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Benčič A, Toplak N, Koren S, Bogožalec Košir A, Milavec M, Tomič V, Lužnik D, Dreo T. Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum. mSystems 2024:e0073524. [PMID: 39150245 DOI: 10.1128/msystems.00735-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024] Open
Abstract
Targeted high-throughput sequencing (HTS) has revolutionized the way we look at bacterial communities. It can be used for the species-specific detection of bacteria as well as for the determination of the microbiome and resistome and can be applied to samples from almost any environment. However, the results of targeted HTS can be influenced by many factors, which poses a major challenge for its use in clinical diagnostics. In this study, we investigated the impact of the DNA extraction method on the determination of the bacterial microbiome and resistome by targeted HTS using principles from metrology and diagnostics such as repeatability and analytical sensitivity. Sputum samples spiked with Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa at three different concentrations (103-106 cells/mL) were used. DNA was extracted from each sample on 2 separate days in three replicates each using three different extraction methods based on cetrimonium bromide, magnetic beads, and silica membranes. All three spiked bacteria were detected in sputum, and the DNA extraction method had no significant effect on detection. However, the DNA extraction method had significant effects on the composition of the microbiome and the resistome. The sequencing results were repeatable in the majority of cases. The silica membrane-based DNA extraction kit provided the most repeatable results and the highest diversity of the microbiome and resistome. Targeted HTS has been shown to be a reliable tool for determining the microbiome and resistome; however, the method of DNA extraction should be carefully selected to minimize its impact on the results. IMPORTANCE High-throughput sequencing (HTS) is one of the crucial new technologies that gives us insights into previously hidden parts of microbial communities. The DNA extraction method is an important step that can have a major impact on the results, and understanding this impact is of paramount importance for their reliable interpretation. Our results are of great value for the interpretation of sputum microbiome and resistome results obtained by targeted HTS. Our findings allow for a more rational design of future microbiome studies, which would lead to higher repeatability of results and easier comparison between different laboratories. This could also facilitate the introduction of targeted HTS in clinical microbiology for reliable identification of pathogenic bacteria and testing for antimicrobial resistance (AMR). As AMR is a major threat to public health, the improved methods for determining AMR would bring great benefits to both the healthcare system and society as a whole.
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Affiliation(s)
- Aleksander Benčič
- 1Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | | | | | - Alexandra Bogožalec Košir
- 1Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Mojca Milavec
- 1Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Viktorija Tomič
- University Clinic of Pulmonary and Allergic Diseases Golnik, Laboratory for Respiratory Microbiology, Golnik, Slovenia
| | - Dane Lužnik
- University Clinic of Pulmonary and Allergic Diseases Golnik, Laboratory for Respiratory Microbiology, Golnik, Slovenia
| | - Tanja Dreo
- 1Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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2
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Jabeen MF, Sanderson ND, Foster D, Crook DW, Cane JL, Borg C, Connolly C, Thulborn S, Pavord ID, Klenerman P, Street TL, Hinks TSC. Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies. Microbiol Spectr 2022; 10:e0227921. [PMID: 35323032 PMCID: PMC9045196 DOI: 10.1128/spectrum.02279-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
Previous metagenomic studies in asthma have been limited by inadequate sequencing depth for species-level bacterial identification and by heterogeneity in clinical phenotyping. We hypothesize that chronic bacterial airways infection is a key "treatable trait" whose prevalence, clinical phenotype and reliable biomarkers need definition. In this study, we have applied a method for Oxford Nanopore sequencing for the unbiased metagenomic characterization of severe asthma. We optimized methods to compare performance of Illumina MiSeq, Nanopore sequencing, and RT-qPCR on total sputum DNA extracts against culture/MALDI-TOF for analysis of induced sputum samples from highly phenotyped severe asthma during clinical stability. In participants with severe asthma (n = 23) H. influenzae was commonly cultured (n = 8) and identified as the dominant bacterial species by metagenomic sequencing using an optimized method for Illumina MiSeq and Oxford Nanopore. Alongside superior operational characteristics, Oxford Nanopore achieved near complete genome coverage of H. influenzae and demonstrated a high level of agreement with Illumina MiSeq data. Clinically significant infection was confirmed with validated H. influenzae plasmid-based quantitative PCR assay. H. influenzae positive patients were found to have sputum neutrophilia and lower FeNO. In conclusion, using an optimized method of direct sequencing of induced sputum samples, H. influenzae was identified as a clinically relevant pathogen in severe asthma and was identified reliably using metagenomic sequencing. Application of these protocols in ongoing analysis of large patient cohorts will allow full characterization of this clinical phenotype. IMPORTANCE The human airways were once thought sterile in health. Now metagenomic techniques suggest bacteria may be present, but their role in asthma is not understood. Traditional culture lacks sensitivity and current sequencing techniques are limited by operational problems and limited ability to identify pathogens at species level. We optimized a new sequencing technique-Oxford Nanopore technologies (ONT)-for use on human sputum samples and compared it with existing methods. We found ONT was effective for rapidly analyzing samples and could identify bacteria at the species level. We used this to show Haemophilus influenzae was a dominant bacterium in the airways in people with severe asthma. The presence of Haemophilus was associated with a "neutrophilic" form of asthma - a subgroup for which we currently lack specific treatments. Therefore, this technique could be used to target chronic antibiotic therapy and in research to characterize the full breadth of bacteria in the airways.
