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Einarsson GG, Sherrard LJ, Hatch JE, Zorn B, Johnston E, McGettigan C, O'Neill K, Gilpin DF, Downey DG, Murray M, Lavelle G, McElvaney G, Wolfgang MC, Boucher R, Muhlebach MS, Bradbury I, Elborn JS, Tunney MM. Longitudinal changes in the cystic fibrosis airway microbiota with time and treatment. J Cyst Fibros 2024; 23:252-261. [PMID: 38158284 DOI: 10.1016/j.jcf.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Whether there is any benefit in integrating culture-independent molecular analysis of the lower airway microbiota of people with cystic fibrosis into clinical care is unclear. This study determined the longitudinal trajectory of the microbiota and if there were microbiota characteristics that corresponded with response to treatment or predicted a future pulmonary exacerbation. METHODS At least one sputum sample was collected from 149 participants enrolled in this prospective longitudinal multi-centre study and total bacterial density and microbiota community measurements were determined and compared with clinical parameters. RESULTS In 114 participants with paired samples when clinically stable, ∼8 months apart, the microbiota remained conserved between timepoints, regardless of whether participants received acute intravenous antibiotic treatment or not. In 62 participants, who presented with an acute exacerbation, a decrease in community richness correlated best with patient response to antibiotic treatment. Analysis of baseline samples from 30 participants who exacerbated within 4 months of their stable sample being collected and 72 participants who remained stable throughout the study showed that community characteristics such as lower richness at baseline may be predictive of an exacerbation in addition to several clinical parameters. However, lasso regression analysis indicated that only lung function (p = 0.014) was associated with a future exacerbation. CONCLUSIONS The airway microbiota remains stable over periods <1 year with modest shifts related to treatment apparent which might provide some additional insights to patient-level measurements.
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Affiliation(s)
| | | | - Joseph E Hatch
- University of North Carolina, Chapel Hill, NC, United States
| | - Bryan Zorn
- University of North Carolina, Chapel Hill, NC, United States
| | | | | | | | | | | | - Michelle Murray
- Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Gillian Lavelle
- Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Gerry McElvaney
- Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | | | - Richard Boucher
- University of North Carolina, Chapel Hill, NC, United States
| | | | - Ian Bradbury
- Frontier Science (Scotland) Ltd., Kincraig, United Kingdom
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Assessment of Long-Term Macrolide Exposure on the Oropharyngeal Microbiome and Macrolide Resistance in Healthy Adults and Consequences for Onward Transmission of Resistance. Antimicrob Agents Chemother 2022; 66:e0224621. [PMID: 35293783 DOI: 10.1128/aac.02246-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While the use of long-term macrolide therapy to prevent exacerbations in chronic respiratory diseases is widespread, its impact on the oropharyngeal microbiota and macrolide resistance, and the potential for onward transmission of resistance to close contacts are poorly understood. We determined the effects of long-term exposure to azithromycin or erythromycin on phenotypic and genotypic macrolide resistance within the oropharyngeal microbiome of healthy adults and their close contacts in a randomized, single-blinded, parallel-group trial of 4 weeks of twice-daily oral 400 mg erythromycin ethylsuccinate or twice-daily oral 125 mg azithromycin. Using oropharyngeal swabs collected from 20 index healthy adults and 20 paired close contacts, the oropharyngeal microbial composition and macrolide resistance in streptococci were assessed by 16S rRNA sequencing and antibiotic susceptibility testing of oropharyngeal cultures, respectively, at baseline and weeks 4 and 8 (washout). Targeted quantitative PCR of antibiotic resistance genes was performed to evaluate paired changes in resistance gene levels in index patients and close contacts and to relate the potential transmission of antibiotic resistance. Neither azithromycin nor erythromycin altered oropharyngeal microbiota characteristics significantly. Proportional macrolide resistance in oropharyngeal streptococci increased with both erythromycin and azithromycin, remaining above baseline levels for the azithromycin group at washout. Levels of resistance genes increased significantly with azithromycin[erm(B) and mef] and erythromycin (mef), returning to baseline levels at washout only for the erythromycin group. We found no evidence of onward transmission of resistance to close contacts, as indicated by the lack of concomitant changes in resistance gene levels detected in close contacts. (This study has been registered with the Australian and New Zealand Clinical Trials Registry under identifier ACTRN12617000278336.).
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Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study). J Cyst Fibros 2021; 21:e158-e164. [PMID: 34756681 DOI: 10.1016/j.jcf.2021.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/31/2021] [Accepted: 10/06/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Various bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term lung function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF. METHODS As part of the 'Mucoviscidosis, respiratory VIruses, intracellular Bacteria and fastidious organisms'' project, children with CF were longitudinally followed in a Swiss multicentric study. Respiratory samples included mainly throat swabs and sputa samples for bacterial culture and 16S rRNA metagenomics and nasopharyngeal swabs for respiratory virus detection by molecular assays. Percentage of predicted Forced Expiratory Volume in one second (FEV1%) and Lung Clearance Index (LCI) were recorded. RESULTS Sixty-one children, of whom 20 (32.8%) presented with at least one pulmonary exacerbation, were included. Almost half of the 363 nasopharyngeal swabs tested by RT-PCR were positive for a respiratory virus, mainly rhinovirus (26.5%). From linear mixed-effects regression models, P. aeruginosa (-11.35, 95%CI [-17.90; -4.80], p = 0.001) was significantly associated with a decreased FEV1%, whereas rhinovirus was associated with a significantly higher FEV1% (+4.24 95%CI [1.67; 6.81], p = 0.001). Compared to conventional culture, 16S rRNA metagenomics showed a sensitivity and specificity of 80.0% and 85.4%, respectively for detection of typical CF pathogens. However, metagenomics detected a bacteria almost twice more often than culture. CONCLUSIONS As expected, P. aeruginosa impacted negatively on FEV1% while rhinovirus was surprisingly associated with better FEV1%. Culture-free assays identifies significantly more pathogens than standard culture, with disputable clinical correlation.
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Reece E, Bettio PHDA, Renwick J. Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10070827. [PMID: 34356747 PMCID: PMC8300716 DOI: 10.3390/antibiotics10070827] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most dominant pathogens in cystic fibrosis (CF) airway disease and contributes to significant inflammation, airway damage, and poorer disease outcomes. The CF airway is now known to be host to a complex community of microorganisms, and polymicrobial interactions have been shown to play an important role in shaping P. aeruginosa pathogenicity and resistance. P. aeruginosa can cause chronic infections that once established are almost impossible to eradicate with antibiotics. CF patients that develop chronic P. aeruginosa infection have poorer lung function, higher morbidity, and a reduced life expectancy. P. aeruginosa adapts to the CF airway and quickly develops resistance to several antibiotics. A perplexing phenomenon is the disparity between in vitro antimicrobial sensitivity testing and clinical response. Considering the CF airway is host to a diverse community of microorganisms or 'microbiome' and that these microorganisms are known to interact, the antimicrobial resistance and progression of P. aeruginosa infection is likely influenced by these microbial relationships. This review combines the literature to date on interactions between P. aeruginosa and other airway microorganisms and the influence of these interactions on P. aeruginosa tolerance to antimicrobials.
