Cystic fibrosis microbiome: analysis of nasal middle meatus and sputum in different lung disease stages

BACKGROUND: Culture independent methods of molecular detection of microbiome have shown the polymicrobial nature of respiratory infections in cystic fibrosis, with pathogenic agents undetectable in conventional culture methods. Composition and diversity of the airway microbiome are still poorly understood. METHODOLOGY: This study evaluated the airway microbiome in 31 adult cystic fibrosis patients via the analysis of 16S rRNA se- quences by next generation sequencing. RESULTS: Staphylococcus, Streptococcus and Corynebacterium were the most abundant genera in the middle meatus, and Pseudo- monas, Haemophilus and Prevotella were the most abundant in sputum. In patients with advanced disease (FEV1< 50%), there was an increase in the prevalence of Pseudomonas in both sample types when studied separately. In each patient, in a paired analysis, the sputum and middle meatus showed similar microbiome composition in mild or moderate disease (FEV1≥ 50%). In patients with severe lung disease, the relative abundance of Pseudomonas had a positive correlation in both collection sites. CONCLUSIONS: This is the first Brazilian study to evaluate the airway microbiome in cystic fibrosis patients. Our findings agree with those in the international literature and indicate the role of Pseudomonas in the sputum and middle meatus in patients with advanced disease.

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Yakult Intestinal Flora-SCAN: A Novel Culture-Independent Analytical Method for Detection of Bacteria in the Bloodstream

Annals of Nutrition and Metabolism ◽

10.1159/000479917 ◽

2017 ◽

Vol 71 (Suppl. 1) ◽

pp. 4-10 ◽

Cited By ~ 2

Author(s):

Hirokazu Tsuji ◽

Koji Nomoto

Keyword(s):

Gastrointestinal Surgery ◽

Intestinal Flora ◽

Infectious Complications ◽

Analytical Sensitivity ◽

Culture Methods ◽

Rna Molecules ◽

Conventional Culture ◽

Highly Sensitive ◽

Culture Independent ◽

Analytical System

We have developed a highly sensitive microbial analytical system, the Yakult Intestinal Flora-SCAN (YIF-SCAN), based on reverse transcription-quantitative PCR, to quantify the intestinal microbiota. Targeting ribosomal RNA “molecules,” which are present in abundant copies in the microorganisms, YIF-SCAN is at least hundreds of times more sensitive (detection limits: 102-3 cells/g feces, 1 cell/mL blood) than conventional DNA-based methods, and hence enables highly sensitive and precise detection of viable microorganisms in various types of samples, such as stools, blood etc. Specifically, this high analytical sensitivity enables more accurate and reliable detection (compared with conventional culture methods) of microorganisms migrating in the blood, bacteremia, in patients with different diseases such as pediatric patients with febrile neutropenia, neonates with clinically diagnosed sepsis, and patients with type 2 diabetes mellitus or ischemic stroke. Such detection of bacteremia during gastrointestinal surgery can also be particularly effective for preventing postoperative infectious complications. Herein, we review some of the studies corroborating the potential application and clinical significance of YIF-SCAN in diagnosing bacteremia (even at marginable levels) in patients with different diseases.

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Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis

mSystems ◽

10.1128/msystems.00178-21 ◽

2021 ◽

Vol 6 (4) ◽

Author(s):

Stephen C. Watts ◽

Louise M. Judd ◽

Rosemary Carzino ◽

Sarath Ranganathan ◽

Kathryn E. Holt

Keyword(s):

Cystic Fibrosis ◽

Antimicrobial Resistance ◽

Young Children ◽

Lung Disease ◽

Respiratory Infections ◽

Genomic Diversity ◽

Disease Development ◽

Acute Respiratory Infections ◽

Early Disease ◽

Advanced Stages

Cystic fibrosis (CF) lung disease begins during infancy, and acute respiratory infections increase the risk of early disease development and progression. Microbes involved in advanced stages of CF are well characterized, but less is known about early respiratory colonizers.

