An exploratory study of microbial diversity in sinus infections of cystic fibrosis patients by molecular methods

Rudkjøbing, Vibeke Børsholt; Aanæs, Kasper; Wolff, Tine Yding; Buchwald, Christian von; Johansen, Helle Krogh; Thomsen, Trine Rolighed

doi:10.1016/j.jcf.2014.02.008

Cited by 17 publications

(10 citation statements)

References 29 publications

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“…Similarly, the role of medical therapy for CRS in PCD, such as saline irrigation, topical nasal corticosteroids, topical antibiotics, and long‐term macrolide therapy, is uncertain. We isolated sinus and lung pathogens using standard culture methods, which may ignore difficult‐to‐grow bacteria . Our study is strengthened by the prospective design; by 1 experienced surgeon being involved in all steps in all patients; by following a standardized program for surgery, a standardized sample collection procedure, and postoperative adjuvant therapy, and scheduled clinical follow‐ups.…”

Section: Discussionmentioning

confidence: 99%

Sinus surgery can improve quality of life, lung infections, and lung function in patients with primary ciliary dyskinesia

Alanin

Aanæs

Høiby

et al. 2016

Int Forum Allergy Rhinol

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Section: Discussionmentioning

confidence: 99%

Sinus surgery can improve quality of life, lung infections, and lung function in patients with primary ciliary dyskinesia

Alanin

Aanæs

Høiby

et al. 2016

Int Forum Allergy Rhinol

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“…The libraries consisted of near full length 16S rRNA genes ( E. coli position 26–1390) which were obtained as described previously [27, 28]. Briefly, PCR amplicons were cloned using the TOPO TA Cloning ® kit (Invitrogen) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

Rudkjøbing

Thomsen

et al. 2016

BMC Infect Dis

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BackgroundNecrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture.MethodsIn this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples.ResultsFor 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods.Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum.ConclusionThe study emphasizes that many pathogens can be involved in NSTIs, and that no specific “NSTI causing” combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI.

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“…While P. aeruginosa and S. aureus represent two of the most common organisms isolated from the sinuses in CF subjects (30, 31), culture-independent studies suggest that the CF sinuses are also colonized by an abundance of anaerobes ( e.g. Propionibacterium acnes ) and other non-canonical pathogens that are infrequently detected by clinical culture (30). These data are consistent with microbiome surveys of CF lung disease, which is now widely recognized to have a polymicrobial etiology (5–9).…”

Section: Introductionmentioning

confidence: 99%

16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients

Yang

Dunitz

et al. 2017

Preprint

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RationaleChronic rhinosinusitis (CRS) is an inflammatory disorder of the sinonasal mucosa associated with microbial colonization. Metastasis of sinus microbiota into the lower airways is thought have significant implications in the development of chronic respiratory disease. However, this dynamic has not been thoroughly investigated in cystic fibrosis (CF) patients, where lower airway infections are the primary driver of patient mortality. Given the high prevalence of CRS in CF patients and the proposed infection dynamic between the upper and lower airways, a better understanding of sinus-lung continuum is warranted.ObjectiveTo compare the microbiome of matched sinus mucus and lung sputum samples from CF subjects undergoing functional endoscopic sinus surgery (FESS) for treatment of CRS.MethodsMucus was isolated from the sinuses and lungs of twelve CF patients undergoing FESS. 16S ribosomal RNA gene sequencing was then performed to compare bacterial communities of the CF lung and sinus niches. Finally, functional profiling was performed to predict bacterial metagenomes from the 16S dataset, and was used to compare pathogenic bacterial phenotypes between the upper and lower airways.Measurements and Main ResultsBacterial richness was comparable between airway sites, though sinus and lung environments differed in community evenness, with the sinuses harboring a higher prevalence of dominant microorganisms. Beta diversity metrics also revealed that samples clustered more consistently by airway niche rather than by individual. Finally, predicted metagenomes showed that anaerobic metabolism was enriched in the lung environment, while genes associated with both biofilm formation and Gram identity were not variable between sites.ConclusionsSinus and lung microbiomes are distinct with respect to richness and evenness, while sinus communities have a higher incidence of a dominant taxon. Additionally, ordination analyses point to sinus and lung environments as being stronger determinants of microbial community structure than the individual patient. Finally, BugBase-predicted metagenomes revealed anaerobic phenotypes to be in higher abundance in the lung relative to the sinuses. Our findings indicate that while the paranasal sinuses and lungs may still comprise a unified airway in which lower airways are seeded by sinus microbiota, these discrete airway microenvironments harbor distinct bacterial communities.

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An exploratory study of microbial diversity in sinus infections of cystic fibrosis patients by molecular methods

Abstract: The results indicate that the culture methods in some cases may not be suitable as stand-alone method for this patient group, as diversity may be underestimated and important species undetected.

Cited by 17 publications

References 29 publications

Sinus surgery can improve quality of life, lung infections, and lung function in patients with primary ciliary dyskinesia

Sinus surgery can improve quality of life, lung infections, and lung function in patients with primary ciliary dyskinesia

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients

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