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5
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Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis. Nat Rev Microbiol 2021; 19:331-342. [PMID: 33214718 DOI: 10.1038/s41579-020-00477-5] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
Intense genome sequencing of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) airways has shown inefficient eradication of the infecting bacteria, as well as previously undocumented patient-to-patient transmission of adapted clones. However, genome sequencing has limited potential as a predictor of chronic infection and of the adaptive state during infection, and thus there is increasing interest in linking phenotypic traits to the genome sequences. Phenotypic information ranges from genome-wide transcriptomic analysis of patient samples to determination of more specific traits associated with metabolic changes, stress responses, antibiotic resistance and tolerance, biofilm formation and slow growth. Environmental conditions in the CF lung shape both genetic and phenotypic changes of P. aeruginosa during infection. In this Review, we discuss the adaptive and evolutionary trajectories that lead to early diversification and late convergence, which enable P. aeruginosa to succeed in this niche, and we point out how knowledge of these biological features may be used to guide diagnosis and therapy.
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6
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Acosta N, Thornton CS, Surette MG, Somayaji R, Rossi L, Rabin HR, Parkins MD. Azithromycin and the microbiota of cystic fibrosis sputum. BMC Microbiol 2021; 21:96. [PMID: 33784986 PMCID: PMC8008652 DOI: 10.1186/s12866-021-02159-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Azithromycin is commonly prescribed drug for individuals with cystic fibrosis (CF), with demonstrated benefits in reducing lung function decline, exacerbation occurrence and improving nutrition. As azithromycin has antimicrobial activity against components of the uncultured microbiome and increasingly the CF microbiome is implicated in disease pathogenesis – we postulated azithromycin may act through its manipulation. Herein we sought to determine if the CF microbiome changed following azithromycin use and if clinical benefit observed during azithromycin use associated with baseline community structure. Results Drawing from a prospectively collected biobank we identified patients with sputum samples prior to, during and after initiating azithromycin and determined the composition of the CF microbial community by sequencing the V3-V4 region of the 16S rRNA gene. We categorized patients as responders if their rate of lung function decline improved after azithromycin initiation. Thirty-eight adults comprised our cohort, nine who had not utilized azithromycin in at least 3 years, and 29 who were completely naïve. We did not observe a major impact in the microbial community structure of CF sputum in the 2 years following azithromycin usage in either alpha or beta-diversity metrics. Seventeen patients (45%) were classified as Responders – demonstrating reduced lung function decline after azithromycin. Responders who were naïve to azithromycin had a modest clustering effect distinguishing them from those who were non-Responders, and had communities enriched with several organisms including Stenotrophomonas, but not Pseudomonas. Conclusions Azithromycin treatment did not associate with subsequent large changes in the CF microbiome structure. However, we found that baseline community structure associated with subsequent azithromycin response in CF adults. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02159-5.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada
| | - Christina S Thornton
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada
| | - Michael G Surette
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada. .,Department of Medicine, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada.
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7
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Frost F, Young GR, Wright L, Miah N, Smith DL, Winstanley C, Walshaw MJ, Fothergill JL, Nazareth D. The clinical and microbiological utility of inhaled aztreonam lysine for the treatment of acute pulmonary exacerbations of cystic fibrosis: An open-label randomised crossover study (AZTEC-CF). J Cyst Fibros 2020; 20:994-1002. [PMID: 33358119 DOI: 10.1016/j.jcf.2020.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND The objective of this study was to explore the clinical and microbiological outcomes associated with substituting inhaled aztreonam lysine for an intravenous antibiotic in the treatment of acute pulmonary exacerbations of CF. METHODS An open-label randomised crossover pilot trial was conducted at a UK CF centre among 16 adults with CF and P. aeruginosa infection. Median [IQR] age was 29.5 [24.5-32.5], mean ± SD forced expiratory volume in 1 second (FEV1) was 52.4 ± 14.7 % predicted. Over the course of two exacerbations, participants were randomised to sequentially receive 14 days of inhaled aztreonam lysine plus IV colistimethate (AZLI+IV), or dual IV antibiotics (IV+IV). Primary outcome was absolute change in % predicted FEV1. Other outcomes evaluated changes in quality of life, bacterial load and the lung microbiota. RESULTS The difference between mean change in lung function at day 14 between AZLI+IV and IV+IV was +4.6% (95% CI 2.1-7.2, p=0.002). The minimum clinically important difference of the Cystic Fibrosis Revised Questionnaire (CFQ-R) was achieved more frequently with AZLI+IV (10/12, 83.3%) than IV+IV (7/16, 43.8%), p=0.05. No differences were observed for modulation of serum white cell count, C-reactive protein or sputum bacterial load. Microbiome compositional changes were observed with IV+IV (Bray-Curtis r2=0.14, p=0.02), but not AZLI+IV (r2=0.03, p=0.64). CONCLUSION In adults with CF and P. aeruginosa infection experiencing an acute pulmonary exacerbation, AZLI+IV improved lung function and quality of life compared to the current standard treatment. These findings support the need for larger definitive trials of inhaled antibiotics in the acute setting. CLINICAL TRIAL REGISTRATION EudraCT 2016-002832-34 ClinicalTrials.org NCT02894684.
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Affiliation(s)
- Freddy Frost
- Adult CF Centre, Liverpool Heart & Chest Hospital, UK; Institute of Infection & Global Health, University of Liverpool, UK.
| | - Gregory R Young
- Faculty of Health and Life Sciences, University of Northumbria, UK
| | - Laura Wright
- Institute of Infection & Global Health, University of Liverpool, UK
| | - Nahida Miah
- Institute of Infection & Global Health, University of Liverpool, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, University of Northumbria, UK
| | - Craig Winstanley
- Institute of Infection & Global Health, University of Liverpool, UK
| | - Martin J Walshaw
- Adult CF Centre, Liverpool Heart & Chest Hospital, UK; Institute of Infection & Global Health, University of Liverpool, UK
| | | | - Dilip Nazareth
- Adult CF Centre, Liverpool Heart & Chest Hospital, UK; Institute of Infection & Global Health, University of Liverpool, UK
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8
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Vandeplassche E, Sass A, Ostyn L, Burmølle M, Kragh KN, Bjarnsholt T, Coenye T, Crabbé A. Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm. Biofilm 2020; 2:100031. [PMID: 33447816 PMCID: PMC7798459 DOI: 10.1016/j.bioflm.2020.100031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
The lungs of cystic fibrosis (CF) patients are often chronically colonized by multiple microbial species that can form biofilms, including the major CF pathogen Pseudomonas aeruginosa. Herewith, lower microbial diversity in CF airways is typically associated with worse health outcomes. In an attempt to treat CF lung infections patients are frequently exposed to antibiotics, which may affect microbial diversity. This study aimed at understanding if common antibiotics that target P. aeruginosa influence microbial diversity. To this end, a microaerophilic multispecies biofilm model of frequently co-isolated members of the CF lung microbiome (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus anginosus, Achromobacter xylosoxidans, Rothia mucilaginosa, and Gemella haemolysans) was exposed to antipseudomonal antibiotics. We found that antibiotics that affected several dominant species (i.e. ceftazidime, tobramycin) resulted in higher species evenness compared to colistin, which is only active against P. aeruginosa. Furthermore, susceptibility of individual species in the multispecies biofilm following antibiotic treatment was compared to that of the respective single-species biofilms, showing no differences. Adding three anaerobic species (Prevotella melaninogenica, Veillonella parvula, and Fusobacterium nucleatum) to the multispecies biofilm did not influence antibiotic susceptibility. In conclusion, our study demonstrates antibiotic-dependent effects on microbial community diversity of multispecies biofilms comprised of CF microbiome members.