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Defective Ion Channel in Cystic Fibrosis: Current Development in Treatment of Cystic Fibrosis

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2020/v4i130099 ◽

2020 ◽

pp. 28-34

Author(s):

Ngoga Godfrey ◽

M. M. Ganyam ◽

G.O. Ibiang ◽

C. A. Difa ◽

Nelson Christian

Keyword(s):

Cystic Fibrosis ◽

Ion Transport ◽

Ion Channel ◽

Lung Disease ◽

Defense Mechanisms ◽

Respiratory Infections ◽

The Body ◽

Transmembrane Conductance Regulator ◽

Transmembrane Conductance ◽

Airway Defense

Cystic fibrosis is an inherited disorder that causes severe damage to the lungs, digestive system and other organs in the body. Cystic fibrosis transmembrane conductance regulator (CFTR) is involved in the production of mucus, sweat and digestive juices. These secreted fluids are normally thin and slippery. But in people with cystic fibrosis, a defective gene in CFTR causes the secretions to become sticky and thick. Instead of acting as a lubricant, the secretions plug up tubes, ducts and passage ways, especially in the lungs and pancreas. This mucus leads to the formation of bacterial microenvironments known as biofilms (a niche that harbors bacteria; Staphylococcus aureus, Haemophilus influenzae, and Pseudomonas aeruginosa ) that are difficult for immune cells and antibiotics to penetrate. Viscous secretions and persistent respiratory infections repeatedly damage the lung by gradually remodeling the airways, which makes infection even more difficult to eradicate. CFTR, a Cl– selective ion channel, is a prototypic member of the ATP-binding cassette transporter super family that is expressed in several organs. Understanding how these complexes regulate the intracellular trafficking and activity of CFTR provides a unique insight into the aetiology of cystic fibrosis and other diseases associated to it. Cystic fibrosis patients exhibit lung disease consistent with a failure of innate airway defense mechanisms. The link between abnormal ion transport, disease initiation and progression is not fully understood, but airway mucus dehydration seems paramount in the initiation of CF lung disease. New therapies are currently in development that target the ion transport defects in CF with the intention of rehydrating airway surfaces.

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Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease

Microorganisms ◽

10.3390/microorganisms8071003 ◽

2020 ◽

Vol 8 (7) ◽

pp. 1003 ◽

Cited By ~ 1

Author(s):

Giovanni Bacci ◽

Giovanni Taccetti ◽

Daniela Dolce ◽

Federica Armanini ◽

Nicola Segata ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Disease ◽

Temporal Dynamics ◽

Clinical Status ◽

Antibiotic Resistance Genes ◽

Lower Airway ◽

Metagenomic Sequencing ◽

Taxonomic Profiling ◽

Shotgun Metagenomic Sequencing ◽

Airway Microbiome

Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.

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Allergic Bronchopulmonary Aspergillosis in Children with Cystic Fibrosis: An Update on the Newest Diagnostic Tools and Therapeutic Approaches

Pathogens ◽

10.3390/pathogens9090716 ◽

2020 ◽

Vol 9 (9) ◽

pp. 716

Author(s):

Claudia Lattanzi ◽

Giulia Messina ◽

Valentina Fainardi ◽

Maria Candida Tripodi ◽

Giovanna Pisi ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Disease ◽

Diagnostic Criteria ◽

Respiratory Infections ◽

Fungal Infections ◽

Early Recognition ◽

Allergic Bronchopulmonary Aspergillosis ◽

Clinical Manifestations ◽

Diagnostic Tools ◽

The Impact

Cystic fibrosis (CF), the most common autosomal-recessive genetic disease in the Caucasian population, is characterized by frequent respiratory infections and progressive lung disease. Fungal species are commonly found in patients with CF, and among them, Aspergillus fumigatus is the most frequently isolated. While bacteria, particularly Pseudomonas aeruginosa, have a well-established negative effect on CF lung disease, the impact of fungal infections remains unclear. In patients with CF, inhalation of Aspergillus conidia can cause allergic bronchopulmonary aspergillosis (ABPA), a Th2-mediated lung disease that can contribute to disease progression. Clinical features, diagnostic criteria and treatment of ABPA are still a matter of debate. Given the consequences of a late ABPA diagnosis or the risk of ABPA overdiagnosis, it is imperative that the diagnostic criteria guidelines are reviewed and standardized. Along with traditional criteria, radiological features are emerging as tools for further classification as well as novel immunological tests. Corticosteroids, itraconazole and voriconazole continue to be the bedrock of ABPA therapy, but other molecules, such as posaconazole, vitamin D, recombinant INF-γ and Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) modulators, have been showing positive results. However, few studies have been conducted recruiting CF patients, and more research is needed to improve the prevention and the classification of clinical manifestations as well as to personalize treatment. Early recognition and early treatment of fungal infections may be fundamental to prevent progression of CF disease. The aim of this narrative review is to give an update on ABPA in children with CF.

