1
|
Thornton CS, Caverly LJ, Kalikin LM, Carmody LA, McClellan S, LeBar W, Sanders DB, West NE, Goss CH, Flume PA, Heltshe SL, VanDevanter DR, LiPuma JJ. Prevalence and Clinical Impact of Respiratory Viral Infections from the STOP2 Study of Cystic Fibrosis Pulmonary Exacerbations. Ann Am Thorac Soc 2024; 21:595-603. [PMID: 37963297 PMCID: PMC10995546 DOI: 10.1513/annalsats.202306-576oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023] Open
Abstract
Rationale: Rates of viral respiratory infection (VRI) are similar in people with cystic fibrosis (CF) and the general population; however, the associations between VRI and CF pulmonary exacerbations (PEx) require further elucidation.Objectives: To determine VRI prevalence during CF PEx and evaluate associations between VRI, clinical presentation, and treatment response.Methods: The STOP2 (Standardized Treatment of Pulmonary Exacerbations II) study was a multicenter randomized trial to evaluate different durations of intravenous antibiotic therapy for PEx. In this ancillary study, participant sputum samples from up to three study visits were tested for respiratory viruses using multiplex polymerase chain reactions. Baselines and treatment-associated changes in mean lung function (percent predicted forced expiratory volume in 1 s), respiratory symptoms (Chronic Respiratory Infection Symptom Score), weight, and C-reactive protein were compared as a function of virus detection. Odds of PEx retreatment within 30 days and future PEx hazard were modeled by logistic and Cox proportional hazards regression, respectively.Results: A total of 1,254 sputum samples from 621 study participants were analyzed. One or more respiratory viruses were detected in sputum samples from 245 participants (39.5%). Virus-positive participants were more likely to be receiving CF transmembrane conductance regulator modulator therapy (45% vs. 34%) and/or chronic azithromycin therapy (54% vs. 44%) and more likely to have received treatment for nontuberculous Mycobacterium infection in the preceding 2 years (7% vs. 3%). At study visit 1, virus-positive participants were more symptomatic (mean Chronic Respiratory Infection Symptom Score, 53.8 vs. 51.1), had evidence of greater systemic inflammation (log10 C-reactive protein concentration, 1.32 log10 mg/L vs. 1.23 log10 mg/L), and had a greater drop in percent predicted forced expiratory volume in 1 second from the prior 6-month baseline (5.8 vs. 3.6). Virus positivity was associated with reduced risk of future PEx (hazard ratio, 0.82; 95% confidence interval, 0.69-0.99; P = 0.034) and longer median time to next PEx (255 d vs. 172 d; P = 0.021) compared with virus negativity.Conclusions: More than one-third of STOP2 participants treated for a PEx had a positive test result for a respiratory virus with more symptomatic initial presentation compared with virus-negative participants, but favorable long-term outcomes. More refined phenotyping of PEx, taking VRIs into account, may aid in optimizing personalized management of PEx.Clinical trial registered with www.clinicaltrials.gov (NCT02781610).
