Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota

Brown, Perry; Pope, Charles E.; Marsh, Robyn L.; Qin, Xuan; McNamara, Sharon; Gibson, Ronald L.; Burns, Jane L.; Deutsch, Gail H.; Hoffman, Lucas R.

doi:10.1513/annalsats.201311-383oc

Cited by 68 publications

(52 citation statements)

References 38 publications

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“…A recent study of otherwise healthy children with pneumonia found reduced upper airway microbial diversity,36 whilst the lower airway microbiota of adults with end-stage CF lung disease is dominated by a relatively homogenous population of typical CF pathogens 7 13. In cross-sectional studies of adults, increased microbial diversity is associated with clinical stability and improved pulmonary function,12 37 although microbial diversity was also maintained in tissue samples obtained at lobectomy from a 3 year old with severe, localised CF lung disease 38. While it was not possible to exclude the potentially confounding effect of cumulative antibiotic use, our study of young children, whose lifetime antibiotic exposure is likely considerably less than their adult counterparts, suggests that microbial diversity decreases when known pathogens emerge.…”

Section: Discussionmentioning

confidence: 99%

The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis

Frayman

Armstrong

Carzino

et al. 2017

Thorax

101

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Section: Discussionmentioning

confidence: 99%

The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis

Frayman

Armstrong

Carzino

et al. 2017

Thorax

101

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“…These results are consistent with those of Tunney et al (23), who used culturebased analyses to show that anaerobic bacteria were most often present in equal or greater numbers than P. aeruginosa in CF sputum samples. The concern that anaerobic species merely represent contamination from the upper airway has been further assuaged by a study that identified anaerobic species in deep tissue samples of lung resected from a child with CF (27) and by other recent work that provides evidence of microbial anaerobic respiration in CF airways (28,29).…”

Section: Discussionmentioning

confidence: 99%

Culture-Based and Culture-Independent Bacteriologic Analysis of Cystic Fibrosis Respiratory Specimens

et al. 2016

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bCystic fibrosis (CF) is characterized by chronic infection and inflammation of the airways. In vitro culture of select bacterial species from respiratory specimens has been used to guide antimicrobial therapy in CF for the past few decades. More recently, DNA sequence-based, culture-independent approaches have been used to assess CF airway microbiology, although the role that these methods will (or should) have in routine microbiologic analysis of CF respiratory specimens is unclear. We performed DNA sequence analyses to detect bacterial species in 945 CF sputum samples that had been previously analyzed by selective CF culture. We determined the concordance of results based on culture and sequence analysis, highlighting the comparison of the results for the most prevalent genera. Although overall prevalence rates were comparable between the two methods, results varied by genus. While sequence analysis was more likely to detect Achromobacter, Stenotrophomonas, and Burkholderia, it was less likely to detect Staphylococcus. Streptococcus spp. were rarely reported in culture results but were the most frequently detected species by sequence analysis. A variety of obligate and facultative anaerobic species, not reported by culture, was also detected with high prevalence by sequence analysis. Sequence analysis indicated that in a considerable proportion of samples, taxa not reported by selective culture constituted a relatively high proportion of the total bacterial load, suggesting that routine CF culture may underrepresent significant segments of the bacterial communities inhabiting CF airways.A hallmark of cystic fibrosis (CF) is chronic bacterial infection of the respiratory tract. Infection and the associated inflammation contribute to progressive lung damage, which ultimately results in respiratory failure, the leading cause of death in CF. For the past few decades, an important aspect of CF care has been the use of intensive antimicrobial therapy. Although therapy in younger patients is often provided in an attempt to eradicate initial infection, antibiotics in older patients are typically prescribed to suppress chronic infection or to treat the intermittent exacerbations of respiratory symptoms characteristic of CF. In vitro culture of CF respiratory specimens (most often expectorated sputum) has been used to guide the choice of antibiotics and has focused on the selective recovery of a relatively small suite of bacterial species believed to contribute to lung disease in CF. Historically, this set included Staphylococcus aureus, Haemophilus influenzae, and Pseudomonas aeruginosa (1). Since the 1990s, the list of CF species of interest has expanded to include a small number of other opportunistic bacterial pathogens, including Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and the Burkholderia cepacia complex, which also have been associated with disease progression in CF (2).During the past decade, the microbiology of CF respiratory tract infection has been further explored through the use of method...

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“…However, the low detection rate of the traditional method limits the discovery of pathogens present at low abundance. Assisted by next generation of sequencing, 16S rDNA detection of microbiota provides more complete information regarding the flora of the respiratory tract in PBB infants (3)(4)(5).…”

Section: Introductionmentioning

confidence: 99%

Bronchoalveolar lavage fluid microbiota dysbiosis in infants with protracted bacterial bronchitis

Bao

Li²,

Qiu³

et al. 2018

J. Thorac. Dis.

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Background: Protracted bacterial bronchitis (PBB) is a chronic purulent bronchitis which could cause recurrent coughing and wheezing in infants. Based on previous reports, main pathogens which caused PBB were identified in the patients, but their impacts on lung microbiota dysbiosis remain unclear.Methods: In this study, bronchoalveolar lavage fluid (BALF) was collected from PBB infants and tracheomalacia (TM) infants younger than 3 years old under the instruction of Shenzhen Children's Hospital, and 12 samples were randomly selected for 16S rDNA analysis in each group. Based on the results of bacterial composition, the microbiota diversity and co-occurrence network in PBB and TM group were detected and compared. Results: Microbiota diversity was significantly lower in PBB group than it in TM group (P<0.001 for the comparison of Shannon and Simpson indexes). The PBB group was found to harbor 25 accumulated bacterial agents by comparison with TM group, including Haemophilus (P<0.001) and Bacteroides (P<0.001). Whilst, the populations of Lactococcus (P<0.001) and Lactobacillus (P<0.001) were dramatically smaller in PBB group.The co-occurrence network in PBB group also differed from that of TM group. It contained four core nodes in PBB patients, including Haemophilus, Parabacteroides, Porphyromonas, and Cronobacter. Haemophilus was found to be negatively associated with most counterparts, including Clostridium and Bacillus. Conclusions: PBB infants contained discrepant lung genera and co-occurrence network when compared with TM infants. This retrospective study may deepen our understanding of PBB pathogenesis, and it also provided a foundation for bacterial adjunctive therapy of infantile PBB in accordance with clinical treatment.

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Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota

Cited by 68 publications

References 38 publications

The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis

The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis

Culture-Based and Culture-Independent Bacteriologic Analysis of Cystic Fibrosis Respiratory Specimens

Bronchoalveolar lavage fluid microbiota dysbiosis in infants with protracted bacterial bronchitis

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