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The polymicrobial nature of airway infections in cystic fibrosis: Cangene Gold Medal LectureThis article is based on a presentation by Dr. Christopher Sibley at the 60th Annual Meeting of the Canadian Society of Microbiologists in Hamilton, Ontario, on 15 June 2010. Dr. Sibley was the recipient of the 2010 Cangene Gold Medal as the Canadian Graduate Student Microbiologist of the Year, an annual award sponsored by Cangene Corporation intended to recognize excellence in graduate research.

Canadian Journal of Microbiology ◽

10.1139/w10-105 ◽

2011 ◽

Vol 57 (2) ◽

pp. 69-77 ◽

Cited By ~ 37

Author(s):

Christopher D. Sibley ◽

Michael G. Surette

Keyword(s):

Cystic Fibrosis ◽

Microbial Communities ◽

Gold Medal ◽

Emergent Properties ◽

Host Interactions ◽

Airway Infections ◽

Future Challenges ◽

Culture Independent ◽

Airway Microbiome ◽

Dynamic Communities

Microbial communities characterize the airways of cystic fibrosis (CF) patients. Members of these diverse and dynamic communities can be thought of as pathogens, benign commensals, or synergens — organisms not considered pathogens in the traditional sense but with the capacity to alter the pathogenesis of the community through microbe–microbe or polymicrobe–host interactions. Very few bacterial pathogens have been implicated as clinically relevant in CF; however, the CF airway microbiome can be a reservoir of previously unrecognized but clinically relevant organisms. A combination of culture-dependent and culture-independent approaches provides a more comprehensive perspective of CF microbiology than either approach alone. Here we review these concepts, highlight the future challenges for CF microbiology, and discuss the implications for the management of CF airway infections. We suggest that the success of treatment interventions for chronic CF lung disease will rely on the context of the microbes within microbial communities. The microbiology of CF airways may serve as a model to investigate the emergent properties of other clinically relevant microbial communities in the human body.

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Respiratory infection rates differ between geographically distant paediatric cystic fibrosis cohorts

ERJ Open Research ◽

10.1183/23120541.00014-2016 ◽

2016 ◽

Vol 2 (3) ◽

pp. 00014-2016 ◽

Cited By ~ 5

Author(s):

Kathryn A. Ramsey ◽

Emily Hart ◽

Lidija Turkovic ◽

Marc Padros-Goossens ◽

Stephen M. Stick ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Disease ◽

Respiratory Infections ◽

Age Groups ◽

Similar Rate ◽

Lower Airway ◽

Annual Review ◽

Respiratory Pathogens ◽

Geographical Differences ◽

Old Patients

Respiratory infections are a major cause of pulmonary decline in children with cystic fibrosis (CF). We compared the prevalence of infection in early life at geographically distant CF treatment centres participating in the same surveillance programme in Australia.Lower airway microbiology, inflammation and structural lung disease at annual review were evaluated for 260 children 0–8 years old with CF at 1032 visits to CF treatment centres in Melbourne or Perth.Melbourne patients were more likely to be culture-positive for common respiratory pathogens at all age groups (odds ratio (OR) 1.85, 95% CI 1.33–2.58). Subjects <2 years old in Melbourne were also more likely to have neutrophil elastase present (OR 3.11, 95% CI 1.62–5.95). Bronchiectasis (OR 2.02, 95% CI 1.21–3.38) and air trapping (OR 2.53, 95% CI 1.42–4.51) in subjects 2–5 years old was more common in Melbourne subjects. The severity of structural lung disease was also worse in Melbourne patients >5 years old. Patients at both centres had a similar rate of hospitalisations and prescribed antibiotics.No procedural differences were identified that could explain the disparity between pathogen prevalence. Geographical differences in early acquisition of infection may contribute to variability in outcomes between CF centres.

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Cystic Fibrosis Airway Microbiome: Overturning the Old, Opening the Way for the New

Journal of Bacteriology ◽

10.1128/jb.00561-17 ◽

2017 ◽

Vol 200 (4) ◽

Cited By ~ 21

Author(s):

George A. O'Toole

Keyword(s):

Cystic Fibrosis ◽

Bronchoalveolar Lavage Fluid ◽

Lavage Fluid ◽

Chronic Infections ◽

Cystic Fibrosis Airway ◽

Airway Infections ◽

Culture Independent ◽

Airway Microbiome ◽

New Strategies ◽

The Way

ABSTRACTThe genetic disease cystic fibrosis (CF) is associated with chronic airway infections that are a proximal cause of death in many patients with this affliction. Classic microbiology studies focusing on canonical pathogens resulted in the development of a common set of views regarding the nature of the airway infections associated with this disease, and these ideas have influenced everything from the way infections are treated to how clinical trials for new CF-targeted antibiotics are designed and the focus of CF-related research topics. Recent culture-independent studies have prompted us to rethink, and in some cases discard, some of these long-held views. In this piece, I argue that an updated view of the complicated chronic infections associated with CF, thanks in large part to culture-independent studies of sputum and bronchoalveolar lavage fluid samples, should be leveraged to develop new strategies to treat these recalcitrant infections.

