Molecular detection of CF lung pathogens: Current status and future potential

Pattison, S.; Rogers, Geraint B.; Crockard, Martin; Elborn, J. Stuart; Tunney, Michael

doi:10.1016/j.jcf.2013.01.007

Cited by 25 publications

(30 citation statements)

References 78 publications

(100 reference statements)

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“…Due to their known virulence in CF, the major pathogens P. aeruginosa and S. aureus must be treated in priority. However, as described by Aravantagi et al [11], some patients receiving [21]. It should be noticed that even if Beucher et al [7] suggested that the association Nocardia/Pseudomonas seems to be correlated to increased symptoms, in our study, only four sputa contained P. aeruginosa and only two of them were associated with acute exacerbations.…”

Section: Discussionsupporting

confidence: 44%

A French multicentric study and review of pulmonary Nocardia spp. in cystic fibrosis patients

Rodríguez-Nava

Durupt

Chyderiotis

et al. 2014

Med Microbiol Immunol

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Some bacterial species recovered from the airways of cystic fibrosis (CF) patients are indisputably associated with lung infections, whereas the clinical relevance of others, such as Nocardia spp., remains unclear. Sixteen French CF cases of colonization/infection with Nocardia spp. were reviewed in order to evaluate the epidemiology, the clinical impact and the potential treatment of these bacteria, and results were compared to those of the literature. Five Nocardia species were identified, Nocardia cyriacigeorgica being the major species (50 % of cases). At first isolation, Nocardia was the sole pathogen recovered in six patients. Seven patients presented pulmonary exacerbation. For 12 patients, antimicrobial treatment against Nocardia was started immediately, mainly based on cotrimoxazole (6 of the 12 cases). In this study, we highlight the heterogeneity of the clinical management of Nocardia spp. in CF. Guidelines for the clinical management of Nocardia infections in CF patients are proposed.

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Section: Discussionsupporting

confidence: 44%

A French multicentric study and review of pulmonary Nocardia spp. in cystic fibrosis patients

Rodríguez-Nava

Durupt

Chyderiotis

et al. 2014

Med Microbiol Immunol

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“…2 and Table S1). A probable reason for the higher prevalences is the increased sensitivity inherent in molecular-based approaches when compared to culture-based methods [7]. SIMPER analysis revealed that all recognised pathogen OTUs, with the exception of A. xylosoxidans, contributed substantially to the dissimilarity between lung disease categories ( Table 2).…”

Section: Discussionmentioning

confidence: 99%

“…A relatively small group of bacterial species, all of which can be readily isolated using conventional aerobic culture-based approaches, are associated with chronic lower respiratory infection in CF, including Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia cepacia complex, Haemophilus influenzae, Stenotrophomonas maltophilia and Achromobacter xylosoxidans [1]. Culture-based approaches have influenced everything from the way infections are treated to informing national CF registries on changing pathogen prevalences with age [6,7]. However, molecular approaches have elucidated a much more complex picture of polymicrobial lower airway infection in this disease [8][9][10].…”

Section: Introductionmentioning

confidence: 99%

“…However, molecular approaches have elucidated a much more complex picture of polymicrobial lower airway infection in this disease [8][9][10]. In light of the recognition that CF lung microbiota are multifarious, the limitations of culture-based diagnostic microbiology to characterise CF lung infections have become increasingly apparent [7]. The traditional 'one microbe, one disease' concept of infection pathogenesis and infection control in CF management has therefore been brought into question [6,11,12].…”

Section: Introductionmentioning

confidence: 99%

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Lung function and microbiota diversity in cystic fibrosis

et al. 2020

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Background: Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, involving a lung microbiota, infection surveillance and control approaches remain underpinned by classical aerobic culture-based microbiology. How to use microbiomics to direct clinical management of CF airway infections remains a crucial challenge. A pivotal step towards leveraging microbiome approaches in CF clinical care is to understand the ecology of the CF lung microbiome and identify ecological patterns of CF microbiota across a wide spectrum of lung disease. Assessing sputum samples from 299 patients attending 13 CF centres in Europe and the USA, we determined whether the emerging relationship of decreasing microbiota diversity with worsening lung function could be considered a generalised pattern of CF lung microbiota and explored its potential as an informative indicator of lung disease state in CF. Results:We tested and found decreasing microbiota diversity with a reduction in lung function to be a significant ecological pattern. Moreover, the loss of diversity was accompanied by an increase in microbiota dominance. Subsequently, we stratified patients into lung disease categories of increasing disease severity to further investigate relationships between microbiota characteristics and lung function, and the factors contributing to microbiota variance. Core taxa group composition became highly conserved within the severe disease category, while the rarer satellite taxa underpinned the high variability observed in the microbiota diversity. Further, the lung microbiota of individual patient were increasingly dominated by recognised CF pathogens as lung function decreased. Conversely, other bacteria, especially obligate anaerobes, increasingly dominated in those with better lung function. Ordination analyses revealed lung function and antibiotics to be main explanators of compositional variance in the microbiota and the core and satellite taxa. Biogeography was found to influence acquisition of the rarer satellite taxa. (Continued on next page)Conclusions: Our findings demonstrate that microbiota diversity and dominance, as well as the identity of the dominant bacterial species, in combination with measures of lung function, can be used as informative indicators of disease state in CF.

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“…At present, there is no readily available methodology to identify all of these organisms in a way that makes this information valuable for clinical treatment (77). Studies are under way to develop technologies to allow molecular identification without prior culture (78). The choice of antibiotics for pulmonary exacerbations associated with multiple bacteria is an area that has not been extensively studied.…”

Section: Treating Multiple Infectionsmentioning

confidence: 99%

Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

et al. 2014

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Despite significant advances in treatment strategies targeting the underlying defect in cystic fibrosis (CF), airway infection remains an important cause of lung disease. In this two-part series, we review recent evidence related to the complexity of CF airway infection, explore data suggesting the relevance of individual microbial species, and discuss current and future treatment options. In Part I, the evidence with respect to the spectrum of bacteria present in the CF airway, known as the lung microbiome is discussed. Subsequently, the current approach to treat methicillin-resistant Staphylococcus aureus, gram-negative bacteria, as well as multiple coinfections is reviewed. Newer molecular techniques have demonstrated that the airway microbiome consists of a large number of microbes, and the balance between microbes, rather than the mere presence of a single species, may be relevant for disease pathophysiology. A better understanding of this complex environment could help define optimal treatment regimens that target pathogens without affecting others. Although relevance of these organisms is unclear, the pathologic consequences of methicillin-resistant S. aureus infection in patients with CF have been recently determined. New strategies for eradication and treatment of both acute and chronic infections are discussed. Pseudomonas aeruginosa plays a prominent role in CF lung disease, but many other nonfermenting gram-negative bacteria are also found in the CF airway. Many new inhaled antibiotics specifically targeting P. aeruginosa have become available with the hope that they will improve the quality of life for patients. Part I concludes with a discussion of how best to treat patients with multiple coinfections.

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Molecular detection of CF lung pathogens: Current status and future potential

Cited by 25 publications

References 78 publications

A French multicentric study and review of pulmonary Nocardia spp. in cystic fibrosis patients

A French multicentric study and review of pulmonary Nocardia spp. in cystic fibrosis patients

Lung function and microbiota diversity in cystic fibrosis

Antibiotic Management of Lung Infections in Cystic Fibrosis. I. The Microbiome, Methicillin-Resistant Staphylococcus aureus, Gram-Negative Bacteria, and Multiple Infections

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