Collapse
Affiliation(s)
| | | | | | | | - Scott McClellan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - William LeBar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Don B. Sanders
- Department of Pediatrics, Indiana University, Indianapolis, Indiana
| | - Natalie E. West
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Christopher H. Goss
- Department of Medicine and
- Department of Pediatrics, University of Washington, Seattle, Washington
- CF Therapeutics Development Network Coordinating Center, Seattle Children’s Research Institute, Seattle, Washington
| | - Patrick A. Flume
- Department of Medicine and
- Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina; and
| | - Sonya L. Heltshe
- Department of Pediatrics, University of Washington, Seattle, Washington
- CF Therapeutics Development Network Coordinating Center, Seattle Children’s Research Institute, Seattle, Washington
| | - Donald R. VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | |
Collapse
|
2
|
Widder S, Opron K, Carmody LA, Kalikin LM, Caverly LJ, LiPuma JJ. Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis. bioRxiv 2023:2023.07.21.550012. [PMID: 37546739 PMCID: PMC10401930 DOI: 10.1101/2023.07.21.550012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease (COPD). Intermittent pulmonary exacerbations (PEx) in these conditions are associated with lung function decline and higher mortality rates. An understanding of the microbial underpinnings of PEx is challenged by high inter-patient variability in airway microbial community profiles. We analyzed 880 near-daily CF sputum samples and developed non-standard microbiome descriptors to model community reorganization prior and during 18 PEx. We identified two communal microbial regimes with opposing ecology and dynamics. Whereas pathogen-governed dysbiosis showed hierarchical community organization and reduced diversity, anaerobic bloom dysbiosis displayed stochasticity and increased diversity. Microbiome organization modulated the relevance of pathogens and a simulation of antimicrobial treatment predicted better efficacy for hierarchically organized microbiota. This causal link between PEx, microbiome organization, and treatment success advances the development of personalized dysbiosis management in CF and, potentially, other obstructive lung diseases.
Collapse
|
3
|
Thornton CS, Carmody LA, Kalikin LM, Opron K, Caverly LJ, LiPuma JJ. Airway bacterial community composition in persons with advanced cystic fibrosis lung disease. J Cyst Fibros 2023; 22:623-629. [PMID: 36628831 DOI: 10.1016/j.jcf.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
BACKGROUND The progression of lung disease in people with cystic fibrosis (pwCF) has been associated with a decrease in the diversity of airway bacterial communities. How often low diversity communities occur in advanced CF lung disease and how they may be associated with clinical outcomes is not clear, however. METHODS We sequenced a region of the bacterial 16S ribosomal RNA gene to characterize bacterial communities in sputum from 190 pwCF with advanced lung disease (FEV1≤40% predicted), with particular attention to the prevalence and relative abundance of dominant genera. We evaluated relationships between community diversity and clinical outcomes. RESULTS Although most of the 190 pwCF with advanced lung disease had airway bacterial communities characterized by low diversity with a dominant genus, a considerable minority (40%) did not. The absence of a dominant genus, presence of methicillin-susceptible Staphylococcus aureus, and greater bacterial richness positively correlated with lung function. Higher relative abundance of the dominant genus and greater antimicrobial use negatively correlated with lung function. PwCF with a low diversity community and dominant genus had reduced lung transplant-free survival compared to those without (median survival of 1.6 vs 2.9 years). CONCLUSIONS A considerable proportion of pwCF with advanced lung disease do not have airway bacterial communities characterized by low diversity and a dominant genus and these individuals had better survival. An understanding of the antecedents of low diversity airway communities- and the impact these may have on lung disease trajectory - may provide avenues for improved management strategies.
Collapse
Affiliation(s)
- Christina S Thornton
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
4
|
Thornton CS, Magaret AS, Carmody LA, Kalikin LM, Simon RH, LiPuma JJ, Caverly LJ. Quantifying variation in home spirometry in people with cystic fibrosis during baseline health, and associations with clinical outcomes. J Cyst Fibros 2023:S1569-1993(23)00141-8. [PMID: 37244842 PMCID: PMC10674030 DOI: 10.1016/j.jcf.2023.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Home spirometry is increasingly used to monitor lung function in people with cystic fibrosis (pwCF). Although decreases in lung function in the setting of increased respiratory symptoms are consistent with a pulmonary exacerbation (PEx), the interpretation of home spirometry during asymptomatic periods of baseline health is unclear. The aims of this study were to determine the variation in home spirometry in pwCF during asymptomatic periods of baseline health and to identify associations between this variation and PEx. METHODS Near-daily home spirometry measurements were obtained from a cohort of pwCF enrolled in a long-term study of the airway microbiome. Associations between the degree of variation in home spirometry and the time to next PEx were evaluated. RESULTS Thirteen subjects (mean age of 29 years and mean percent predicted forced expiratory volume in one second [ppFEV1] of 60) provided a median of 204 spirometry readings taken during 40 periods of baseline health. The mean week-to-week within-subject level of variation in ppFEV1 was 15.2 ± 6.2%. The degree of variation in ppFEV1 during baseline health was not associated with time to PEx. CONCLUSIONS Variation in ppFEV1 measured with near-daily home spirometry in pwCF during periods of baseline health exceeded the variation in ppFEV1 expected in clinic spirometry (based on ATS guidelines). The degree of variation in ppFEV1 during baseline health was not associated with time to PEx. These data are relevant for guiding interpretation of home spirometry.
