Interlobar differences in bronchoalveolar lavage fluid from children with cystic fibrosis

Exhaled breath profiles to detect lung infection with Staphylococcus aureus in children with cystic fibrosis

BACKGROUND

An electronic nose (eNose) can be used to detect volatile organic compounds (VOCs). Exhaled breath contains numerous VOCs and individuals' VOCs mixtures create distinct breath profiles. Previous reports have shown that eNose can detect lung infections. Whether eNose can detect Staphylococcus aureus airway infections in breath of children with cystic fibrosis (CF) is currently unclear.

METHODS

In this cross-sectional observational study, a cloud-connected eNose was used for breath profile analysis of clinically stable paediatric CF patients with airway microbiology cultures positive or negative for CF pathogens. Data-analysis involved advanced signal processing, ambient correction and statistics based on linear discriminant and receiver operating characteristics (ROC) analyses.

RESULTS

Breath profiles from 100 children with CF (median predicted FEV1 91%) were obtained and analysed. CF patients with positive airway cultures for any CF pathogen were distinguishable from no CF pathogens (no growth or usual respiratory flora) with accuracy of 79.0% (AUC-ROC 0.791; 95% CI: 0.669-0.913) and between patients positive for Staphylococcus aureus (SA) only and no CF pathogen with accuracy of 74.0% (AUC-ROC 0.797; 95% CI: 0.698-0.896). Similar differences were seen for Pseudomonas aeruginosa (PA) infection vs no CF pathogens (78.0% accuracy, AUC-ROC 0.876, 95% CI: 0.794-0.958). SA- and PA-specific signatures were driven by different sensors in the SpiroNose suggesting pathogen-specific breath signatures.

CONCLUSIONS

Breath profiles of CF patients with SA in airway cultures are distinct from those with no infection or PA infection, suggesting the utility of eNose technology in the detection of this early CF pathogen in children with CF.

The clinical yield of bronchoscopy in the management of cystic fibrosis: A retrospective multicenter study

BACKGROUND

Pulmonary disease is the leading cause of morbidity and mortality in people with cystic fibrosis (pwCF). Several studies have shown no benefit for bronchoscopy and bronchoalveolar lavage (BAL) over sputum to obtain microbiological cultures, hence the role of bronchoscopy in pwCF is unclear.

AIM

To analyze how bronchoscopy results affected clinical decision-making in pwCF and assess safety.

METHODS

A retrospective analysis of all charts of pwCF from three CF centers in Israel, between the years 2008 and 2019. We collected BAL culture results as well as sputum cultures obtained within 1 month of the BAL sample. A meaningful yield was defined as a decision to start antibiotics, change the antibiotic regimen, hospitalize the patient for treatment, or the resolution of the problem that led to bronchoscopy (e.g., atelectasis or hemoptysis).

RESULTS

During the study years, of the 428 consecutive patient charts screened, 72 patients had 154 bronchoscopies (2.14 bronchoscopies/patient). Forty-five percent of the bronchoscopies had a meaningful clinical yield. The finding of copious sputum on bronchoscopy was strongly associated with a change in treatment (OR: 5.25, 95%CI: 2.1-13.07, p < 0.001). BAL culture results were strongly associated with a meaningful yield, specifically isolation of Aspergillus spp. (p = 0.003), Haemophilus influenza (p = 0.001). Eight minor adverse events following bronchoscopy were recorded.

CONCLUSIONS

In this multicenter retrospective analysis of bronchoscopy procedures from three CF centers, we have shown that a significant proportion of bronchoscopies led to a change in treatment, with no serious adverse events. Our findings suggest that bronchoscopy is a safe procedure that may assist in guiding treatment in some pwCF. Future studies should evaluate whether BAL-guided decision-making may also lead to a change in clinical outcomes in pwCF.

AtbFinder Diagnostic Test System Improves Optimal Selection of Antibiotic Therapy in Persons with Cystic Fibrosis

Cystic fibrosis (CF) is characterized by mutations of CFTR that lead to increased viscous secretions, bacterial colonization, and recurrent infections. Chronic Pseudomonas aeruginosa infection in persons with CF is associated with progressive and accelerated lung function decline despite aggressive antibiotic treatment. We report the management of respiratory infections in persons with CF with antibiotic therapy that was based on the recommendations of AtbFinder, a novel, rapid, culture-based diagnostic test system that employs a novel paradigm of antibiotic selection. AtbFinder mimics bacterial interactions with antibiotics at concentrations that can be achieved in affected tissues or organs and models conditions of interbacterial interactions within polymicrobial biofilms. This open-label, single-arm, investigator-initiated clinical study was designed to identify the efficacy of antibiotics selected using AtbFinder in persons with CF. Microbiological and clinical parameters were assessed following the change of antibiotic therapy to antibiotics selected with AtbFinder between January 2016 and December 2018 and retrospectively compared with clinical data collected between January 2013 and December 2015. We enrolled 35 persons with CF (33 with chronic P. aeruginosa colonization). Antibiotics selected using AtbFinder resulted in clearance of P. aeruginosa in 81.8% of subsequent cultures, decreased pulmonary exacerbations from 1.21 per patient per annum to 0, and an increase in predicted percent predicted forced expiratory volume in 1 s up to 28.4% from baseline. The number of systemic antibiotic courses used in patients after switching to the AtbFinder-selected therapy was reduced from 355 to 178. These findings describe the superiority of antibiotic regimens selected with AtbFinder compared with routine antimicrobial susceptibility testing.

Pilot study of inflammatory biomarkers in matched induced sputum and bronchoalveolar lavage of 2-year-olds with cystic fibrosis

BACKGROUND

In this pilot study, we investigated whether induced sputum (IS) could serve as a viable alternative to bronchoalveolar lavage (BAL) and yield robust inflammatory biomarkers in toddlers with cystic fibrosis (CF) featuring minimal structural lung disease.

METHODS

We collected IS, BAL (right middle lobe and lingula), and blood, and performed chest computed tomography (CT) scans from 2-year-olds with CF (N = 11), all within a single visit. Inflammatory biomarkers included 20 soluble immune mediators and neutrophil elastase (NE), as well as frequency and phenotype of T cells, monocytes/macrophages, and neutrophils.

RESULTS

At the molecular level, nine mediators showed similar levels in IS and BAL (CXCL1, CXCL8, IL-1α, IL-1RA, IL-6, CCL2, CXCL10, M-CSF, VEGF-A), four were higher in IS than in BAL (CXCL5, IL-1β, CXCL11, TNFSF10), and two were present in IS, but undetectable in BAL (IL-10, IFN-γ). Meanwhile, soluble NE had lower activity in IS than in BAL. At the cellular level, T-cell frequency was lower in IS than in BAL. Monocytes/macrophages were dominant in IS and BAL with similar frequencies, but differing expression of CD16 (lower in IS), CD115, and surface-associated NE (higher in IS). Neutrophil frequency and phenotype did not differ between IS and BAL. Finally, neutrophil frequency in IS correlated positively with air trapping.

CONCLUSIONS

IS collected from 2-year-olds with CF yields biomarkers of early airway inflammation with good agreement with BAL, notably with regard to molecular and cellular outcomes related to neutrophils and monocytes/macrophages.

