
    Issue number1
    DOIs
    Publication statusPublished - 16 Oct 2018

    Fingerprint

    Nasal Polyps
    Polyps
    Staphylococcus aureus
    Microbial Genome
    Phenotype
    Genome-Wide Association Study
    Genome
    Single Nucleotide Polymorphism
    Virulence
    Microbial Genetics
    Bacitracin
    Superantigens
    Microbial Drug Resistance
    Genomics
    Genetic Markers
    Genetic Promoter Regions
    Carrier Proteins
    Adenosine Triphosphate
    Genes
    Proteins

    Cite this

    Bardy, Jake Jervis ; Sarovich, Derek S. ; Price, Erin P. ; Steinig, Eike ; Tong, Steven ; Drilling, Amanda ; Ou, Judy ; Vreugde, Sarah ; Wormald, Peter John ; Psaltis, Alkis J. / Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes. In: BMC Ear, Nose and Throat Disorders. 2018 ; Vol. 18, No. 1. pp. 1-8.
    @article{8cac34b9ed95423588731e3ec1c28464,
    title = "Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes",
    abstract = "Background: Staphylococcus aureus has a high prevalence in chronic rhinosinusitis (CRS) patients and is suggested to play a more etiopathogenic role in CRS patients with nasal polyps (CRSwNP), a severe form of the CRS spectrum with poorer surgical outcomes. We performed a microbial genome-wide association study (mGWAS) to investigate whether S. aureus isolates from CRS patients have particular genetic markers associated with CRS with nasal polyps (CRSwNP) or CRS without nasal polyps (CRSsNP). Methods: Whole genome sequencing was performed on S. aureus isolates collected from 28 CRSsNP and 30 CRSwNP patients. A mGWAS approach was employed using large-scale comparative genomics to identify genetic variation within our dataset. Results: Considerable genetic variation was observed, with > 90,000 single nucleotide polymorphisms (SNPs) sites identified. There was little correlation with CRS subtype based on SNPs and Insertion/Delection (Indels). One indel was found to significantly correlate with CRSwNP and occurred in the promoter region of a bacitracin transport system ATP-binding protein. Additionally, two variants of the highly variable superantigen-like (SSL) proteins were found to significantly correlate with each CRS phenotype. No significant association with other virulence or antibiotic resistance genes were observed, consistent with previous studies. Conclusion: To our knowledge this study is the first to use mGWAS to investigate the contribution of microbial genetic variation to CRS presentations. Utilising the most comprehensive genome-wide analysis methods available, our results suggest that CRS phenotype may be influenced by genetic factors other than specific virulence mechanisms within the S. aureus genome.",
    keywords = "Chronic rhinosinusitis, Genome-wide association study, Microbial genomics, Staphylococcus aureus, Whole genome sequencing",
    author = "Bardy, {Jake Jervis} and Sarovich, {Derek S.} and Price, {Erin P.} and Eike Steinig and Steven Tong and Amanda Drilling and Judy Ou and Sarah Vreugde and Wormald, {Peter John} and Psaltis, {Alkis J.}",
    year = "2018",
    month = "10",
    day = "16",
    doi = "10.1186/s12901-018-0064-1",
    language = "English",
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    Bardy, JJ, Sarovich, DS, Price, EP, Steinig, E, Tong, S, Drilling, A, Ou, J, Vreugde, S, Wormald, PJ & Psaltis, AJ 2018, 'Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes', BMC Ear, Nose and Throat Disorders, vol. 18, no. 1, 16, pp. 1-8. https://doi.org/10.1186/s12901-018-0064-1

    Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes. / Bardy, Jake Jervis; Sarovich, Derek S.; Price, Erin P.; Steinig, Eike; Tong, Steven; Drilling, Amanda; Ou, Judy; Vreugde, Sarah; Wormald, Peter John; Psaltis, Alkis J.

    In: BMC Ear, Nose and Throat Disorders, Vol. 18, No. 1, 16, 16.10.2018, p. 1-8.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes

    AU - Bardy, Jake Jervis

    AU - Sarovich, Derek S.