Collapse
Affiliation(s)
- Christina S Thornton
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amalia S Magaret
- Departments of Pediatrics and Biostatistics, University of Washington, Seattle, Washington, USA
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Richard H Simon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| |
Collapse
|
5
|
Carmody LA, Kalikin LM, VanDevanter DR, Li G, Opron K, Simon RH, Caverly LJ, LiPuma JJ. Changes in airway bacterial communities occur soon after initiation of antibiotic treatment of pulmonary exacerbations in cystic fibrosis. J Cyst Fibros 2022; 21:766-768. [PMID: 35667975 PMCID: PMC10440828 DOI: 10.1016/j.jcf.2022.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/02/2022] [Accepted: 05/29/2022] [Indexed: 01/04/2023]
Abstract
Chronic polymicrobial airway infections are a hallmark of cystic fibrosis (CF) lung disease. Antibiotic therapy is a primary treatment of CF pulmonary exacerbations (PEx); however, the impact of episodic antibiotic treatment on airway bacterial communities has not been well described. We analyzed sputum samples from adults with CF obtained immediately before and during antibiotic treatment of PEx. Sequencing of the V4 region of the bacterial 16S ribosomal RNA gene was used to assess changes in bacterial community structure during antibiotic treatment. The peak impact of antibiotic treatment was observed by day four or five of treatment. These findings advance our understanding of bacterial community dynamics during antibiotic treatment of PEx and complement recent and ongoing studies evaluating the optimal duration of antibiotic therapy for PEx.
Collapse
Affiliation(s)
- Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, United States
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, United States
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Gen Li
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Richard H Simon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, United States
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, United States.
| |
Collapse
|
6
|
Widder S, Zhao J, Carmody LA, Zhang Q, Kalikin LM, Schloss PD, LiPuma JJ. Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways. ISME J 2022; 16:905-914. [PMID: 34689185 PMCID: PMC8941020 DOI: 10.1038/s41396-021-01129-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022]
Abstract
Bacterial infection and inflammation of the airways are the leading causes of morbidity and mortality in persons with cystic fibrosis (CF). The ecology of the bacterial communities inhabiting CF airways is poorly understood, especially with respect to how community structure, dynamics, and microbial metabolic activity relate to clinical outcomes. In this study, the bacterial communities in 818 sputum samples from 109 persons with CF were analyzed by sequencing bacterial 16S rRNA gene amplicons. We identified eight alternative community types (pulmotypes) by using a Dirichlet multinomial mixture model and studied their temporal dynamics in the cohort. Across patients, the pulmotypes displayed chronological patterns in the transition among each other. Furthermore, significant correlations between pulmotypes and patient clinical status were detected by using multinomial mixed effects models, principal components regression, and statistical testing. Constructing pulmotype-specific metabolic activity profiles, we found that pulmotype microbiota drive distinct community functions including mucus degradation or increased acid production. These results indicate that pulmotypes are the result of ordered, underlying drivers such as predominant metabolism, ecological competition, and niche construction and can form the basis for quantitative, predictive models supporting clinical treatment decisions.
Collapse
Affiliation(s)
- Stefanie Widder
- Department of Medicine 1, Research Laboratory of Infection Biology, Medical University of Vienna, Vienna, Austria.