Mucosal Immunity in Cystic Fibrosis

The highly complex and variable genotype-phenotype relationships observed in cystic fibrosis (CF) have been an area of growing interest since the discovery of the CF transmembrane conductance regulator (CFTR) gene >30 y ago. The consistently observed excessive, yet ineffective, activation of both the innate and adaptive host immune systems and the establishment of chronic infections within the lung, leading to destruction and functional decline, remain the primary causes of morbidity and mortality in CF. The fact that both inflammation and pathogenic bacteria persist despite the introduction of modulator therapies targeting the defective protein, CFTR, highlights that we still have much to discover regarding mucosal immunity determinants in CF. Gene modifier studies have overwhelmingly implicated immune genes in the pulmonary phenotype of the disease. In this context, we aim to review recent advances in our understanding of the innate and adaptive immune systems in CF lung disease.

Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways

Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing.

Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing. A better understanding of the ecological dynamics of this ecosystem may enable clinicians to harness these interactions and thereby improve treatment outcomes. Like all ecosystems, the CF lung microbial community develops through a series of stages, each of which may present with distinct microbial communities that generate unique host-microbe and microbe-microbe interactions, metabolic profiles, and clinical phenotypes. While insightful models have been developed to explain some of these stages and interactions, there is no unifying model to describe how these infections develop and persist. Here, we review current perspectives on the ecology of the CF airway and present the CF Ecological Succession (CFES) model that aims to capture the spatial and temporal complexity of CF lung infection, address current challenges in disease management, and inform the development of ecologically driven therapeutic strategies.

Impact of Pseudomonas aeruginosa Infection on Patients with Chronic Inflammatory Airway Diseases

Pseudomonas aeruginosa (P. aeruginosa) is a ubiquitous and opportunistic microorganism and is considered one of the most significant pathogens that produce chronic colonization and infection of the lower respiratory tract, especially in people with chronic inflammatory airway diseases such as asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and bronchiectasis. From a microbiological viewpoint, the presence and persistence of P. aeruginosa over time are characterized by adaptation within the host that precludes any rapid, devastating injury to the host. Moreover, this microorganism usually develops antibiotic resistance, which is accelerated in chronic infections especially in those situations where the frequent use of antimicrobials facilitates the selection of “hypermutator P. aeruginosa strain”. This phenomenon has been observed in people with bronchiectasis, CF, and the “exacerbator” COPD phenotype. From a clinical point of view, a chronic bronchial infection of P. aeruginosa has been related to more severity and poor prognosis in people with CF, bronchiectasis, and probably in COPD, but little is known on the effect of this microorganism infection in people with asthma. The relationship between the impact and treatment of P. aeruginosa infection in people with airway diseases emerges as an important future challenge and it is the most important objective of this review.

mSphere of Influence: a Community To Study Communities

Dominique Limoli studies polymicrobial interactions during cystic fibrosis respiratory disease. In this mSphere of Influence article, she reflects on how two papers (D. A. Hogan, S. D. Willger, E. L. Dolben, T. H. Hampton, et al., PLoS One 11:e0149998, 2016, https://doi.org/10.1371/journal.pone.0149998, and P. Jorth, B.

Dominique Limoli studies polymicrobial interactions during cystic fibrosis respiratory disease. In this mSphere of Influence article, she reflects on how two papers (D. A. Hogan, S. D. Willger, E. L. Dolben, T. H. Hampton, et al., PLoS One 11:e0149998, 2016, https://doi.org/10.1371/journal.pone.0149998, and P. Jorth, B. J. Staudinger, X. Wu, K. B. Hisert, et al., Cell Host & Microbe 18:307–319, 2015, https://doi.org/10.1016/j.chom.2015.07.006) have influenced her thinking and research direction, which aims to understand interspecies bacterial communication during airway infections. These studies highlighted for her a need for new perspectives on the pathology of chronic infections in order to improve interventions.

Regional differences in infection and structural lung disease in infants and young children with cystic fibrosis

BACKGROUND

Both infection and inflammation are critical to the progression of cystic fibrosis (CF) lung disease. Potential anatomical differences in lower airway infection, inflammation and bronchiectasis in young children with CF raise questions regarding the pathogenesis of early structural lung disease.

METHODS

A longitudinal multi-centre birth cohort study of infants newly diagnosed with CF was conducted. Paired bronchoalveolar lavage (BAL) samples were obtained from the right middle lobe (RML) and lingula bronchi. Chest computed tomography (CT) was performed biennially and analysed using the modified CF-CT scoring system.

RESULTS

One hundred and twenty-four children (0.11 - 7.0 years) contributed 527 BAL samples and underwent 388 CT chest scans. Pro-inflammatory microbes were detected in 279 BAL samples (53%), either in both lingula and RML samples (69%), in the lingula alone (24%), or in the RML alone in only 7% of samples. Overall, the prevalence of structural lung disease was greater in the setting of pro-inflammatory microbes. Although infection was less commonly isolated in the right lung, bronchiectasis was more commonly detected in the right lung compared with the left. No anatomical differences in the presence of air trapping were detected.

CONCLUSION

Overall, the detection of pro-inflammatory microbes in the lower airways was associated with increased risk of both air trapping and bronchiectasis. However, the apparent discordance between commonest sites of isolation of pro-inflammatory microbes and the anatomical site of early bronchiectasis warrants further exploration.

Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface

In human pathophysiology, the clash between microbial infection and host immunity contributes to multiple diseases. Cystic fibrosis (CF) is a classical example of this phenomenon, wherein a dysfunctional, hyperinflammatory immune response combined with chronic pulmonary infections wreak havoc upon the airway, leading to a disease course of substantial morbidity and shortened life span. Pseudomonas aeruginosa is an opportunistic pathogen that commonly infects the CF lung, promoting an accelerated decline of pulmonary function. Importantly, P. aeruginosa exhibits significant resistance to innate immune effectors and to antibiotics, in part, by expressing specific virulence factors (e.g., antioxidants and exopolysaccharides) and by acquiring adaptive mutations during chronic infection. In an effort to review our current understanding of the host-pathogen interface driving CF pulmonary disease, we discuss (i) the progression of disease within the primitive CF lung, specifically focusing on the role of host versus bacterial factors; (ii) critical, neutrophil-derived innate immune effectors that are implicated in CF pulmonary disease, including reactive oxygen species (ROS) and antimicrobial peptides (e.g., LL-37); (iii) P. aeruginosa virulence factors and adaptive mutations that enable evasion of the host response; and (iv) ongoing work examining the distribution and colocalization of host and bacterial factors within distinct anatomical niches of the CF lung.

Mucoid Pseudomonas aeruginosa and regional inflammation in the cystic fibrosis lung

BACKGROUND

Pseudomonas aeruginosa is the prominent bacterial pathogen in the cystic fibrosis (CF) lung and contributes to significant morbidity and mortality. Though P. aeruginosa strains initially colonizing the CF lung have a nonmucoid colony morphology, they often mutate into mucoid variants that are associated with clinical deterioration. Both nonmucoid and mucoid P. aeruginosa variants are often co-isolated on microbiological cultures of sputum collected from CF patients. With regional variation in bronchiectasis, tissue damage, inflammation, and microbial colonization, lobar distribution of nonmucoid and mucoid P. aeruginosa variants may impact local microenvironments in the CF lung, but this has not been well-studied.