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Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Mette Burmølle
- Department of Microbiology, University of Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
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9
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Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors. Sci Rep 2020; 10:2316. [PMID: 32047185 PMCID: PMC7012823 DOI: 10.1038/s41598-020-59048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/08/2020] [Indexed: 12/23/2022] Open
Abstract
Interactions between bacteria govern the progression of respiratory infections; however, the mechanisms underpinning these interactions are still unclear. Understanding how a bacterial species comes to dominate infectious communities associated with respiratory infections has direct relevance to treatment. In this study, Burkholderia, Pseudomonas, and Staphylococcus species were isolated from the sputum of an individual with Cystic Fibrosis and assembled in a fully factorial design to create simple microcosms. Measurements of growth and habitat modification were recorded over time, the later using proton Nuclear Magnetic Resonance spectra. The results showed interactions between the bacteria became increasingly neutral over time. Concurrently, the bacteria significantly altered their ability to modify the environment, with Pseudomonas able to utilise secondary metabolites produced by the other two isolates, whereas the reverse was not observed. This study indicates the importance of including data about the habitat modification of a community, to better elucidate the mechanisms of bacterial interactions.
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Taylor SL, O'Farrell HE, Simpson JL, Yang IA, Rogers GB. The contribution of respiratory microbiome analysis to a treatable traits model of care. Respirology 2018; 24:19-28. [PMID: 30282116 DOI: 10.1111/resp.13411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/13/2018] [Accepted: 09/09/2018] [Indexed: 12/15/2022]
Abstract
The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.
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Affiliation(s)
- Steven L Taylor
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Hannah E O'Farrell
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Jodie L Simpson
- Respiratory and Sleep Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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11
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Zhao J, Cheng W, He X, Liu Y. The co-colonization prevalence of Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis: A systematic review and meta-analysis. Microb Pathog 2018; 125:122-128. [PMID: 30217514 DOI: 10.1016/j.micpath.2018.09.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/26/2018] [Accepted: 09/05/2018] [Indexed: 12/29/2022]
Abstract
PURPOSE The co-colonization prevalence of P. aeruginosa and A. fumigatus in cystic fibrosis (CF) has been inconsistently reported. The purpose of this systematic review and meta-analysis was to estimate the overall co-colonization prevalence of P. aeruginosa and A. fumigatus in CF. METHODS The Embase, PubMed and Web of Science databases were systematically searched for studies reporting the co-colonization prevalence of P. aeruginosa and A. fumigatus in CF. The co-colonization prevalence of two pathogenic microorganisms in the individual studies was assessed by calculating the proportion and 95% confidence interval (CI). The random effects model was used to calculate the pooled prevalence. The I2 test was used to assess statistical heterogeneity. The funnel plot and two statistical methods were used to assess publication bias. RESULTS Twenty-three eligible studies were included in this analysis. The pooled co-colonization prevalence of P. aeruginosa and A. fumigatus in CF patients was 15.8% (95% CI: 9.9-21.8). The co-colonization prevalence of P. aeruginosa and A. fumigatus chronic colonization was lower than that of intermittent colonization, higher in sputum cultures than in bronchoalveolar lavage (BAL) cultures, and lower in children than in adults. There was a statistically significant difference in co-colonization prevalence among studies from different decades, but the prevalence was similar in different geographical regions and with different study types. CONCLUSIONS The co-colonization prevalence of P. aeruginosa and A. fumigatus in the lower respiratory tract of CF patients was high. The anti-infective treatment in exacerbation of CF should be considered to cover the two pathogenic microorganisms simultaneously. Large-scale research is still needed to obtain more accurate co-colonization data.
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Affiliation(s)
- Jingming Zhao
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, 16#, Jiangsu Road, Qingdao, 266003, PR China.
| | - Wei Cheng
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, 16#, Jiangsu Road, Qingdao, 266003, PR China
| | - Xigang He
- Department of Respiratory Medicine, People's Hospital of Rizhao Lanshan, 566#, Lanshan Xi Road, Lanshan District, Rizhao, 276807, PR China
| | - Yanli Liu
- Department of Respiratory Medicine, The Affiliated Hospital of Qingdao University, 16#, Jiangsu Road, Qingdao, 266003, PR China
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The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning 16 Years. Ann Am Thorac Soc 2018; 14:1288-1297. [PMID: 28541746 DOI: 10.1513/annalsats.201609-668oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RATIONALE The cystic fibrosis (CF) airways are infected with a diverse polymicrobial community. OBJECTIVES Understanding how changes in the CF microbiome have occurred over time, similar to the observed changes in the prevalence of cultured pathogens, is key in understanding the microbiome's role in disease. METHODS Drawing from a prospectively collected and maintained sputum biobank, we identified 45 patients with sputum samples collected between the ages of 18 and 21 years in three successive cohorts of adults transitioning to our CF clinic: A (1997-2000), B (2004-2007), and C (2010-2013). Patient demographics, clinical status, and medications were collected from detailed chart review. Microbial communities were assessed by Ilumina MiSeq sequencing of the variable 3 (V3) region of the 16S rDNA. RESULTS The three cohorts were similar with respect to baseline demographics. There was a trend toward improved health and use of disease-modifying therapies in each successive cohort. Shannon diversity increased in the most recent cohort, suggesting an increase in the diversity of organisms between cohorts. Furthermore, the proportion of samples with Pseudomonas-dominated communities decreased over time, whereas Streptococcus increased. Although β-diversity was associated with transition cohort, the greatest predictor of diversity remained lung function. Furthermore, core microbiome constituents were preserved across cohorts. CONCLUSIONS Modest changes in the composition and structure of the microbiome of three successive cohorts of young adults with CF were observed, occurring in parallel with successive improvements in clinical status. Importantly, however, the core microbiome constituents were preserved across cohorts.
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13
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How can the cystic fibrosis respiratory microbiome influence our clinical decision-making? Curr Opin Pulm Med 2018; 23:536-543. [PMID: 28786882 DOI: 10.1097/mcp.0000000000000419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Almost 15 years have now passed since bacterial community profiling techniques were first used to analyse respiratory samples from people with cystic fibrosis. Since then, many different analytical approaches have been used to try to better understand the contribution of the cystic fibrosis lung microbiota to disease, with varying degrees of success. We examine the extent to which cystic fibrosis respiratory microbiome research has been successful in informing clinical decision-making, and highlight areas that we believe have the potential to yield important insight. RECENT FINDINGS Recent research on the cystic fibrosis lung microbiome can be broadly divided into efforts to better characterize microbiota composition, particularly relative to key clinical events, and attempts to understand the cystic fibrosis lung microbiology as an interactive microbial system. The latter, in particular, has led to the development of a number of models in which microbiome-mediated processes precipitate clinical events. SUMMARY Growing technological sophistication is enabling increasingly detailed microbiological data to be generated from cystic fibrosis respiratory samples. However, translating these data into clinically useful measures that accurately predict outcomes and guide treatments remains a formidable challenge. The development of systems biology approaches that enable the integration of complex microbiome and host-derived data provide an exciting opportunity to address this goal.