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Lisa A Carmody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Qingyang Zhang
- Department of Mathematical Science, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Linda M Kalikin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, 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, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| |
Collapse
|
7
|
Mustafa M, Bogdanet D, Khattak A, Carmody LA, Kirwan B, Gaffney G, O'Shea PM, Dunne F. Early gestational diabetes mellitus (GDM) is associated with worse pregnancy outcomes compared with GDM diagnosed at 24-28 weeks gestation despite early treatment. QJM 2021; 114:17-24. [PMID: 32413109 DOI: 10.1093/qjmed/hcaa167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/03/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) is associated+ with adverse pregnancy outcomes compared with women with normal glucose tolerance in pregnancy. The WHO recommends screening at 24-28 weeks gestation for GDM. Women who are diagnosed before 24-28 weeks gestation have a longer intervention period which may impact positively on pregnancy outcomes. AIM This study aimed to examine pregnancy outcomes of women with GDM diagnosed <24 weeks gestation compared with those diagnosed at 24-28 weeks in a large Irish cohort. METHODS A retrospective cohort study of 1471 pregnancies in women with GDM diagnosed using IADPSG criteria between September 2012 and April 2016 was conducted. At GDM diagnosis, women were classified as early GDM <24 weeks or standard GDM 24-28 weeks gestation. RESULTS Women with early GDM had a significantly greater risk of pregnancy-induced hypertension (12.4% vs. 5.3%; P < 0.05), post-partum haemorrhage (8.7% vs. 2.4%; P < 0.05) and post-partum glucose abnormalities (32% vs. 15.6%; P < 0.05). Their offspring had a greater risk of pre-maturity (10.9% vs. 6.6%; P < 0.05), stillbirth (1.4% vs. 0.5%; P < 0.05), large for gestational age (19.1% vs. 13.4% P < 0.05) and need neonatal intensive care (30.7% vs. 22.1%; P < 0.05) compared with offspring of women with standard GDM. Rates of C-section and pre-maturity were still higher in the early GDM group when the two groups where compared based on their post-natal OGTT. CONCLUSION Early GDM women and their offspring are at greater risk of an adverse pregnancy outcome compared with those diagnosed at 24-28 weeks. In view of the abnormal post-natal glucose findings, early GDM may reflect a more advanced state in diabetes pathogenesis.
Collapse
Affiliation(s)
- M Mustafa
- Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group (SUHCG), Galway University Hospitals (GUH), Newcastle Rd, Galway, H91 YR71, Ireland
- Department of Endocrine, College of Medicine, National University Ireland, University Road, Galway, H91 TK33, Ireland
| | - D Bogdanet
- Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group (SUHCG), Galway University Hospitals (GUH), Newcastle Rd, Galway, H91 YR71, Ireland
- Department of Endocrine, College of Medicine, National University Ireland, University Road, Galway, H91 TK33, Ireland
| | - A Khattak
- Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group (SUHCG), Galway University Hospitals (GUH), Newcastle Rd, Galway, H91 YR71, Ireland
| | - L A Carmody
- Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group (SUHCG), Galway University Hospitals (GUH), Newcastle Rd, Galway, H91 YR71, Ireland
| | - B Kirwan
- Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group (SUHCG), Galway University Hospitals (GUH), Newcastle Rd, Galway, H91 YR71, Ireland
| | - G Gaffney
- Department of Endocrine, College of Medicine, National University Ireland, University Road, Galway, H91 TK33, Ireland
- Department of Obstetrics and Gynecology, Galway University Hospital, Saolta University Health Care Group (SHCG), Newcastle Rd, Galway, H91 YR71, Ireland
| | - P M O'Shea
- Department of Endocrine, College of Medicine, National University Ireland, University Road, Galway, H91 TK33, Ireland
- Department of Clinical Biochemistry, Galway University Hospital, Newcastle Rd, Galway, H91 YR71, Ireland
| | - F Dunne
- Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group (SUHCG), Galway University Hospitals (GUH), Newcastle Rd, Galway, H91 YR71, Ireland
- Department of Endocrine, College of Medicine, National University Ireland, University Road, Galway, H91 TK33, Ireland
| |
Collapse
|
8
|