METHODS

We prospectively collected lobe-specific bronchoalveolar lavage (BAL) fluid from a CF patient cohort (n = 14) using a standardized bronchoscopic protocol where collection was performed in 6 lobar regions. The lobar BAL specimens were plated on P. aeruginosa-selective media and proinflammatory cytokines (IL-1, TNF, IL-6 and IL-8) were measured via cytokine array. Correlations between infecting P. aeruginosa variants (nonmucoid, mucoid, or mixed-variant populations), the lobar regions in which these variants were found, and regional proinflammatory cytokine concentrations were measured.

RESULTS

P. aeruginosa mucoid and nonmucoid variants were homogenously distributed throughout the CF lung. However, infection with mucoid variants (found within single- or mixed-variant populations) was associated with significantly greater regional inflammation. The upper and lower lobes of the CF lung did not exhibit differences in inflammatory cytokine concentrations.

CONCLUSIONS

Mucoid P. aeruginosa infection is a microbial determinant of regional inflammation within the CF lung.

No benefit of longer eradication therapy of Pseudomonas aeruginosa primoinfections in pediatric cystic fibrosis

OBJECTIVE

Patients with cystic fibrosis are more susceptible than members of the general population to lung infections. Infections with Pseudomonas aeruginosa require particular attention, because they may accelerate the deterioration of lung function if not adequately treated. This study assessed the eradication rate of P. aeruginosa primoinfections, with a protocol of inhaled tobramycin and oral ciprofloxacin over a 3 months' period.

RESULTS

Retrospective single-center study from June 1st, 2007 to December 31st, 2015. Inclusion of 28 pediatric patients (11 females, 17 males), with a total of 49 primoinfections. Overall success rate of 67.3%, which is similar or even inferior to figures published in the literature.

Phenotyping and outcomes of hospitalized COPD patients using rapid molecular diagnostics on sputum samples

Background

Etiologies of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are heterogeneous. We phenotyped severe AECOPD based on molecular pathogen detection of sputum samples collected at hospitalization of COPD patients and determined their outcomes.

Methods

We phenotyped 72 sputum samples of COPD patients who were hospitalized with a primary diagnosis of AECOPD using a molecular array that detected common bacterial and viral respiratory pathogens. Based on these results, the patients were classified into positive or negative pathogen groups. The pathogen-positive group was further divided into virus or bacteria subgroups. Admission day 1 blood samples were assayed for N-terminal prohormone brain natriuretic peptide, CRP, and complete blood counts.

Results

A total of 52 patients had a positive result on the array, while 20 patients had no pathogens detected. The most common bacterial pathogen detected was Haemophilus influenzae and the most common virus was rhinovirus. The pathogen-negative group had the worse outcomes with longer hospital stays (median 6.5 vs 5 days for bacteria-positive group, P=0.02) and a trend toward increased 1-year mortality (P=0.052). The bacteria-positive group had the best prognosis, whereas the virus-positive group had outcomes somewhere in between the bacteria-positive and pathogen-negative groups.

Conclusion

Molecular diagnostics on sputum can rapidly phenotype serious AECOPD into bacteria-, virus-, or pathogen-negative groups. The bacteria-positive group appears to have the best prognosis, while pathogen-negative group has the worst. These data suggest that AECOPD is a heterogeneous event and that accurate phenotyping of AECOPD may lead to novel management strategies that are personalized and more precise.

Differences in the lower airway microbiota of infants with and without cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) lung disease commences in infancy, and understanding the role of the microbiota in disease pathogenesis is critical. This study examined and compared the lower airway microbiota of infants with and without CF and its relationship to airway inflammation in the first months of life.

METHODS

Infants newly-diagnosed with CF were recruited into a single-centre study in Melbourne, Australia from 1992 to 2001. Bronchoalveolar lavage was performed at study entry. Healthy infants undergoing bronchoscopy to investigate chronic stridor acted as controls. Quantitative microbiological culture was performed and inflammatory markers were measured contemporaneously. 16S ribosomal RNA gene analysis was performed on stored samples.

RESULTS

Thirteen bronchoalveolar samples from infants with CF and nine from control infants, collected at median ages of 1.8-months (25th-75th percentile 1.5 to 3.1-months) and 5-months (25th-75th percentile 2.9 to 8.2-months) respectively, provided 16S rRNA gene data. Bacterial biomass was positively associated with inflammation. Alpha diversity was reduced in infants with CF and between-group compositional differences were apparent. These differences were driven by increased Staphylococcus and decreased Fusobacterium and were most apparent in symptomatic infants with CF.

CONCLUSION

In CF lung disease, differences in lower airway microbial community composition and structure are established by age 6-months.

Comparison of the upper and lower airway microbiota in children with chronic lung diseases

Rationale

The lower airway microbiota is important in normal immunological development and chronic lung diseases (CLDs). Young children cannot expectorate and because of the uncertainty whether upper airway samples reflect the lower airway microbiota, there have been few longitudinal paediatric studies to date.

Objectives

To assess whether throat swabs (TS) and cough swabs (CS) are representative of the lower airway microbiota.

Methods

TS, CS, bronchoalveolar lavage and bronchial brushings were prospectively collected from 49 children undergoing fibreoptic bronchoscopy for CLDs. Bacterial DNA was extracted and the 16S rRNA gene V4 region sequenced using the Illumina MiSeq.

Results

5.97 million high quality reads were obtained from 168 samples (47 TS, 37 CS, 42 BALF and 42 bronchial brushings). CS sequenced poorly. At a community level, no difference in alpha diversity (richness, evenness or Shannon Diversity Index) was seen between lower airway samples and TS (P > 0.05). Less than 6.31% of beta diversity variation related to sampling method for TS (P = 0.001). Variation between pathologies and individual patients was greater (20%, 54% respectively P ≤ 0.001) than between TS and lower airway samples. There was strong correlation in the relative abundance of genera between samples (r = 0.78, P < 0.001). Similarity between upper and lower airway samples was observed to be less for individuals where one sample type was dominated by a single organism.

Conclusions

At the community structure level, TS correlate with lower airway samples and distinguish between different CLDs. TS may be a useful sample for the study of the differences in longitudinal changes in the respiratory microbiota between different CLDs. Differences are too great however for TS to be used for clinical decision making.

The airway microbiota in early cystic fibrosis lung disease

Infection plays a critical role in the pathogenesis of cystic fibrosis (CF) lung disease. Over the past two decades, the application of molecular and extended culture-based techniques to microbial analysis has changed our understanding of the lungs in both health and disease. CF lung disease is a polymicrobial disorder, with obligate and facultative anaerobes recovered alongside traditional pathogens in varying proportions, with some differences observed to correlate with disease stage. While healthy lungs are not sterile, differences between the lower airway microbiota of individuals with CF and disease-controls are already apparent in childhood. Understanding the evolution of the CF airway microbiota, and its relationship with clinical treatments and outcome at each disease stage, will improve our understanding of the pathogenesis of CF lung disease and potentially inform clinical management. This review summarizes current knowledge of the early development of the respiratory microbiota in healthy children and then discusses what is known about the airway microbiota in individuals with CF, including how it evolves over time and where future research priorities lie.