    AU - Price, Erin P.

    AU - Steinig, Eike

    AU - Tong, Steven

    AU - Drilling, Amanda

    AU - Ou, Judy

    AU - Vreugde, Sarah

    AU - Wormald, Peter John

    AU - Psaltis, Alkis J.

    PY - 2018/10/16

    Y1 - 2018/10/16

    N2 - Background: Staphylococcus aureus has a high prevalence in chronic rhinosinusitis (CRS) patients and is suggested to play a more etiopathogenic role in CRS patients with nasal polyps (CRSwNP), a severe form of the CRS spectrum with poorer surgical outcomes. We performed a microbial genome-wide association study (mGWAS) to investigate whether S. aureus isolates from CRS patients have particular genetic markers associated with CRS with nasal polyps (CRSwNP) or CRS without nasal polyps (CRSsNP). Methods: Whole genome sequencing was performed on S. aureus isolates collected from 28 CRSsNP and 30 CRSwNP patients. A mGWAS approach was employed using large-scale comparative genomics to identify genetic variation within our dataset. Results: Considerable genetic variation was observed, with > 90,000 single nucleotide polymorphisms (SNPs) sites identified. There was little correlation with CRS subtype based on SNPs and Insertion/Delection (Indels). One indel was found to significantly correlate with CRSwNP and occurred in the promoter region of a bacitracin transport system ATP-binding protein. Additionally, two variants of the highly variable superantigen-like (SSL) proteins were found to significantly correlate with each CRS phenotype. No significant association with other virulence or antibiotic resistance genes were observed, consistent with previous studies. Conclusion: To our knowledge this study is the first to use mGWAS to investigate the contribution of microbial genetic variation to CRS presentations. Utilising the most comprehensive genome-wide analysis methods available, our results suggest that CRS phenotype may be influenced by genetic factors other than specific virulence mechanisms within the S. aureus genome.

    AB - Background: Staphylococcus aureus has a high prevalence in chronic rhinosinusitis (CRS) patients and is suggested to play a more etiopathogenic role in CRS patients with nasal polyps (CRSwNP), a severe form of the CRS spectrum with poorer surgical outcomes. We performed a microbial genome-wide association study (mGWAS) to investigate whether S. aureus isolates from CRS patients have particular genetic markers associated with CRS with nasal polyps (CRSwNP) or CRS without nasal polyps (CRSsNP). Methods: Whole genome sequencing was performed on S. aureus isolates collected from 28 CRSsNP and 30 CRSwNP patients. A mGWAS approach was employed using large-scale comparative genomics to identify genetic variation within our dataset. Results: Considerable genetic variation was observed, with > 90,000 single nucleotide polymorphisms (SNPs) sites identified. There was little correlation with CRS subtype based on SNPs and Insertion/Delection (Indels). One indel was found to significantly correlate with CRSwNP and occurred in the promoter region of a bacitracin transport system ATP-binding protein. Additionally, two variants of the highly variable superantigen-like (SSL) proteins were found to significantly correlate with each CRS phenotype. No significant association with other virulence or antibiotic resistance genes were observed, consistent with previous studies. Conclusion: To our knowledge this study is the first to use mGWAS to investigate the contribution of microbial genetic variation to CRS presentations. Utilising the most comprehensive genome-wide analysis methods available, our results suggest that CRS phenotype may be influenced by genetic factors other than specific virulence mechanisms within the S. aureus genome.

    KW - Chronic rhinosinusitis

    KW - Genome-wide association study

    KW - Microbial genomics

    KW - Staphylococcus aureus

    KW - Whole genome sequencing

    UR - http://www.scopus.com/inward/record.url?scp=85055009764&partnerID=8YFLogxK

    U2 - 10.1186/s12901-018-0064-1

    DO - 10.1186/s12901-018-0064-1

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    SP - 1

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    JO - BMC Ear, Nose and Throat Disorders

    JF - BMC Ear, Nose and Throat Disorders

    SN - 1472-6815

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