Caverly LJ, Lu J, Carmody LA, Kalikin LM, Shedden K, Opron K, Azar M, Cahalan S, Foster B, VanDevanter DR, Simon RH, LiPuma JJ. Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability. Ann Am Thorac Soc 2019; 16:1534-1542. [PMID: 31415187 PMCID: PMC6956830 DOI: 10.1513/annalsats.201903-270oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/15/2019] [Indexed: 12/18/2022] Open
Abstract
Rationale: Differences in cystic fibrosis (CF) airway microbiota between periods of clinical stability and exacerbation of respiratory symptoms have been investigated in efforts to better understand microbial triggers of CF exacerbations. Prior studies have often relied on a single sample or a limited number of samples to represent airway microbiota. However, the variability in airway microbiota during periods of clinical stability is not well known.Objectives: To determine the temporal variability of measures of airway microbiota during periods of clinical stability, and to identify factors associated with this variability.Methods: Sputum samples (N = 527), obtained daily from six adults with CF during 10 periods of clinical stability, underwent sequencing of the V4 region of the bacterial 16S ribosomal RNA gene. The variability in airway microbiota among samples within each period of clinical stability was calculated as the average of the Bray-Curtis similarity measures of each sample to every other sample within the same period. Outlier samples were defined as samples outside 1.5 times the interquartile range within a baseline period with respect to the average Bray-Curtis similarity. Total bacterial load was measured with droplet digital polymerase chain reaction.Results: The variation in Bray-Curtis similarity and total bacterial load among samples within the same baseline period was greater than the variation observed in technical replicate control samples. Overall, 6% of samples were identified as outliers. Within baseline periods, changes in bacterial community structure occurred coincident with changes in maintenance antibiotics (P < 0.05, analysis of molecular variance). Within subjects, bacterial community structure changed between baseline periods (P < 0.01, analysis of molecular variance). Sample-to-sample similarity within baseline periods was greater with fewer interval days between sampling.Conclusions: During periods of clinical stability, airway bacterial community structure and bacterial load vary among daily sputum samples from adults with CF. This day-to-day variation has bearing on study design and interpretation of results, particularly in analyses that rely on single samples to represent periods of interest (e.g., clinical stability vs. pulmonary exacerbation). These data also emphasize the importance of accounting for maintenance antibiotic use and granularity of sample collection in studies designed to assess the dynamics of CF airway microbiota relative to changes in clinical state.
Collapse
Affiliation(s)
| | | | | | | | - Kerby Shedden
- Department of Statistics and Biostatistics, University of Michigan, Ann Arbor, Michigan; and
| | - Kristopher Opron
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | | | | | | | - Donald R. VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Richard H. Simon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | | |
Collapse
|
9
|
Carmody LA, Caverly LJ, Foster BK, Rogers MAM, Kalikin LM, Simon RH, VanDevanter DR, LiPuma JJ. Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis. PLoS One 2018. [PMID: 29522532 PMCID: PMC5844593 DOI: 10.1371/journal.pone.0194060] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteria that infect the airways of persons with cystic fibrosis (CF) include a group of well-described opportunistic pathogens as well as numerous, mainly obligate or facultative anaerobic species typically not reported by standard sputum culture. We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 sputum specimens collected from 111 CF patients over 10 years. We describe fluctuations in the relative abundances of typical CF pathogens, as well as anaerobic species, in relation to changes in patients’ clinical state and lung disease stage. Both bacterial community diversity and the relative abundance of anaerobes increased during exacerbation of symptoms (prior to antibiotic treatment), although this trend was not observed uniformly across disease stages. Community diversity and the relative abundance of anaerobic species decreased during antibiotic treatment. These results support current hypotheses regarding the role of anaerobes in CF pulmonary exacerbations and lung disease progression.