Is bronchoscopy an obsolete tool in cystic fibrosis? The role of bronchoscopy in cystic fibrosis and its clinical use

Cystic fibrosis (CF) is a progressive life threatening multisystem genetic disease which affects the CF transmembrane conductance regulator channel. Respiratory causes remain the most common mortality in CF. With the onset of newborn screening, initiating treatments both for prophylaxis and disease management, optimizing nutritional support, and developing therapies targeting CF transmembrane conductance regulator protein, this has significantly changed the face of managing this devastating disease. Bronchoscopy and related procedures such as bronchoalveolar lavage (BAL), transbronchial biopsies, and protected brush sampling have been looked at in the management of CF as patients with CF continue to live longer with the help of newer therapies, the microbiome in the lung becomes less diverse along with increased occurrences for noninfectious causes of airway diseases. Though bronchoscopy has been used in conjunction with other modalities such as computed tomography and sputum induction providing a better understanding of the progression of the disease, it still remains valuable in the diagnosis and management of CF.

Dysregulated Chemokine Signaling in Cystic Fibrosis Lung Disease: A Potential Therapeutic Target

CF lung disease is characterized by a chronic and non-resolving activation of the innate immune system with excessive release of chemokines/cytokines including IL-8 and persistent infiltration of immune cells, mainly neutrophils, into the airways. Chronic infection and impaired immune response eventually lead to pulmonary damage characterized by bronchiectasis, emphysema, and lung fibrosis. As a complete knowledge of the pathways responsible for the exaggerated inflammatory response in CF lung disease is lacking, understanding these pathways could reveal new therapeutic targets, and lead to novel treatments. Therefore, there is a strong rationale for the identification of mechanisms and pathways underlying the exaggerated inflammatory response in CF lung disease. This article reviews the role of inflammation in the pathogenesis of CF lung disease, with a focus on the dysregulated signaling involved in the overexpression of chemokine IL-8 and excessive recruitment of neutrophils in CF airways. The findings suggest that targeting the exaggerated IL-8/IL-8 receptor (mainly CXCR2) signaling pathway in immune cells (especially neutrophils) may represent a potential therapeutic strategy for CF lung disease.

Clinical implications of Pseudomonas aeruginosa location in the lungs of patients with cystic fibrosis

WHAT IS KNOWN AND OBJECTIVE

Pseudomonas aeruginosa is the leading cause of lung infection in patients with cystic fibrosis (CF) and is associated with significant morbidity and mortality. Antibiotics are regarded as the foundational pharmacological treatment for the suppressive management of chronic P. aeruginosa infections and to eradicate the first infection by P. aeruginosa. Inhalation remains a preferred route for drug administration, providing direct access to the site of infection while minimizing systemic side effects. Effective suppressive management of P. aeruginosa infections, however, requires an understanding of the location of the bacteria in the lungs and consideration of the factors that could limit access of the inhaled antibiotic to the infected area. This review provides a systematic assessment of the scientific literature to gain insight into the location of P. aeruginosa in the lungs of patients with CF and its clinical implications. The characteristics of antibiotic inhalation systems are also discussed in this context.

METHODS

We reviewed evidence-based literature from both human and animal studies in which P. aeruginosa lung location was reported. Relevant publications were identified through a screening strategy and summarized by reported P. aeruginosa location.

RESULTS AND DISCUSSION

Most areas of the conductive and respiratory zones of the lungs are susceptible to P. aeruginosa colonization. Deposition of an inhaled antibiotic is dependent on the device and formulation characteristics, as well as the ability of the patient to generate sufficient inhaled volume. As patients with CF often experience a decline in lung function, the challenge is to ensure that the inhaled antibiotic can be delivered throughout the bronchial tree.

WHAT IS NEW AND CONCLUSION

An effective drug delivery system that can target P. aeruginosa in both the respiratory and conductive zones is required. The chosen inhalation device should also offer a drug formulation that can be quickly and effectively delivered to specific lung locations, with minimal inspiratory effort from the patient.

Induced sputum to detect lung pathogens in young children with cystic fibrosis

INTRODUCTION

Induced sputum sampling holds promise as a method for obtaining samples representative of the lower airways in young children. Collection of induced sputum samples in young children differs from older children and adults' as pharyngeal suctioning is often required. Our aim was to determine the sensitivity and specificity of induced sputum with and without airway clearance techniques to detect lower airway pathogens in children less than age 7 with cystic fibrosis.

METHODS

Microbiological culture results were compared between 61 paired induced sputum and bronchoalveolar lavage fluid samples from young children with cystic fibrosis. The first cohort received no airway clearance and the second cohort received airway clearance. Induced sputum was sampled within 7 days of bronchoscopy.

RESULTS

Median age (range) of participants was 3.3 years (0.9-6.7). Sensitivity and specificity (95%CI) of induced sputum was 36.8% (16.3, 61.6), and 69% (52.9, 82.4), respectively (N = 61). In subgroup analysis, induced sputum with (N = 31) and without airway clearance (N = 30) demonstrated sensitivity of 50% (15.7, 84.3) and 27.3% (6.0, 61.0), respectively, and specificity of 60.9% (38.5, 80.3), and 78.9% (54.4, 93.9), respectively.

CONCLUSION

Induced sputum is not highly sensitive or specific as routine surveillance for detection of lower airway pathogens in young children with cystic fibrosis. Pediatr Pulmonol. 2017;52:182-189. © 2016 Wiley Periodicals, Inc.

Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis

Background

Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics.

Methods

BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening. BALF was analyzed for total bacterial load by qPCR and for bacterial community composition by 16S ribosomal RNA sequencing. Clinical characteristics and standard BALF and NP culture results were recorded over five years of longitudinal follow-up.

Results

12 BALF samples were collected from 8 infants with CF. Streptococcus, Burkholderia, Prevotella, Haemophilus, Porphyromonas, and Veillonella had the highest median relative abundance in infant CF BALF. Two of the 3 infants with repeat BALF had changes in their microbial communities over six months (Morisita-Horn diversity index 0.36, 0.38). Although there was excellent percent agreement between standard NP and BALF cultures, these techniques did not routinely detect all bacteria identified by sequencing.

Conclusions

BALF in asymptomatic CF infants contains complex microbiota, often missed by traditional culture of airway secretions. Anaerobic bacteria are commonly found in the lower airways of CF infants.

Infection and inflammation in induced sputum from preschool children with chronic airways diseases

BACKGROUND

We hypothesized airway inflammation can be detected non-invasively by induced sputum (IS) or peripheral blood eosinophilia, and IS can detect bacterial and viral infection in preschool children with airway disease, with results comparable to broncho-alveolar lavage (BAL).

METHODS

Preschool children with cystic fibrosis, recurrent wheeze, or wet cough underwent IS with nebulized hypertonic saline, chest physiotherapy, and oropharyngeal suction. Samples were analyzed for inflammation by cytology and bacterial culture, viral detection by PCR. Results were compared to BAL and blood in a sub-group undergoing clinically indicated bronchoscopy.