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14
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Inflammatory phenotypes in patients with severe asthma are associated with distinct airway microbiology. J Allergy Clin Immunol 2018; 141:94-103.e15. [DOI: 10.1016/j.jaci.2017.03.044] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 02/28/2017] [Accepted: 03/15/2017] [Indexed: 12/31/2022]
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15
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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Kramná L, Dřevínek P, Lin J, Kulich M, Cinek O. Changes in the lung bacteriome in relation to antipseudomonal therapy in children with cystic fibrosis. Folia Microbiol (Praha) 2017; 63:237-248. [PMID: 29127619 DOI: 10.1007/s12223-017-0562-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 10/30/2017] [Indexed: 12/28/2022]
Abstract
The lung in cystic fibrosis (CF) is home to numerous pathogens that shorten the lives of patients. The aim of the present study was to assess changes in the lung bacteriome following antibiotic therapy targeting Pseudomonas aeruginosa in children with CF. The study included nine children (9-18 years) with CF who were treated for their chronic or intermittent positivity for Pseudomonas aeruginosa. The bacteriomes were determined in 16 pairs of sputa collected at the beginning and at the end of a course of intravenous antibiotic therapy via deep sequencing of the variable region 4 of the 16S rRNA gene, and the total bacterial load and selected specific pathogens were assessed using quantitative real-time PCR. The effect of antipseudomonal antibiotics was observable as a profound decrease in the total 16S rDNA load (p = 0.001) as well as in a broad range of individual taxa including Staphylococcus aureus (p = 0.03) and several members of the Streptococcus mitis group (S. oralis, S. mitis, and S. infantis) (p = 0.003). Improvements in forced expiratory volume (FEV1) were associated with an increase in Granulicatella sp. (p = 0.004), whereas a negative association was noted between the total bacterial load and white blood cell count (p = 0.007). In conclusion, the data show how microbial communities differ in reaction to antipseudomonal treatment, suggesting that certain rare species may be associated with clinical parameters. Our work also demonstrates the utility of absolute quantification of bacterial load in addition to the 16S rDNA profiling.
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Affiliation(s)
- Lenka Kramná
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Úvalu 84, 15006, Prague 5, Czech Republic
| | - Pavel Dřevínek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jake Lin
- BioMediTech, Computational Biology, University of Tampere, Tampere, Finland
| | - Michal Kulich
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Ondrej Cinek
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Úvalu 84, 15006, Prague 5, Czech Republic.
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Botterel F, Angebault C, Cabaret O, Stressmann FA, Costa JM, Wallet F, Wallaert B, Bruce K, Delhaes L. Fungal and Bacterial Diversity of Airway Microbiota in Adults with Cystic Fibrosis: Concordance Between Conventional Methods and Ultra-Deep Sequencing, and Their Practical use in the Clinical Laboratory. Mycopathologia 2017; 183:171-183. [DOI: 10.1007/s11046-017-0185-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/22/2017] [Indexed: 11/29/2022]
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Narayanamurthy V, Sweetnam JM, Denner DR, Chen LW, Naureckas ET, Laxman B, White SR. The metabolic footprint of the airway bacterial community in cystic fibrosis. MICROBIOME 2017; 5:67. [PMID: 28666467 PMCID: PMC5493850 DOI: 10.1186/s40168-017-0289-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF. METHODS Expectorated sputum was collected from 16 CF subjects and 8 control subjects. The Biolog Gen III Microplate was used in a community-level physiological profiling (CLPP)-based assay to examine oxidative metabolic activity. 16S rRNA V4 amplicon sequencing was used to characterize the taxonomy and diversity of the samples. Correlations were then identified among the oxidative activity and taxonomy data. In an additional paired analysis, sputum from seven CF subjects were collected at two separate clinic visits and compared for oxidative activity, taxonomy, and diversity. RESULTS Significant differences in oxidative metabolic activity, microbial taxonomy, and diversity were found between the CF and control sputum samples. Oxidative activity correlated positively with total genera but not with other measures of diversity or taxonomy, demonstrating that the metabolic assay complements the structural aspects of the microbiome. As expected, Pseudomonas was significantly enriched in CF samples, while Streptococcus and Prevotella were similarly abundant in both CF and control samples. Paired analysis of CF samples at separate clinic visits revealed comparable oxidative activity that correlated with similar stability in taxonomy and diversity. CONCLUSIONS The CLPP assay used in this study complements existing sequencing methods to delineate the oxidative metabolic footprint of the CF airway bacterial community. This method may be useful to study the CF microbial community over time and with changes in disease state.
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Affiliation(s)
- Vaishnavi Narayanamurthy
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637 USA
| | - John M. Sweetnam
- Present address: Medical College of Georgia, Augusta University, Augusta, GA 30912 USA
| | - Darcy R. Denner
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637 USA
| | - Lena W. Chen
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637 USA
| | - Edward T. Naureckas
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637 USA
| | - Bharathi Laxman
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637 USA
| | - Steven R. White
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL 60637 USA
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Stokell JR, Hamp TJ, Steck TR. Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR. Antonie van Leeuwenhoek 2016; 109:1161-6. [PMID: 27160743 DOI: 10.1007/s10482-016-0707-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/27/2016] [Indexed: 02/06/2023]
Abstract
Changes in the composition of microbial communities are often examined using high-throughput sequencing (HTS). Here we analyzed bar-coded Illumina sequencing data from a previous work describing the microbial community found in the sputum of a cystic fibrosis patient by itself or in combination with qPCR to measure the absolute abundance of Pseudomonas aeruginosa and Burkholderia multivorans. Through this comparison we were able to determine the computational analysis accuracy of sequencing data to measure the relative abundance of specific taxa. While no correlation was found between relative abundance and absolute abundance of P. aeruginosa or B. multivorans, we did find conclusions derived from HTS data alone differed from those derived from a combination of HTS and qPCR. Our results highlight the importance of using qPCR with HTS when characterizing organisms in microbial communities having a dominant taxon.
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Affiliation(s)
- Joshua R Stokell
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Timothy J Hamp
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.,PerkinElmer, Inc., 940 Winter Street, Waltham, MA, 02451, USA
| | - Todd R Steck
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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Denny JE, Powell WL, Schmidt NW. Local and Long-Distance Calling: Conversations between the Gut Microbiota and Intra- and Extra-Gastrointestinal Tract Infections. Front Cell Infect Microbiol 2016; 6:41. [PMID: 27148490 PMCID: PMC4826874 DOI: 10.3389/fcimb.2016.00041] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
Preservation of health from infectious diseases depends upon both mucosal and systemic immunity via the collaborative effort of innate and adaptive immune responses. The proficiency of host immunity stems from robust defense mechanisms—physical barriers and specialized immune cells—and a failure of these mechanisms leads to pathology. Intriguingly, immunocompetence to pathogens can be shaped by the gut microbiome as recent publications highlight a dynamic interplay between the gut microbiome and host susceptibility to infection. Modulation of host immunity to enteric pathogens has long been studied where gut bacteria shape multiple facts of both innate and adaptive immunity. Conversely, the impact of gut commensals on host immunity to extra-gastrointestinal (GI) tract infections has only recently been recognized. In this context, the gut microbiome can augment host immunity to extra-GI tract bacterial, viral, and parasitic pathogens. This review explores the research that affords insight into the role of the gut microbiome in various infectious diseases, with a particular emphasis on extra-GI tract infections. A better understanding of the link between the gut microbiome and infectious disease will be critical for improving global health in the years ahead.
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Affiliation(s)
- Joshua E Denny
- Department of Microbiology and Immunology, University of Louisville Louisville, KY, USA
| | - Whitney L Powell
- Department of Microbiology and Immunology, University of Louisville Louisville, KY, USA
| | - Nathan W Schmidt
- Department of Microbiology and Immunology, University of Louisville Louisville, KY, USA
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22
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Lim MY, Yoon HS, Rho M, Sung J, Song YM, Lee K, Ko G. Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans. Sci Rep 2016; 6:23745. [PMID: 27030383 PMCID: PMC4814871 DOI: 10.1038/srep23745] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/14/2016] [Indexed: 01/30/2023] Open
Abstract
Recent studies showing clear differences in the airway microbiota between healthy and diseased individuals shed light on the importance of the airway microbiota in health. Here, we report the associations of host genetics and lifestyles such as smoking, alcohol consumption, and physical activity with the composition of the sputum microbiota using 16S rRNA gene sequence data generated from 257 sputum samples of Korean twin-family cohort. By estimating the heritability of each microbial taxon, we found that several taxa, including Providencia and Bacteroides, were significantly influenced by host genetic factors. Smoking had the strongest effect on the overall microbial community structure among the tested lifestyle factors. The abundances of Veillonella and Megasphaera were higher in current-smokers, and increased with the pack-year value and the Fagerstrom Test of Nicotine Dependence (FTND) score. In contrast, Haemophilus decreased with the pack-year of smoking and the FTND score. Co-occurrence network analysis showed that the taxa were clustered according to the direction of associations with smoking, and that the taxa influenced by host genetics were found together. These results demonstrate that the relationships among sputum microbial taxa are closely associated with not only smoking but also host genetics.