Collapse
Affiliation(s)
- Lisa A. Carmody
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lindsay J. Caverly
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Bridget K. Foster
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mary A. M. Rogers
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Linda M. Kalikin
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Richard H. Simon
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Donald R. VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - John J. LiPuma
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
10
|
Caverly LJ, Carmody LA, Haig SJ, Kotlarz N, Kalikin LM, Raskin L, LiPuma JJ. Culture-Independent Identification of Nontuberculous Mycobacteria in Cystic Fibrosis Respiratory Samples. PLoS One 2016; 11:e0153876. [PMID: 27093603 PMCID: PMC4836755 DOI: 10.1371/journal.pone.0153876] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/05/2016] [Indexed: 11/19/2022] Open
Abstract
Respiratory tract infections with nontuberculous mycobacteria (NTM) are increasing in prevalence and are a significant cause of lung function decline in individuals with cystic fibrosis (CF). NTM have been detected in culture-independent analyses of CF airway microbiota at lower rates than would be expected based on published prevalence data, likely due to poor lysing of the NTM cell wall during DNA extraction. We compared a standard bacterial lysis protocol with a modified method by measuring NTM DNA extraction by qPCR and NTM detection with bacterial 16S rRNA gene sequencing. The modified method improved NTM DNA recovery from spiked CF sputum samples by a mean of 0.53 log10 copies/mL for M. abscessus complex and by a mean of 0.43 log10 copies/mL for M. avium complex as measured by qPCR targeting the atpE gene. The modified method also improved DNA sequence based NTM detection in NTM culture-positive CF sputum and bronchoalveolar lavage samples; however, both qPCR and 16S rRNA gene sequencing remained less sensitive than culture for NTM detection. We highlight the limitations of culture-independent identification of NTM from CF respiratory samples, and illustrate how alterations in the bacterial lysis and DNA extraction process can be employed to improve NTM detection with both qPCR and 16S rRNA gene sequencing.
Collapse
Affiliation(s)
- Lindsay J. Caverly
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Lisa A. Carmody
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sarah-Jane Haig
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nadine Kotlarz
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Linda M. Kalikin
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lutgarde Raskin
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - John J. LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| |
Collapse
|
11
|
Zhao J, Evans CR, Carmody LA, LiPuma JJ. Impact of storage conditions on metabolite profiles of sputum samples from persons with cystic fibrosis. J Cyst Fibros 2015; 14:468-73. [PMID: 25725986 DOI: 10.1016/j.jcf.2015.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Although recent studies have begun to elucidate how airway microbial community structure relates to lung disease in cystic fibrosis (CF), microbial community activity and the host's response to changes in this activity are poorly understood. Metabolomic profiling provides a means to investigate microbial activity and human cell activity within diseased airways. However, variables in sample storage and shipping likely affect downstream analyses and standards for sample handling are lacking. METHODS We assessed the impact of sample storage conditions on liquid chromatography mass spectrometry analysis of CF sputum samples. RESULTS Significant changes in global metabolomic profiles occurred in samples stored at room temperature or at 4°C for longer than one day. Untargeted metabolomic profiles were stable in sputum samples stored at -20°C or -80°C for at least 28 days. Quorum sensing molecules and phenazines, both considered important to the in vivo activity of Pseudomonas during airway infection, were detected after sample storage at room temperature for five days. CONCLUSIONS Sputum samples can be stored at -20°C or -80°C for weeks with minimal effect on global metabolomic profiles. This observation provides guidance in designing metabolomic studies that have the potential to deepen our understanding of how airway microbial communities impact lung disease progression in CF.