RESULTS

64 children (median age 33 [7-76] months) underwent IS without adverse events. IS was obtained from 61/64. Twenty out of sixty-four underwent BAL and IS, no IS was obtained in 2/23. Thirteen out of twenty-one (62%) had matching bacteria and viruses, 4/21 had positive BAL bacterial growth with negative IS, and 3/21 had negative BAL growth with positive IS. 67% of sputum samples were processed for cytology, 46% had <80% squamous cells; the proportion of squamous cells reduced with increasing age (r = -0.55, P < 0.01). IS was significantly more neutrophilic and less eosinophilic than BAL; 2/21 IS samples contained eosinophils compared to 17/23 BAL. There was a positive correlation between blood and BAL eosinophilia (r = 0.75, P < 0.01).

CONCLUSION

IS from preschool children can be used to assess infection. BAL and IS culture concurred in approximately two-thirds. However, inflammation was measureable in only one-third of IS samples and the cell differential was predominantly neutrophilic compared to BAL. Blood eosinophils may provide a better reflection of lower airway eosinophilia in this age group. Pediatr Pulmonol. 2016;51:778-786. © 2015 WileyPeriodicals, Inc.

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease

Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV₁>50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease.

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation

The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1) with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from different patients, providing a poignant example of parallel evolution. Together, this combined clinical-genomic approach provides a high-resolution portrait of the fungal microbiome of cystic fibrosis patient lungs and identifies a genetic basis of pathogen adaptation.

Microbial cells vastly outnumber human cells in our bodies, yet we are only beginning to understand how these microbes influence human health and disease. One disease for which microbial communities are especially important is cystic fibrosis, where persistent lung infections can be lethal. Fungi are associated with poor respiratory function, but how fungal communities change with disease progression or treatment remains enigmatic. Here, we assess the dynamics of fungal communities by combining high-throughput sequencing of sputum samples from 28 patients with detailed analysis of phenotypes and genotypes of 1,603 fungal isolates. We found stable communities dominated by Candida and Aspergillus, and diversity in traits important for host adaptation. Antifungal drug resistance varied largely between species, while morphogenesis varied within species. For Candida species, the capacity to transition between yeast and filaments is a key virulence trait that is normally regulated by inducing cues, however, 28 isolates grew as filaments without such cues. Filamentation was due to loss-of-function mutations in the transcriptional regulator NRG1 in most isolates, which conferred resistance to the filament-repressive effects of a common bacterial pathogen. This work provides a portrait of the fungal microbiome associated with a lethal disease, and illuminates a genetic basis of pathogen adaptation.

Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough

Identification of bacteria causing lower-airway infections is important to determine appropriate antimicrobial therapy. Flexible bronchoscopy with bronchoalveolar lavage (BAL) is used to obtain lower-airway specimens in young children. The first lavage (lavage-1) is typically used for bacterial culture. However, no studies in children have compared the detection of cultivable bacteria from sequential lavages of the same lobe. BAL fluid was collected from two sequential lavages of the same lobe in 79 children enrolled in our prospective studies of chronic cough. The respiratory bacteria Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Haemophilus parainfluenzae were isolated and identified using standard published methods. H. influenzae was differentiated from Haemophilus haemolyticus using PCR assays. Lower-airway infection was defined as ≥ 104 c.f.u. ml- 1 BAL fluid. We compared cultivable bacteria from lavage-1 with those from the second lavage (lavage-2) using the κ statistic. Lower-airway infections by any pathogen were detected in 46% of first lavages and 39% of second lavages. Detection was similar in both lavages for all pathogens; the κ statistic was 0.7-0.8 for all bacteria except H. parainfluenzae. Of all infections detected in either lavage, 90% were detected in lavage-1 and 78  in lavage-2. However, culture of lavage-2 identified infections that would have been missed in 8% of children, including infections by additional Streptococcus pneumoniae serotypes. Our findings support the continued use of lavage-1 for bacterial culture; however, culture of lavage-2 may yield additional identifications of bacterial pathogens in lower-airway infections.

Biomarkers in Paediatric Cystic Fibrosis Lung Disease

Biomarkers in cystic fibrosis are used i. for the measurement of cystic fibrosis transmembrane regulator function in order to diagnose cystic fibrosis, and ii. to assess aspects of lung disease severity (e.g. inflammation, infection). Effective biomarkers can aid disease monitoring and contribute to the development of new therapies. The tests of cystic fibrosis transmembrane regulator function each have unique strengths and weaknesses, and biomarkers of inflammation, infection and tissue destruction have the potential to enhance the management of cystic fibrosis through the early detection of disease processes. The development of biomarkers of cystic fibrosis lung disease, in particular airway inflammation and infection, is influenced by the challenges of obtaining relevant samples from infants and children for whom early detection and treatment of disease might have the greatest long term benefits.

Use of ibuprofen to assess inflammatory biomarkers in induced sputum: Implications for clinical trials in cystic fibrosis

BACKGROUND

High-dose ibuprofen (HDI) is a clinically beneficial anti-inflammatory regimen that may be a useful reagent to study induced sputum inflammatory marker changes over short study periods appropriate for early-phase CF clinical trials.

METHODS

We conducted a 28-day, open-label, randomized, controlled trial among 72 clinically stable CF subjects (FEV1≥40% predicted) randomized to HDI or routine care that assessed IL-6, IL-8, TNF-α, IL-1-β, free neutrophil elastase, and white cell counts with differentials change from baseline in induced sputum.

RESULTS

IL-6 was the only biomarker with significant within-group change: 0.13 log10 pg/mL mean reduction among ibuprofen-treated subjects (p=0.04); and no change in the control group. IL-6 change between groups was statistically significant (p=0.024). No other inflammatory biomarker differences were observed between groups after 28 days.

CONCLUSION

Although we studied only one agent, HDI, these results suggest that one month may be inadequate to assess anti-inflammatory candidates using markers from induced sputum.

The findings of a clinical surveillance bronchoalveolar lavage programme in pre-school patients with cystic fibrosis

BACKGROUND

Evidence suggests infection is present in the lower airways of young children with cystic fibrosis (CF), even when clinically stable. Oropharyngeal samples (OPS) are typically used for airway surveillance in these children but have been shown to have low positive predictive values and low sensitivity in detecting lower airway infection when compared with the reference standard, bronchoalveolar lavage (BAL).

METHODS

The aim of this study was to determine the prevalence of pathogens in lower airway samples detected as part of a pilot clinical BAL surveillance programme, in young children aged from one to six years old, and to ascertain if their detection resulted in a change in treatment.

RESULTS

During the study 78 bronchoscopies were performed on 38 patients. The average age at the time of bronchoscopy was 2.7 years (range 0.3-7.0 year). A significant organism was detected in 58 (74.5%) BALs. Haemophilus influenzae was detected in 27 (34.6%) samples, 16 (20.5%) samples had Staphylococcus aureus, and nine (11.5%) had Pseudomonas aeruginosa. Change in treatment occurred after 46 (58.9%) BALs.

CONCLUSIONS

This study suggests that, in young non-expectorating children with CF, routine surveillance bronchoscopy allows the detection of significant lower airway pathogens and provides the opportunity for targeted treatment of sub-clinical infection.