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Evolution and adaptation of Pseudomonas aeruginosa in the paranasal sinuses of people with cystic fibrosis

10.1101/2020.10.29.359844 ◽

2020 ◽

Author(s):

Catherine R. Armbruster ◽

Christopher W. Marshall ◽

Jeffrey A. Melvin ◽

Anna C. Zemke ◽

Arkadiy I. Garber ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Lung Disease ◽

Respiratory Infections ◽

Genetic Disorder ◽

List Type ◽

Host Restriction ◽

Single Clone ◽

Lung Infections ◽

End Stage

AbstractPeople with the genetic disorder cystic fibrosis (CF) harbor lifelong respiratory infections, with morbidity and mortality frequently linked to chronic lung infections dominated by the opportunistically pathogenic bacterium Pseudomonas aeruginosa. During chronic CF lung infections, a single clone of P. aeruginosa can persist for decades and dominate end-stage CF lung disease due to its propensity to adaptively evolve to the respiratory environment, a process termed “pathoadaptation”. Chronic rhinosinusitis (CRS), chronic inflammation and infection of the sinonasal space, is highly prevalent in CF and the sinuses may serve as the first site in the respiratory tract to become colonized by bacteria that then proceed to seed lung infections. We identified three evolutionary genetic routes by which P. aeruginosa evolves in the sinuses of people with CF, including through the evolution of mutator lineages and proliferative insertion sequences and culminating in early genomic signatures of host-restriction. Our findings raise the question of whether a significant portion of the pathoadaptive phenotypes previously thought to have evolved in response to selective pressures in the CF lungs may have first arisen in the sinuses and underscore the link between sinonasal and lung disease in CF.Graphical abstract and highlightsPseudomonas aeruginosa undergoes adaptive evolution in the sinuses of people with CFOver time, pathoadapted strains display early signatures of genome degradation consistent with recent host restrictionMutations previously thought to occur in CF lungs may have first evolved in sinuses

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Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

mBio ◽

10.1128/mbio.02863-20 ◽

2021 ◽

Vol 12 (2) ◽

Author(s):

Marija Dmitrijeva ◽

Christian R. Kahlert ◽

Rounak Feigelman ◽

Rebekka L. Kleiner ◽

Oliver Nolte ◽

...

Keyword(s):

Cystic Fibrosis ◽

Disease Progression ◽

Respiratory Infections ◽

Cystic Fibrosis Lung ◽

Shotgun Metagenomics ◽

Lung Microbiome ◽

Longitudinal Tracking ◽

Culture Independent ◽

Repeated Sampling

ABSTRACT In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals can colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting lineages. Routine clinical protocols, however, provide a limited overview of the colonizer populations. Therefore, a more comprehensive and precise identification and characterization of infecting lineages could assist in making corresponding decisions on treatment. Here, we describe longitudinal tracking for four cystic fibrosis patients who exhibited extreme clinical phenotypes and, thus, were selected from a pilot cohort of 11 patients with repeated sampling for more than a year. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sublineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences. Our study showcases a culture-independent shotgun metagenomics approach for longitudinal tracking of sublineage pathogen dynamics, opening up the possibility of using such methods to assist in monitoring disease progression through providing high-resolution routine characterization of the cystic fibrosis lung microbiome. IMPORTANCE Cystic fibrosis patients frequently suffer from recurring respiratory infections caused by colonizing pathogenic and commensal bacteria. Although modern therapies can sometimes alleviate respiratory symptoms by ameliorating residual function of the protein responsible for the disorder, management of chronic respiratory infections remains an issue. Here, we propose a minimally invasive and culture-independent method to monitor microbial lung content in patients with cystic fibrosis at minimal additional effort on the patient’s part. Through repeated sampling and metagenomics sequencing of our selected cystic fibrosis patients, we successfully classify infecting bacterial lineages and deconvolute multiple lineage variants of the same species within a given patient. This study explores the application of modern computational methods for deconvoluting lineages in the cystic fibrosis lung microbiome, an environment known to be inhabited by a heterogeneous pathogen population that complicates management of the disorder.

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