Collapse
Affiliation(s)
- Jiangchao Zhao
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Charles R Evans
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Lisa A Carmody
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
| |
Collapse
|
12
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
13
|
Noctor E, Crowe C, Carmody LA, Avalos GM, Kirwan B, Infanti JJ, O'Dea A, Gillespie P, Newell J, McGuire B, O'Neill C, O'Shea PM, Dunne FP. ATLANTIC DIP: simplifying the follow-up of women with previous gestational diabetes. Eur J Endocrinol 2013; 169:681-7. [PMID: 24092597 DOI: 10.1530/eje-13-0491] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Previous gestational diabetes (GDM) is associated with a significant lifetime risk of type 2 diabetes. In this study, we assessed the performance of HbA1c and fasting plasma glucose (FPG) measurements against that of 75 g oral glucose tolerance testing (OGTT) for the follow-up screening of women with previous GDM. METHODS Two hundred and sixty-six women with previous GDM underwent the follow-up testing (mean of 2.6 years (s.d. 1.0) post-index pregnancy) using HbA1c (100%), and 75 g OGTT (89%) or FPG (11%). American Diabetes Association (ADA) criteria for abnormal glucose tolerance were used. DESIGN, COHORT STUDY, AND RESULTS The ADA HbA1c high-risk cut-off of 39 mmol/mol yielded sensitivity of 45% (95% CI 32, 59), specificity of 84% (95% CI 78, 88), negative predictive value (NPV) of 87% (95% CI 82, 91) and positive predictive value (PPV) of 39% (95% CI 27, 52) for detecting abnormal glucose tolerance. ADA high-risk criterion for FPG of 5.6 mmol/l showed sensitivity of 80% (95% CI 66, 89), specificity of 100% (95% CI 98, 100), NPV of 96% (95% CI 92, 98) and PPV of 100% (95% CI 91, 100). Combining HbA1c ≥39 mmol/mol with FPG ≥5.6 mmol/l yielded sensitivity of 90% (95% CI 78, 96), specificity of 84% (95% CI 78, 88), NPV of 97% (95% CI 94, 99) and PPV of 56% (95% CI 45, 66). CONCLUSIONS Combining test cut-offs of 5.6 mmol/l and HbA1c 39 mmol/mol identifies 90% of women with abnormal glucose tolerance post-GDM (mean 2.6 years (s.d.1.0) post-index pregnancy). Applying this follow-up strategy will reduce the number of OGTT tests required by 70%, will be more convenient for women and their practitioners, and is likely to lead to increased uptake of long-term retesting by these women whose risk for type 2 diabetes is substantially increased.
Collapse
Affiliation(s)
- E Noctor
- Galway Diabetes Research Centre, National University of Ireland, Galway, Ireland
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Crowe C, Noctor E, Carmody LA, Wickham B, Avalos G, Gaffney G, O’Shea P, Dunne F. The prevalence of metabolic syndrome up to 5 years post-partum in patients with a history of gestational diabetes mellitus. BMC Proc 2012. [PMCID: PMC3426054 DOI: 10.1186/1753-6561-6-s4-p44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
15
|
Crowe C, Noctor E, Carmody LA, Wickham B, Avalos G, Gaffney G, O’Shea P, Dunne F. Validation of a diabetes risk score in identifying patients at risk of progression to abnormal glucose tolerance post partum. BMC Proc 2012. [PMCID: PMC3426002 DOI: 10.1186/1753-6561-6-s4-o36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- C Crowe
- Department of Medicine, University Hospital Galway and National University of Ireland, Galway, Ireland
| | - E Noctor
- Department of Medicine, University Hospital Galway and National University of Ireland, Galway, Ireland
| | - LA Carmody
- Department of Medicine, University Hospital Galway and National University of Ireland, Galway, Ireland
| | - B Wickham
- Department of Medicine, University Hospital Galway and National University of Ireland, Galway, Ireland
| | - G Avalos
- Department of Medicine, University Hospital Galway and National University of Ireland, Galway, Ireland
| | - G Gaffney
- Department of Obstetrics and Gynaecology, University Hospital Galway, Ireland
| | - P O’Shea
- Department of Clinical Biochemistry, University Hospital Galway, Ireland