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Affiliation(s)
- Mi Young Lim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Hyo Shin Yoon
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Mina Rho
- Division of Computer Science and Engineering, College of Engineering, Hanyang University, Seoul, Republic of Korea
| | - Joohon Sung
- Department of Epidemiology, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kayoung Lee
- Department of Family Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Center for Human and Environmental Microbiome, Seoul National University, Seoul, Republic of Korea
- N-Bio, Seoul National University, Seoul, Republic of Korea
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Understanding persistent bacterial lung infections: clinical implications informed by the biology of the microbiota and biofilms. ACTA ACUST UNITED AC 2016; 23:57-66. [PMID: 27004018 DOI: 10.1097/cpm.0000000000000108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The infections found in chronic obstructive pulmonary disease, cystic fibrosis, and bronchiectasis share a number of clinical similarities, the most striking of which is bacterial persistence despite the use of antibiotics. These infections have been clinically described using culture-based methods usually performed on sputum samples, and treatment has been directed towards the bacteria found in this manner. Unfortunately the clinical response to antibiotics is frequently not predictable based on these cultures, and the role of these cultured organisms in disease progression has been debated. The past 20 years have seen a revolution in the techniques used to describe bacterial populations and their growth patterns. These techniques have revealed these persistent lung infections are vastly more complicated than described by traditional, and still widely relied upon, sputum cultures. A better understanding of the initiation and evolution of these infections, and better clinical tools to describe them, will dramatically alter the way patients are cared for. While clinical tests to more accurately describe these infections are not yet available, the better appreciation of these infections afforded by current science should enlighten practitioners as to the care of their patients with these diseases.
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Affiliation(s)
- Laura M. Filkins
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. THE LANCET RESPIRATORY MEDICINE 2015; 4:73-82. [PMID: 26700443 DOI: 10.1016/s2213-2600(15)00476-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
A decade of rapid technological advances has provided an exciting opportunity to incorporate information relating to a range of potentially important disease determinants in the clinical decision-making process. Access to highly detailed data will enable respiratory medicine to evolve from one-size-fits-all models of care, which are associated with variable clinical effectiveness and high rates of side-effects, to precision approaches, where treatment is tailored to individual patients. The human microbiome has increasingly been recognised as playing an important part in determining disease course and response to treatment. Its inclusion in precision models of respiratory medicine, therefore, is essential. Analysis of the microbiome provides an opportunity to develop novel prognostic markers for airways disease, improve definition of clinical phenotypes, develop additional guidance to aid treatment selection, and increase the accuracy of indicators of treatment effect. In this Review we propose that collaboration between researchers and clinicians is needed if respiratory medicine is to replicate the successes of precision medicine seen in other clinical specialties.
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Affiliation(s)
- Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory Flinders University School of Medicine, Adelaide, SA, Australia.
| | - Steve Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory Flinders University School of Medicine, Adelaide, SA, Australia
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26
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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention. ISME JOURNAL 2015; 10:1081-91. [PMID: 26555248 PMCID: PMC4820042 DOI: 10.1038/ismej.2015.198] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/22/2015] [Indexed: 01/24/2023]
Abstract
Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs to better understand how changes in microbiota are associated with CFPE onset and management. Data were divided into five clinical periods: pre-CFPE baseline, CFPE, antibiotic treatment, recovery, and post-CFPE baseline. Samples were treated with propidium monoazide prior to DNA extraction, to remove the impact of bacterial cell death artefacts following antibiotic treatment, and then characterised by 16S rRNA gene-targeted high-throughput sequencing. Partitioning CF microbiota into core and rare groups revealed compositional resistance to CFPE and resilience to antibiotics interventions. Mixed effects modelling of core microbiota members revealed no significant negative impact on the relative abundance of Pseudomonas aeruginosa across the exacerbation cycle. Our findings have implications for current CFPE management strategies, supporting reassessment of existing antimicrobial treatment regimens, as antimicrobial resistance by pathogens and other members of the microbiota may be significant contributing factors.
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27
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Collie D, Glendinning L, Govan J, Wright S, Thornton E, Tennant P, Doherty C, McLachlan G. Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium. PLoS One 2015; 10:e0142097. [PMID: 26544950 PMCID: PMC4636361 DOI: 10.1371/journal.pone.0142097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/16/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Exacerbations associated with chronic lung infection with Pseudomonas aeruginosa are a major contributor to morbidity, mortality and premature death in cystic fibrosis. Such exacerbations are treated with antibiotics, which generally lead to an improvement in lung function and reduced sputum P. aeruginosa density. This potentially suggests a role for the latter in the pathogenesis of exacerbations. However, other data suggesting that changes in P. aeruginosa sputum culture status may not reliably predict an improvement in clinical status, and data indicating no significant changes in either total bacterial counts or in P. aeruginosa numbers in sputum samples collected prior to pulmonary exacerbation sheds doubt on this assumption. We used our recently developed lung segmental model of chronic Pseudomonas infection in sheep to investigate the lung microbiota changes associated with chronic P. aeruginosa lung infection and the impact of systemic therapy with colistimethate sodium (CMS). METHODOLOGY/PRINCIPAL FINDINGS We collected protected specimen brush (PSB) samples from sheep (n = 8) both prior to and 14 days after establishment of chronic local lung infection with P aeruginosa. Samples were taken from both directly infected lung segments (direct) and segments spatially remote to such sites (remote). Four sheep were treated with daily intravenous injections of CMS between days 7 and 14, and four were treated with a placebo. Necropsy examination at d14 confirmed the presence of chronic local lung infection and lung pathology in every direct lung segment. The predominant orders in lung microbiota communities before infection were Bacillales, Actinomycetales and Clostridiales. While lung microbiota samples were more likely to share similarities with other samples derived from the same lung, considerable within- and between-animal heterogeneity could be appreciated. Pseudomonadales joined the aforementioned list of predominant orders in lung microbiota communities after infection. Whilst treatment with CMS appeared to have little impact on microbial community composition after infection, or the change undergone by communities in reaching that state, when Gram negative organisms (excluding Pseudomonadales) were considered together as a group there was a significant decrease in their relative proportion that was only observed in the sheep treated with CMS. With only one exception the reduction was seen in both direct and remote lung segments. This reduction, coupled with generally increasing or stable levels of Pseudomonadales, meant that the proportion of the latter relative to total Gram negative bacteria increased in all bar one direct and one remote lung segment. CONCLUSIONS/SIGNIFICANCE The proportional increase in Pseudomonadales relative to other Gram negative bacteria in the lungs of sheep treated with systemic CMS highlights the potential for such therapies to inadvertently select or create a niche for bacteria seeding from a persistent source of chronic infection.