How to use: bacterial cultures in diagnosing lower respiratory tract infections in cystic fibrosis

Respiratory infections are the leading cause of morbidity and mortality in cystic fibrosis. Certain bacteria, such as Pseudomonas aeruginosa, are associated with a worse clinical outcome than others, but can be completely eradicated if identified and treated early. The diagnosis of lower respiratory tract infections can be challenging in the non-expectorating patient, in whom upper airway samples, such as cough swabs, are a surrogate for lower airway sampling. However, the results of these often do not fit with the clinical picture, presenting a management dilemma. Frequently, clinicians are faced with a negative culture result in a progressively symptomatic patient and vice versa. When judging the clinical significance of a positive upper airway culture result in an asymptomatic patient, it is important to consider the prognostic significance of the organism cultured. Given that the reported sensitivity of upper airway swabs (which includes throat swabs) is variable, ranging from 35.7% to 71% for Pseudomonas aeruginosa, 50% to 86% for Staphylococcus aureus and 11% to 92% for Haemophilus influenza, upper airway samples may fail to identify lower airway infections. Therefore, in symptomatic children, a repeatedly negative upper airway swab should not be considered as reassuring, and alternative sampling methods, such as induced sputum or bronchoalveolar lavage, should be considered. Here we use some examples of common scenarios to illustrate how best to use bacterial cultures to aid management decisions in cystic fibrosis.

Development of an ex vivo porcine lung model for studying growth, virulence, and signaling of Pseudomonas aeruginosa

Research into chronic infection by bacterial pathogens, such as Pseudomonas aeruginosa, uses various in vitro and live host models. While these have increased our understanding of pathogen growth, virulence, and evolution, each model has certain limitations. In vitro models cannot recapitulate the complex spatial structure of host organs, while experiments on live hosts are limited in terms of sample size and infection duration for ethical reasons; live mammal models also require specialized facilities which are costly to run. To address this, we have developed an ex vivo pig lung (EVPL) model for quantifying Pseudomonas aeruginosa growth, quorum sensing (QS), virulence factor production, and tissue damage in an environment that mimics a chronically infected cystic fibrosis (CF) lung. In a first test of our model, we show that lasR mutants, which do not respond to 3-oxo-C₁₂-homoserine lactone (HSL)-mediated QS, exhibit reduced virulence factor production in EVPL. We also show that lasR mutants grow as well as or better than a corresponding wild-type strain in EVPL. lasR mutants frequently and repeatedly arise during chronic CF lung infection, but the evolutionary forces governing their appearance and spread are not clear. Our data are not consistent with the hypothesis that lasR mutants act as social “cheats” in the lung; rather, our results support the hypothesis that lasR mutants are more adapted to the lung environment. More generally, this model will facilitate improved studies of microbial disease, especially studies of how cells of the same and different species interact in polymicrobial infections in a spatially structured environment.

Single-cell control of initial spatial structure in biofilm development using laser trapping

Biofilms are sessile communities of microbes that are spatially structured by an embedding matrix. Biofilm infections are notoriously intractable. This arises, in part, from changes in the bacterial phenotype that result from spatial structure. Understanding these interactions requires methods to control the spatial structure of biofilms. We present a method for growing biofilms from initiating cells whose positions are controlled with single-cell precision using laser trapping. The native growth, motility, and surface adhesion of positioned microbes are preserved, as we show for model organisms Pseudomonas aeruginosa and Staphylococcus aureus. We demonstrate that laser-trapping and placing bacteria on surfaces can reveal the effects of spatial structure on bacterial growth in early biofilm development.

Multi-modality monitoring of cystic fibrosis lung disease: the role of chest computed tomography

Cystic fibrosis [CF] lung disease is characterized by progressive bronchiectasis and small airways disease. To monitor CF lung disease traditionally spirometry has been the most important modality. In addition to spirometry chest radiography was used to monitor progression of structural lung abnormalities. However, the importance of chest radiography in disease management has been limited due to its poor sensitivity and specificity to detect disease progression. Over the last decade chest CT has become the gold standard for monitoring the severity and progression of bronchiectasis. Small airways disease can be monitored using spirometry, multiple breath washout techniques, and chest CT. In modern CF-care a multi-modality approach is needed to monitor CF lung disease and to personalize treatment for the needs of the patient. When state-of-the-art low dose bi-annual chest CT protocols are used radiation risk is considered to be low. In between chest CT imaging, physiologic measures are important to obtain for monitoring. Stratification of monitoring protocols based on the risk profile of the patient can help us in the future to better care for people with CF.

Challenges and limitations of testing efficacy of aerosol device delivery in young children

An increasing number of medical conditions are chronically or acutely managed with some form of aerosolized therapy. Due to the benefit of directly administering medications to the intended site of action, there is great interest in evaluating treatments for aerosol use. One of the major challenges in selecting and testing new drug-device combinations in children is the uncertainty regarding the appropriate outcome measure to choose. In studies involving adult patients, typically exacerbations of disease or airflow obstruction are assessed as endpoints in drug trials or device assessment. However, in young children, choosing endpoints to assess efficacy is difficult due to the potential lack of sensitive, noninvasive endpoints that are easily performed across sites. In this review, we discuss the challenges and limitations of selecting clinical endpoints for drug-device trials in the youngest population, with a focus on novel emerging technologies. This article provides an overview of preschool and infant pulmonary function testing, multiple-breath washout, imaging techniques including computed tomography and magnetic resonance imaging, flexible bronchoscopy in children, mucociliary clearance scans, and exhaled breath condensate.

Novel end points for clinical trials in young children with cystic fibrosis

Cystic fibrosis (CF) lung disease commences early in the disease progression and is the most common cause of mortality. While new CF disease-modifying agents are currently undergoing clinical trial evaluation, the implementation of such trials in young children is limited by the lack of age-appropriate clinical trial end points. Advances in infant and preschool lung function testing, imaging of the chest and the development of biochemical biomarkers have led to increased possibility of quantifying mild lung disease in young children with CF and objectively monitoring disease progression over the course of an intervention. Despite this, further standardization and development of these techniques is required to provide robust objective measures for clinical trials in this age group.

Bronchoscopy contributes to the clinical management of indigenous children newly diagnosed with bronchiectasis

BACKGROUND

Some pediatric centers perform flexible bronchoscopy (FB) routinely when bronchiectasis is suspected. However, there are no published data evaluating this practice.

OBJECTIVE

To evaluate the contribution of FB and bronchoalveolar lavage (BAL) to the initial management of children newly diagnosed with non-cystic fibrosis (CF) bronchiectasis.

METHOD

We examined FB and BAL data collected prospectively in 56 children aged 0.8-9.8 years during initial investigations for bronchiectasis. Investigations contributed to management if any of the following were identified: (1) airway obstruction requiring additional intervention, (2) lower airway eosinophilia (BAL eosinophils >2.5%), or (3) BAL fluid culture >10(4) colony-forming units/ml of a respiratory bacterial pathogen requiring change from usual empiric antibiotics.

RESULTS

Of the 56 children undergoing FB, there were 25 occasions in 23 children where these procedures altered empiric treatment. Lower airway eosinophilia was identified in 19 (34%) children, BAL microbiology results led to antibiotic changes in 5 (9%) and an unsuspected foreign body was found in another (2%). Strongyloides serology was performed in 38 children, including 12 of the 19 with airway eosinophilia, and was positive in 5 of these 12 children (42%).