| | - F Dunne
- Department of Medicine, University Hospital Galway and National University of Ireland, Galway, Ireland
| |
Collapse
|
16
|
Crowe C, Noctor E, Carmody LA, Wickham B, Avalos G, Gaffney G, O’Shea P, Dunne F. ATLANTIC DIP: The prevalence of pre-diabetes/type 2 diabetes in an Irish population with gestational diabetes mellitus 1-5 years post index pregnancy. BMC Proc 2012. [PMCID: PMC3426151 DOI: 10.1186/1753-6561-6-s4-o35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
17
|
Dunne FP, Avalos G, Durkan M, Mitchell Y, Gallacher T, Keenan M, Hogan M, Carmody LA, Gaffney G. ATLANTIC DIP: pregnancy outcomes for women with type 1 and type 2 diabetes. Ir Med J 2012; 105:6-9. [PMID: 22838098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
ATLANTIC DIP prospectively evaluated the perinatal and maternal outcomes of pregnancies complicated by Type 1 and Type 2 diabetes during 2006/2007 in 5 antenatal centres. All women with established diabetes for at least 6 months prior to the index pregnancy and booking for antenatal care between 1/1/2006 and 31/12/2007 were included in the study. Results were collected electronically via the DIAMOND Diabetes Information System. Pregnancy outcome was compared with that of the background population receiving antenatal care in the region during the same time. There were 104 singleton pregnancies during the period of study. The stillbirth rate (SBR) of 25/1000 was 5 times greater than that reported in the background population at 5/1000 and the perinatal mortality rate (PMR) of 25/1000 was 3.5 times greater than background 7/1000. The congenital malformation rate (CMR) of 24/1000 was twice that observed in the background population. Women were not well prepared for pregnancy with 28% receiving pre pregnancy care (PPC), 43% receiving pre pregnancy folic acid and 51% achieving a HbA1C < = 7% at first antenatal visit. Pregnancy induced hypertension (PIH) and/or pre eclampsia toxaemia (PET) were three times more common than in women in the background population. In conclusion women are not well prepared for pregnancy. Maternal and infant morbidity and infant mortality are greater in women with diabetes. A regional pre pregnancy care (PPC) programme and centralised glucose management are urgently needed.
Collapse
Affiliation(s)
- F P Dunne
- School of Medicine, National University of Ireland, Galway.
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Carmody LA, Gill JJ, Summer EJ, Sajjan US, Gonzalez CF, Young RF, LiPuma JJ. Efficacy of bacteriophage therapy in a model of Burkholderia cenocepacia pulmonary infection. J Infect Dis 2010; 201:264-71. [PMID: 20001604 DOI: 10.1086/649227] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The therapeutic potential of bacteriophages (phages) in a mouse model of acute Burkholderia cenocepacia pulmonary infection was assessed. Phage treatment was administered by either intranasal inhalation or intraperitoneal injection. Bacterial density, macrophage inflammatory protein 2 (MIP-2), and tumor necrosis factor alpha (TNF-alpha) levels were significantly reduced in lungs of mice treated with intraperitoneal phages (P < .05). No significant differences in lung bacterial density or MIP-2 levels were found between untreated mice and mice treated with intranasal phages, intraperitoneal ultraviolet-inactivated phages, or intraperitoneal lambda phage control mice. Mock-infected mice treated with phage showed no significant increase in lung MIP-2 or TNF-alpha levels compared with mock-infected/mock-treated mice. We have demonstrated the efficacy of phage therapy in an acute B. cenocepacia lung infection model. Systemic phage administration was more effective than inhalational administration, suggesting that circulating phages have better access to bacteria in lungs than do topical phages.
Collapse
Affiliation(s)
- Lisa A Carmody
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | | | | | | | | | | | | |
Collapse
|