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Affiliation(s)
- David Collie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - John Govan
- University of Edinburgh, Medical School, Edinburgh, Scotland, United Kingdom
| | - Steven Wright
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Elisabeth Thornton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Tennant
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine Doherty
- University of Edinburgh, Medical School, Edinburgh, Scotland, United Kingdom
| | - Gerry McLachlan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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Elkhatib W, Noreddin A. Efficacy of ciprofloxacin-clarithromycin combination against drug-resistant Pseudomonas aeruginosa mature biofilm using in vitro experimental model. Microb Drug Resist 2015; 20:575-82. [PMID: 25050970 DOI: 10.1089/mdr.2014.0024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is the main cause of mortality in cystic fibrosis patients and eradication of its biofilm represents a substantial problem clinically. In this study, biofilm of a cystic fibrosis strain P. aeruginosa PACI22 was established and confocal laser scanning microscopy was utilized for biofilm visualization. A quantitative time-kill biofilm model was implemented in vitro to assess the biocidal effect of ciprofloxacin, clarithromycin, and their combination at concentration levels ranged from 0.5× to 64× minimum biofilm inhibitory concentrations (MBIC) against the biofilm and the mean log bacterial densities (Log CFU/ml) retrieved from the biofilm were monitored by frequent sampling at 0, 3, 6, 9, 12, and 24 hr throughout the experiment. The results revealed that none of the tested antibiotics alone could completely eradicate the biofilm-ensconced bacteria at 0.5-64× MBIC values after 24 hr of treatment. Conversely, ciprofloxacin-clarithromycin combination at 32-64× MBIC entirely exterminated the biofilm. Furthermore, a substantial in vitro synergism between ciprofloxacin and clarithromycin against the biofilm was experimentally verified. This promising synergism affords scientific rationale for further in vivo investigations to evaluate the therapeutic potential of this combination for treatment of chronic pulmonary infections caused by P. aeruginosa biofilms.
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Affiliation(s)
- Walid Elkhatib
- 1 Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University , Cairo, Egypt
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29
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Huffnagle GB, Dickson RP. The bacterial microbiota in inflammatory lung diseases. Clin Immunol 2015; 159:177-82. [PMID: 26122174 DOI: 10.1016/j.clim.2015.05.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Numerous lines of evidence, ranging from recent studies back to those in the 1920s, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined.
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Affiliation(s)
- Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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30
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Lung microbiota across age and disease stage in cystic fibrosis. Sci Rep 2015; 5:10241. [PMID: 25974282 PMCID: PMC4431465 DOI: 10.1038/srep10241] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/07/2015] [Indexed: 12/13/2022] Open
Abstract
Understanding the significance of bacterial species that colonize and persist in cystic fibrosis (CF) airways requires a detailed examination of bacterial community structure across a broad range of age and disease stage. We used 16S ribosomal RNA sequencing to characterize the lung microbiota in 269 CF patients spanning a 60 year age range, including 76 pediatric samples from patients of age 4-17, and a broad cross-section of disease status to identify features of bacterial community structure and their relationship to disease stage and age. The CF lung microbiota shows significant inter-individual variability in community structure, composition and diversity. The core microbiota consists of five genera - Streptococcus, Prevotella, Rothia, Veillonella and Actinomyces. CF-associated pathogens such as Pseudomonas, Burkholderia, Stenotrophomonas and Achromobacter are less prevalent than core genera, but have a strong tendency to dominate the bacterial community when present. Community diversity and lung function are greatest in patients less than 10 years of age and lower in older age groups, plateauing at approximately age 25. Lower community diversity correlates with worse lung function in a multivariate regression model. Infection by Pseudomonas correlates with age-associated trends in community diversity and lung function.
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31
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Parkins MD, Floto RA. Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis. J Cyst Fibros 2015; 14:293-304. [PMID: 25881770 DOI: 10.1016/j.jcf.2015.03.012] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/21/2015] [Accepted: 03/22/2015] [Indexed: 12/22/2022]
Abstract
Chronic suppurative lower airway infection is a hallmark feature of cystic fibrosis (CF). Decades of experience in clinical microbiology have enabled the development of improved technologies and approaches for the cultivation and identification of microorganisms from sputum. It is increasingly apparent that the microbial constituents of the lower airways in CF exist in a dynamic state. Indeed, while changes in prevalence of various pathogens occur through ageing, differences exist in successive cohorts of patients and between clinics, regions and countries. Classical pathogens such as Pseudomonas aeruginosa, Burkholderia cepacia complex and Staphylococcus aureus are increasingly being supplemented with new and emerging organisms rarely observed in other areas of medicine. Moreover, it is now recognized that common oropharyngeal organisms, previously presumed to be benign colonizers may contribute to disease progression. As infection remains the leading cause of morbidity and mortality in CF, an understanding of the epidemiology, risk factors for acquisition and natural history of infection including interactions between colonizing bacteria is required. Unified approaches to the study and determination of pathogen status are similarly needed. Furthermore, experienced and evidence-based treatment data is necessary to optimize outcomes for individuals with CF.
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Affiliation(s)
- Michael D Parkins
- Department of Medicine, The University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Microbiology, Immunology and Infectious Diseases, The University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
| | - R Andres Floto
- Cambridge Institute for Medical Research, University of Cambridge, Papworth Hospital, Cambridge CB23 3RE, UK; Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge CB23 3RE, UK.
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Bacterial Adaptation during Chronic Respiratory Infections. Pathogens 2015; 4:66-89. [PMID: 25738646 PMCID: PMC4384073 DOI: 10.3390/pathogens4010066] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/15/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023] Open
Abstract
Chronic lung infections are associated with increased morbidity and mortality for individuals with underlying respiratory conditions such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). The process of chronic colonisation allows pathogens to adapt over time to cope with changing selection pressures, co-infecting species and antimicrobial therapies. These adaptations can occur due to environmental pressures in the lung such as inflammatory responses, hypoxia, nutrient deficiency, osmolarity, low pH and antibiotic therapies. Phenotypic adaptations in bacterial pathogens from acute to chronic infection include, but are not limited to, antibiotic resistance, exopolysaccharide production (mucoidy), loss in motility, formation of small colony variants, increased mutation rate, quorum sensing and altered production of virulence factors associated with chronic infection. The evolution of Pseudomonas aeruginosa during chronic lung infection has been widely studied. More recently, the adaptations that other chronically colonising respiratory pathogens, including Staphylococcus aureus, Burkholderia cepacia complex and Haemophilus influenzae undergo during chronic infection have also been investigated. This review aims to examine the adaptations utilised by different bacterial pathogens to aid in their evolution from acute to chronic pathogens of the immunocompromised lung including CF and COPD.
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Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, Schmidt TM, Abdo Z, Schloss PD, LiPuma JJ. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. MICROBIOME 2015; 3:12. [PMID: 25834733 PMCID: PMC4381400 DOI: 10.1186/s40168-015-0074-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway community dynamics during the days corresponding to the onset of symptoms of respiratory exacerbation have not been studied. RESULTS Using 16S rRNA amplicon sequencing of 95 daily sputum specimens collected from four adults with CF, we observed varying degrees of day-to-day stability in airway bacterial community structures during periods of clinical stability. Differences were observed between study subjects with respect to the degree of community changes at the onset of exacerbation. Decreases in the relative abundance of dominant taxa were observed in three subjects at exacerbation. We observed no relationship between total bacterial load and clinical status and detected no viruses by multiplex PCR. CONCLUSION CF airway microbial communities are relatively stable during periods of clinical stability. Changes in microbial community structure are associated with some, but not all, pulmonary exacerbations, supporting previous observations suggesting that distinct types of exacerbations occur in CF. Decreased abundance of species that are dominant at baseline suggests a role for less abundant taxa in some exacerbations. Daily sampling revealed patterns of change in microbial community structures that may prove useful in the prediction and management of CF pulmonary exacerbations.