CONCLUSION

Contrary to some expert recommendations that FB should only be performed when bronchiectasis is localized, our data suggest that FB with BAL should at least be included in the initial investigations of Indigenous children with non-CF bronchiectasis.

Clearance of initial mucoid Pseudomonas aeruginosa in patients with cystic fibrosis

BACKGROUND

Accelerated lung function decline in cystic fibrosis (CF) is associated with mucoid Pseudomonas aeruginosa infection. Recent data suggest that mucoid P. aeruginosa may amenable to elimination from the airway. We aim to determine whether the initiation of an aggressive antibiotic eradication regimen upon initial discovery of mucoid P. aeruginosa in the CF airway could be successful in clearing the organism from the CF lung.

METHODS

We performed a retrospective analysis of patients with CF who demonstrated new growth of mucoid P. aeruginosa in an airway culture between January 2003 and December 2008. The primary endpoint was clearance of mucoid P. aeruginosa, based upon the Leeds criteria, with no further growth of mucoid P. aeruginosa cultures within 12 months of the initial discovery and treatment. Factors associated with successful clearance were also evaluated.

RESULTS

Forty-eight of 355 patients with CF had a new diagnosis of mucoid P. aeruginosa during the study period; 15 patients underwent an eradication attempt, while 33 patients received no increase in therapy. We observed clearance of mucoid P. aeruginosa in 73.3% of patients undergoing an eradication attempt, whereas 36.6% of those that did not undergo attempted eradication cleared the organism at 1 year (P < 0.05). Prolonged mucoid P. aeruginosa airway clearance (>24 months) for mucoid P. aeruginosa was seen in 60.0% in subjects undergoing eradication compared to 21.2% (P = 0.02) in control patients. At the study conclusion, lung function was greater in subjects who underwent an eradication attempt than in patients who did not undergo an eradication attempt (FEV(1) %: 91.7% vs. 75.0%, P = 0.04).

CONCLUSIONS

Clearance of initial mucoid P. aeruginosa from the airways of select patients with CF is possible with current antibiotic regimens, and the attempt may be associated with improved lung function.

Impact of recent antibiotics on nasopharyngeal carriage and lower airway infection in Indigenous Australian children with non-cystic fibrosis bronchiectasis

Indigenous Australian children have increased rates of bronchiectasis. Despite a lack of high-level evidence on effectiveness and antibiotic resistance, these children often receive long-term antibiotics. In this study, we determined the impact of recent macrolide (primarily azithromycin) and β-lactam antibiotic use on nasopharyngeal colonisation, lower airway infection (>10(4) CFU/mL of bronchoalveolar lavage fluid culture) and antibiotic resistance in non-typeable Haemophilus influenzae (NTHi), Streptococcus pneumoniae and Moraxella catarrhalis isolates from 104 Indigenous children with radiographically confirmed bronchiectasis. Recent antibiotic use was associated with significantly reduced nasopharyngeal carriage, especially of S. pneumoniae in 39 children who received macrolides [odds ratio (OR)=0.22, 95% confidence interval (CI) 0.08-0.63] and 26 children who received β-lactams (OR=0.07, 95% CI 0.01-0.32), but had no significant effect on lower airway infection involving any of the three pathogens. Children given macrolides were significantly more likely to carry (OR=4.58, 95% CI 1.14-21.7) and be infected by (OR=8.13, 95% CI 1.47-81.3) azithromycin-resistant S. pneumoniae. Children who received β-lactam antibiotics may be more likely to have lower airway infection with β-lactamase-positive ampicillin-resistant NTHi (OR=4.40, 95% CI 0.85-23.9). The risk of lower airway infection by antibiotic-resistant pathogens in children receiving antibiotics is of concern. Clinical trials to determine the overall benefit of long-term antibiotic therapy are underway.

Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples

Barcoded amplicon sequencing is rapidly becoming a standard method for profiling microbial communities, including the human respiratory microbiome. While this approach has less bias than standard cultivation, several steps can introduce variation including the type of DNA extraction method used. Here we assessed five different extraction methods on pediatric bronchoalveolar lavage (BAL) samples and a mock community comprised of nine bacterial genera to determine method reproducibility and detection limits for these typically low complexity communities. Additionally, using the mock community, we were able to evaluate contamination and select a relative abundance cut-off threshold based on the geometric distribution that optimizes the trade off between detecting bona fide operational taxonomic units and filtering out spurious ones. Using this threshold, the majority of genera in the mock community were predictably detected by all extraction methods including the hard-to-lyse Gram-positive genus Staphylococcus. Differences between extraction methods were significantly greater than between technical replicates for both the mock community and BAL samples emphasizing the importance of using a standardized methodology for microbiome studies. However, regardless of method used, individual patients retained unique diagnostic profiles. Furthermore, despite being stored as raw frozen samples for over five years, community profiles from BAL samples were consistent with historical culturing results. The culture-independent profiling of these samples also identified a number of anaerobic genera that are gaining acceptance as being part of the respiratory microbiome. This study should help guide researchers to formulate sampling, extraction and analysis strategies for respiratory and other human microbiome samples.

Spatial distribution of microbial communities in the cystic fibrosis lung

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.

Airway microbiology and host defences in paediatric non-CF bronchiectasis

Bronchiectasis in children without cystic fibrosis is most common in socioeconomically disadvantaged communities. Recurrent pneumonia in early childhood and defective pulmonary defences are important risk factors. These help establish a 'vicious cycle' of impaired mucociliary clearance, infection, airway inflammation and progressive lung injury. Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis and Pseudomonas aeruginosa are the main infecting pathogens. H. influenzae predominates across all ages, while P. aeruginosa is found in older children with advanced disease. It is uncertain whether viruses and upper airway commensal bacteria play an important aetiological role. Overall, the microbiological data are limited however and there are difficulties obtaining reliable respiratory specimens from young children. Bronchiectasis is a complex disorder resulting from susceptibility to pulmonary infection and poorly regulated respiratory innate and adaptive immunity. Airway inflammatory responses are excessive and persist, even once infection is cleared. Improved specimen collection, molecular techniques and biomarkers are needed to enhance management.

Monocytes from children with clinically stable cystic fibrosis show enhanced expression of Toll-like receptor 4

Lung disease in patients with cystic fibrosis (CF) is characterized by recurrent bacterial respiratory infections and intense airway inflammation. Pattern recognition receptors such as Toll-like receptor 2 (TLR2) and TLR4 identify bacterial pathogens and activate the innate immune response. We therefore hypothesized that increased expression of these receptors would be found on circulating immune cells from children with CF. A cohort of 66 young children (median age 3 years) with CF was studied and compared to both healthy controls (n = 14) and children without CF who were being investigated for recurrent respiratory infections (non-CF disease controls; n = 17) of a similar age. Surface expression of TLR2 and TLR4 on peripheral blood monocytes was analyzed using flow cytometry. TLR4 expression was significantly higher in patients with CF compared to healthy controls (P = 0.017) and non-CF disease controls (P = 0.025) but did not vary according to the presence or absence of pulmonary infection with Gram-negative or Gram-positive bacteria (P = 0.387) in the CF group. In contrast, TLR2 expression was similar across all three study groups (P = 0.930). The increased surface expression of TLR4 seen in young children with CF appears to be related to having CF per se and not related to current pulmonary infection.