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Affiliation(s)
- Lisa A Carmody
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jiangchao Zhao
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Linda M Kalikin
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - William LeBar
- />Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Richard H Simon
- />Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Arvind Venkataraman
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Thomas M Schmidt
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Zaid Abdo
- />USDA-ARS, South Atlantic Area, Athens, GA USA
| | - Patrick D Schloss
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - John J LiPuma
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial. THE LANCET RESPIRATORY MEDICINE 2014; 2:988-96. [DOI: 10.1016/s2213-2600(14)70213-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Williams CA, Saynor ZL, Tomlinson OW, Barker AR. Cystic fibrosis and physiological responses to exercise. Expert Rev Respir Med 2014; 8:751-62. [DOI: 10.1586/17476348.2014.966693] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period. J Clin Microbiol 2014; 53:237-47. [PMID: 25392361 DOI: 10.1128/jcm.02555-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The evolution of pulmonary disease in cystic fibrosis (CF) usually begins when bacteria get trapped in mucus in the lungs and become established as a chronic infection. While most CF patients experience periods of stability, pulmonary exacerbations (PEs) can occur multiple times per year and result in permanent damage to the lungs. Little is known of the shift from a period of stability to a PE, but this shift is likely to be attributed to changes in the bacterial community. Here, we identified changes in the lung microbiota to determine if they reflect patient health, indicate the onset of exacerbations, or are related to antibiotic treatment. In contrast to most bacterial studies on CF, we collected weekly samples from an adult CF patient over a period of 3 years and performed quantitative PCR (qPCR) and Illumina sequencing on those samples. While many DNA-based studies have shown the CF microbiota to be relatively stable, we observed an increase in the total bacterial abundance over time (P < 0.001), while the number of different taxa (bacterial richness) and the number of different taxa and their abundances (diversity) significantly decreased over time (P < 0.03), which was likely due to repeated antibiotic exposure. Using genus-specific primers with qPCR, we observed an increase in the abundance of Burkholderia multivorans, a CF-associated pathogen, prior to the occurrence of a PE (P = 0.006). Combining these DNA-based techniques with frequent sampling identified a potential initiator for exacerbations and described a response of the CF microbiota to time and antibiotic treatment not observed in previous CF microbiota studies.
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Abstract
Cystic fibrosis is characterised by chronic polymicrobial infection and inflammation in the airways of patients. Antibiotic treatment regimens, targeting recognised pathogens, have substantially contributed to increased life expectancy of patients with this disease. Although the emergence of antimicrobial resistance and selection of highly antibiotic-resistant bacterial strains is of major concern, the clinical relevance in cystic fibrosis is yet to be defined. Resistance has been identified in recognised cystic fibrosis pathogens and in other bacteria (eg, Prevotella and Streptococcus spp) detected in the airway microbiota, but their role in the pathophysiology of infection and inflammation in chronic lung disease is unclear. Increased antibiotic resistance in cystic fibrosis might be attributed to a range of complex factors including horizontal gene transfer, hypoxia, and biofilm formation. Strategies to manage antimicrobial resistance consist of new antibiotics or localised delivery of antimicrobial agents, iron sequestration, inhibition of quorum-sensing, and resistome analysis. Determination of the contributions of every bacterial species to lung health or disease in cystic fibrosis might also have an important role in the management of antibiotic resistance.
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Affiliation(s)
- Laura J Sherrard
- CF and Airways Microbiology Group, Queen's University Belfast, Belfast, UK; School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Michael M Tunney
- CF and Airways Microbiology Group, Queen's University Belfast, Belfast, UK; School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - J Stuart Elborn
- CF and Airways Microbiology Group, Queen's University Belfast, Belfast, UK; Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.
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Smith DJ, Badrick AC, Zakrzewski M, Krause L, Bell SC, Anderson GJ, Reid DW. Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics. Eur Respir J 2014; 44:922-30. [DOI: 10.1183/09031936.00203013] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chronic airway infection in adults with cystic fibrosis (CF) is polymicrobial and the impact of intravenous antibiotics on the bacterial community composition is poorly understood. We employed culture-independent molecular techniques to explore the early effects of i.v. antibiotics on the CF airway microbiome.DNA was extracted from sputum samples collected from adult subjects with CF at three time-points (before starting treatment, and at day 3 and day 8–10 of i.v. antibiotics) during treatment of an infective pulmonary exacerbation. Microbial community profiles were derived through analysis of bacterial-derived 16S ribosomal RNA by pyrosequencing and changes over time were compared.59 sputum samples were collected during 24 pulmonary exacerbations from 23 subjects. Between treatment onset and day 3 there was a significant reduction in the relative abundance of Pseudomonas and increased microbial diversity. By day 8–10, bacterial community composition was similar to pre-treatment. Changes in community composition did not predict improvements in lung function.The relative abundance of Pseudomonas falls rapidly in subjects with CF receiving i.v. antibiotic treatment for a pulmonary exacerbation and is accompanied by an increase in overall microbial diversity. However, this effect is not maintained beyond the first week of treatment.
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Abstract
RATIONALE In persons with cystic fibrosis (CF), repeated exacerbations of pulmonary symptoms are associated with a progressive decline in lung function. Changes in the airway microbiota around the time of exacerbations are not well understood. OBJECTIVES To characterize changes in airway bacterial communities around the time of exacerbations and to identify predictors for these changes. METHODS DNA prepared from 68 paired baseline and exacerbation sputum samples collected from 28 patients with CF were subjected to barcoded 16S rRNA gene pyrosequencing. Bacterial density was calculated by quantitative PCR. MEASUREMENTS AND MAIN RESULTS Overall, significant differences in bacterial community diversity and bacterial density between baseline and exacerbation samples were not observed. However, considerable changes in community structures were observed in a subset of patients. In these patients, the dominant taxa and initial level of community diversity were significant predictors of the magnitude of community structure changes at exacerbation. Pseudomonas-dominant communities became more diverse at exacerbation compared with communities with other or no dominant species. The relative abundance of Gemella increased in 24 (83%) of 29 samples at exacerbation and was found to be the most discriminative genus between baseline and exacerbation samples. CONCLUSIONS The magnitude of changes in the CF lung microbiota around the time of exacerbation was found to be largely dependent on community diversity and composition at baseline. Certain genera appear to play important roles in driving change in airway bacterial community composition at exacerbation. Gemella might play a direct role in and/or be a biomarker for pulmonary exacerbation.
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Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, Sogin ML, O’Toole GA. Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. MICROBIOME 2013; 1:27. [PMID: 24451123 PMCID: PMC3971630 DOI: 10.1186/2049-2618-1-27] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 10/04/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is caused by inherited mutations in the cystic fibrosis transmembrane conductance regulator gene and results in a lung environment that is highly conducive to polymicrobial infection. Over a lifetime, decreasing bacterial diversity and the presence of Pseudomonas aeruginosa in the lung are correlated with worsening lung disease. However, to date, no change in community diversity, overall microbial load or individual microbes has been shown to correlate with the onset of an acute exacerbation in CF patients. We followed 17 adult CF patients throughout the course of clinical exacerbation, treatment and recovery, using deep sequencing and quantitative PCR to characterize spontaneously expectorated sputum samples RESULTS We identified approximately 170 bacterial genera, 12 of which accounted for over 90% of the total bacterial load across all patient samples. Genera abundant in any single patient sample tended to be detectable in most samples. We found that clinical stages could not be distinguished by absolute Pseudomonas aeruginosa load, absolute total bacterial load or the relative abundance of any individual genus detected, or community diversity. Instead, we found that the microbial structure of each patient's sputum microbiome was distinct and resilient to exacerbation and antibiotic treatment. CONCLUSION Consistent with previously reported sputum microbiome studies we found that total and relative abundance of genera at the population level were remarkably stable for individual patients regardless of clinical status. Patient-by-patient analysis of diversity and relative abundance of each individual genus revealed a complex microbial landscape and highlighted the difficulty of identifying a universal microbial signature of exacerbation. Overall, at the genus level, we find no evidence of a microbial signature of clinical stage.