Can mucoid Pseudomonas aeruginosa be eradicated in children with cystic fibrosis?

Pseudomonas aeruginosa (PsA) is the most common pathogen to cause chronic lung infection in children with cystic fibrosis (CF), and is associated with an increase in both morbidity and mortality. Whilst the non-mucoid strain can be eradicated, it is believed that mucoid PsA is difficult, if not impossible, to eradicate. We hypothesized that with modern and aggressive antibiotic regimes, mucoid PsA can be eradicated in children with CF. We investigated this hypothesis through a retrospective review of respiratory tract cultures of children with CF at The Royal Brompton Hospital, London. Children aged under 16 with a confirmed diagnosis of CF and mucoid PsA on respiratory tract culture during a defined 9-year period were eligible for inclusion. Respiratory tract culture results were followed up for each patient to establish whether children remained infected with mucoid PsA and specifically to identify clearance of infection. Factors which may have been associated with persistence or clearance were also sought. One hundred sixteen children had the minimum dataset, and of these patients 67 (58%) cleared mucoid PsA for more than 1 year. Of the 67 patients who cleared mucoid PsA for more than 1 year, 38 (57%) patients remained clear of mucoid PsA at the last available culture (median 30, range 2-106 clear cultures, and median 55, 12-103 months clear). We conclude that isolation of mucoid PsA does not necessarily equate to lifelong infection. We suggest that trials of eradication of mucoid PsA at first isolation are required.

Pulmonary exacerbations in cystic fibrosis with negative bacterial cultures

BACKGROUND

Pulmonary exacerbations are a major cause of morbidity in cystic fibrosis (CF) and likely contribute to lung function decline. Exacerbations are often associated with characteristic airway bacteria [CF related bacteria (CFRB)]. However, some patients do not have CFRB detected by culture during exacerbations.

OBJECTIVES

We sought to determine the proportion of airway cultures negative for CFRB during pulmonary exacerbations, and to characterize patients who were CFRB-negative versus CFRB-positive.

METHODS

We performed a retrospective study of patients with CF admitted for a pulmonary exacerbation. Patients were classified as CFRB-positive or CFRB-negative based on admission airway cultures. Demographics, clinical presentation, lung function, history of chronic Pseudomonas aeruginosa infection and improvement in lung function with treatment were compared between groups.

MAIN RESULTS

There were 672 admissions for exacerbation involving 211 patients over 5 years. Seventeen percent were classified as CFRB-negative. Forty-one percent of bronchoalveolar lavage (BAL), 32% of throat and 10% of sputum samples were CFRB-negative. Among patients capable of expectorating sputum, the CFRB-negative group was younger, less likely to have chronic P. aeruginosa, had higher lung function and body mass index (BMI), and had a lower systemic inflammatory response on admission compared to those with CFRB-positive cultures. The two groups had similar numbers of patients with three or more signs and symptoms of a pulmonary exacerbation (88% vs. 92%). Both groups returned to baseline lung function following treatment.

CONCLUSIONS

A significant number of patients with CF and pulmonary exacerbation did not have typical CFRB detected by culture. Patients without CFRB still had characteristic signs and symptoms of pulmonary exacerbation and responded to treatment. Understanding the causes of illness in these patients may improve the diagnosis and treatment of pulmonary exacerbations in CF.

Monitoring respiratory disease severity in cystic fibrosis

Measurements of disease severity provide a guide for the physician to tailor therapies, for the patient and family to gauge progress, and are required for clinical trials. For many respiratory diseases, including cystic fibrosis, sensitive, noninvasive measurements are few, and some of those that are available are applicable only to certain subgroups of patients or lack sufficient sensitivity. We discuss currently available measurements in 4 groups: physiology, infection, inflammation, and radiology. For each group we highlight strengths and weaknesses, ask how we could improve upon these, and provide details of alternative methods.

TLR-4-mediated innate immunity is reduced in cystic fibrosis airway cells

Airway epithelial cells contribute to the inflammatory response of the lung, and their innate immune response is primarily mediated via Toll-like receptor (TLR) signaling. Cystic fibrosis (CF) airways are chronically infected with Pseudomonas aeruginosa, suggesting a modified immune response in CF. We investigated the TLR-4 expression and the inflammatory profile (IL-8 and IL-6 secretion) in CF bronchial epithelial cell line CFBE41o- and its CF transmembrane ion condcutance regulator (CFTR)-corrected counterpart grown under air-liquid interface conditions after stimulation with lipopolysaccharide (LPS) from gram-negative bacteria. In CFTR-corrected cells, IL-8 and IL-6 secretions were constitutively activated but significantly increased after LPS stimulation compared with CFBE41o-. Blocking TLR-4 by a specific antibody significantly inhibited IL-8 secretion only in CFTR-corrected cells. Transfection with specific siRNA directed against TLR-4 mRNA significantly reduced the response to LPS in both cell lines. Fluorescence-activated cell sorter analysis revealed significantly higher levels of TLR-4 surface expression in CFTR-corrected cells. In histologic lung sections of patients with CF, the TLR-4 expression in the bronchial epithelium was significantly reduced compared with healthy control subjects. In CF the loss of CFTR function appears to decrease innate immune responses, possibly by altering the expression of TLR-4 on airway epithelial cells. This may contribute to chronic bacterial infection of CF airways.

Lung disease at diagnosis in infants with cystic fibrosis detected by newborn screening

RATIONALE

The promise of newborn screening (NBS) for cystic fibrosis (CF) has not been fully realized, and the extent of improvement in respiratory outcomes is unclear. We hypothesized that significant lung disease was present at diagnosis.

OBJECTIVES

To determine the extent of lung disease in a geographically defined population of infants with CF diagnosed after detection by NBS.

METHODS

Fifty-seven infants (median age, 3.6 mo) with CF underwent bronchoalveolar lavage and chest computed tomography (CT) using a three-slice inspiratory and expiratory protocol.

MEASUREMENTS AND MAIN RESULTS

Despite the absence of respiratory symptoms in 48 (84.2%) of infants, a substantial proportion had lung disease with bacterial infection detected in 12 (21.1%), including Staphylococcus aureus (n = 4) and Pseudomonas aeruginosa (n = 3); neutrophilic inflammation (41. 4 x 10(3) cells/ml representing 18.7% of total cell count); proinflammatory cytokines, with 44 (77.2%) having detectable IL-8; and 17 (29.8%) having detectable free neutrophil elastase activity. Inflammation was increased in those with infection and respiratory symptoms; however, the majority of those infected were asymptomatic. Radiologic evidence of structural lung disease was common, with 46 (80.7%) having an abnormal CT; 11 (18.6%) had bronchial dilatation, 27 (45.0%) had bronchial wall thickening, and 40 (66.7%) had gas trapping. On multivariate analysis, free neutrophil elastase activity was associated with structural lung disease. Most children with structural lung disease had no clinically apparent lung disease.

CONCLUSIONS

These data support the need for full evaluation in infancy and argue for new treatment strategies, especially those targeting neutrophilic inflammation, if the promise of NBS for CF is to be realized.