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Affiliation(s)
- Katherine E Price
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Alex H Gifford
- Dartmouth-Hitchcock Medical Center, Section of Pulmonary and Critical Care Medicine, Lebanon 03756, New Hampshire, USA
| | - Emily L Dolben
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - George A O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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Complexity, temporal stability, and clinical correlates of airway bacterial community composition in primary ciliary dyskinesia. J Clin Microbiol 2013; 51:4029-35. [PMID: 24068019 DOI: 10.1128/jcm.02164-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. The compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. We describe here the first systematic culture-independent evaluation of lower airway bacteriology in PCD. Thirty-three airway samples (26 from sputum, 7 from bronchoalveolar lavage [BAL] fluid) were collected from 24 PCD patients aged 4 to 73 years. 16S rRNA quantitative PCR and pyrosequencing were used to determine the bacterial loads and community compositions of the samples. Bacterial loads, which ranged from 1.3 × 10(4) to 5.2 × 10(9) CFU/ml, were positively correlated with age (P = 0.002) but not lung function. An analysis of ∼7,000 16S rRNA sequences per sample identified bacterial species belonging to 128 genera. The concurrently collected paired samples showed high bacterial community similarity. The mean relative abundance of the dominant genera was 64.5% (standard deviation [SD], 24.5), including taxa reported through standard diagnostic microbiology (members of the genera Pseudomonas, Haemophilus, and Streptococcus) and those requiring specific ex vivo growth conditions (members of the genera Prevotella and Porphyromonas). The significant correlations observed included a positive relationship between Pseudomonas aeruginosa relative abundance and age and a negative relationship between P. aeruginosa relative abundance and lung function. Members of the genus Ralstonia were also found to contribute substantially to the bacterial communities in a number of patients. Follow-up samples from a subset of patients revealed high levels of bacterial community temporal stability. The detailed microbiological characterization presented here provides a basis for the reassessment of the clinical management of PCD airway infections.
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Dickson RP, Erb-Downward JR, Huffnagle GB. The role of the bacterial microbiome in lung disease. Expert Rev Respir Med 2013; 7:245-57. [PMID: 23734647 PMCID: PMC4007100 DOI: 10.1586/ers.13.24] [Citation(s) in RCA: 266] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Novel culture-independent techniques have recently demonstrated that the lower respiratory tract, historically considered sterile in health, contains diverse communities of microbes: the lung microbiome. Increasing evidence supports the concept that a distinct microbiota of the lower respiratory tract is present both in health and in various respiratory diseases, although the biological and clinical significance of these findings remains undetermined. In this article, the authors review and synthesize published reports of the lung microbiota of healthy and diseased subjects, discuss trends of microbial diversity and constitution across disease states, and look to the extrapulmonary microbiome for hypotheses and future directions for study.
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Affiliation(s)
- Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - John R. Erb-Downward
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Gary B. Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
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Rogers GB, Hoffman LR, Carroll MP, Bruce KD. Interpreting infective microbiota: the importance of an ecological perspective. Trends Microbiol 2013; 21:271-6. [PMID: 23598051 PMCID: PMC3880558 DOI: 10.1016/j.tim.2013.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 01/09/2023]
Abstract
Complex microbiota are being reported increasingly across a range of chronic infections, including those of the cystic fibrosis airways. Such diversity fits poorly into classical models of sterile tissue infections, which generally involve one species, and where microbe-outcome associations usually imply causality. It has been suggested that microbiota at sites of infection could represent pathogenic entities, analogous to individual species. We argue that our ability to identify causality in microbiota-disease associations is, however, inherently confounded. Although particular microbiota may be associated with clinical outcomes, niche characteristics at sites of infection will shape microbiota composition through exerting selective pressures. Here, we suggest that ecological theory can inform clinical understanding.
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Affiliation(s)
- Geraint B Rogers
- Institute of Pharmaceutical Science, Molecular Microbiology Research Laboratory, King's College London, London, UK.
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Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013; 8:e62917. [PMID: 23646159 PMCID: PMC3639911 DOI: 10.1371/journal.pone.0062917] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/27/2013] [Indexed: 12/22/2022] Open
Abstract
Background Pulmonary exacerbations (PEx), frequently associated with airway infection and inflammation, are the leading cause of morbidity in cystic fibrosis (CF). Molecular microbiologic approaches detect complex microbiota from CF airway samples taken during PEx. The relationship between airway microbiota, inflammation, and lung function during CF PEx is not well understood. Objective To determine the relationships between airway microbiota, inflammation, and lung function in CF subjects treated for PEx. Methods Expectorated sputum and blood were collected and lung function testing performed in CF subjects during early (0–3d.) and late treatment (>7d.) for PEx. Sputum was analyzed by culture, pyrosequencing of 16S rRNA amplicons, and quantitative PCR for total and specific bacteria. Sputum IL-8 and neutrophil elastase (NE); and circulating C-reactive protein (CRP) were measured. Results Thirty-seven sputum samples were collected from 21 CF subjects. At early treatment, lower diversity was associated with high relative abundance (RA) of Pseudomonas (r = −0.67, p<0.001), decreased FEV1% predicted (r = 0.49, p = 0.03) and increased CRP (r = −0.58, p = 0.01). In contrast to Pseudomonas, obligate and facultative anaerobic genera were associated with less inflammation and higher FEV1. With treatment, Pseudomonas RA and P. aeruginosa by qPCR decreased while anaerobic genera showed marked variability in response. Change in RA of Prevotella was associated with more variability in FEV1 response to treatment than Pseudomonas or Staphylococcus. Conclusions Anaerobes identified from sputum by sequencing are associated with less inflammation and higher lung function compared to Pseudomonas at early exacerbation. CF PEx treatment results in variable changes of anaerobic genera suggesting the need for larger studies particularly of patients without traditional CF pathogens.
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Affiliation(s)
- Edith T Zemanick
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.
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Pattison SH, Rogers GB, Crockard M, Elborn JS, Tunney MM. Molecular detection of CF lung pathogens: current status and future potential. J Cyst Fibros 2013; 12:194-205. [PMID: 23402821 PMCID: PMC7105241 DOI: 10.1016/j.jcf.2013.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/08/2013] [Accepted: 01/11/2013] [Indexed: 12/24/2022]
Abstract
Molecular diagnostic tests, based on the detection and identification of nucleic acids in human biological samples, are increasingly employed in the diagnosis of infectious diseases and may be of future benefit to CF microbiology services. Our growing understanding of the complex polymicrobial nature of CF airway infection has highlighted current and likely future shortcomings in standard diagnostic practices. Failure to detect fastidious or slow growing microbes and misidentification of newly emerging pathogens could potentially be addressed using culture-independent molecular technologies with high target specificity. This review considers existing molecular diagnostic tests in the context of the key requirements for an envisaged CF microbiology focussed assay. The issues of assay speed, throughput, detection of multiple pathogens, data interpretation and antimicrobial susceptibility testing are discussed.
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Affiliation(s)
- Sally H Pattison
- CF and Airways Microbiology Research Group, Queen's University Belfast, United Kingdom.
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