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Affiliation(s)
- Maisha F. Jabeen
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick W. Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jennifer L. Cane
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Catherine Borg
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Clare Connolly
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Samantha Thulborn
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ian D. Pavord
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Teresa L. Street
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Timothy S. C. Hinks
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
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3
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Rehner J, Schmartz GP, Groeger L, Dastbaz J, Ludwig N, Hannig M, Rupf S, Seitz B, Flockerzi E, Berger T, Reichert MC, Krawczyk M, Meese E, Herr C, Bals R, Becker SL, Keller A, Müller R. Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:405-417. [PMID: 35680095 PMCID: PMC9684153 DOI: 10.1016/j.gpb.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 01/05/2023]
Abstract
High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
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Affiliation(s)
- Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany
| | | | - Laura Groeger
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Jan Dastbaz
- Helmholtz Institute for Pharmaceutical Research Saarland, D-66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, D-66421 Homburg, Germany
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, D-66421 Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Elias Flockerzi
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | | | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, D-66421 Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, D-66421 Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, D-66123 Saarbrücken, Germany
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Terranova L, Risé P, Gramegna A, Pinna C, Agostoni C, Syrén ML, Turolo S, Marchisio P, Amati F, Aliberti S, Sala A, Blasi F. Pro-resolving and pro-inflammatory fatty acid-derived mediators in sputum of stable state bronchiectasis patients. Respir Res 2022; 23:363. [PMID: 36539829 PMCID: PMC9764713 DOI: 10.1186/s12931-022-02301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Bronchiectasis is characterized by neutrophilic inflammation and frequent exacerbations often associated with infections. Lipid mediators play critical roles in the inflammatory response, and the balance between anti-inflammatory and pro-inflammatory mediators could drive to chronic inflammation. The aim of this study was to evaluate the metabolites of docosahexaenoic acid and arachidonic acid in sputum of adults with bronchiectasis defining their associations with clinical data, bacterial load and neutrophil elastase. METHODS An observational, cross-sectional study was conducted at the bronchiectasis program of the Policlinico Hospital in Milan, Italy, where patients were enrolled. Active neutrophil elastase was measured by enzyme-linked immunosorbent assay, pro-resolving and pro-inflammatory fatty acid-derived mediators were evaluated by mass spectrometry and respiratory pathogens were assessed by real-time PCR. Analysis were performed on sputum collected during stable state and clinical data were also collected. RESULTS Levels of pro-inflammatory mediators derived from arachidonic acid metabolism showed association with neutrophil elastase, were proportional to Pseudomonas aeruginosa identifications and were linked with radiological gravity index, while the concentrations of pro-resolution mediators derived from docosahexaenoic acid were associated with a better health status, highlighted by the inverse correlation with radiological gravity index, bacterial infections and sputum volume production. CONCLUSION Pro-inflammatory mediators derived from FA metabolisms are associated with severity of bronchiectasis while DHA-derived metabolites are inversely associated with severity of the disease, which may be used for personized treatment of bronchiectasis.
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Affiliation(s)
- Leonardo Terranova
- grid.414818.00000 0004 1757 8749Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Patrizia Risé
- grid.4708.b0000 0004 1757 2822Department of Pharmaceutical Sciences-DISFARM, University of Milan, 20122 Milan, Italy
| | - Andrea Gramegna
- grid.414818.00000 0004 1757 8749Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Christian Pinna
- grid.4708.b0000 0004 1757 2822Department of Pharmaceutical Sciences-DISFARM, University of Milan, 20122 Milan, Italy
| | - Carlo Agostoni
- grid.414818.00000 0004 1757 8749Pediatric Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Marie-Louise Syrén
- grid.4708.b0000 0004 1757 2822Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Stefano Turolo
- grid.414818.00000 0004 1757 8749Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Paola Marchisio
- grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy ,grid.414818.00000 0004 1757 8749Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Francesco Amati
- grid.452490.eDepartment of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy ,grid.417728.f0000 0004 1756 8807Respiratory Unit, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Stefano Aliberti
- grid.452490.eDepartment of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy ,grid.417728.f0000 0004 1756 8807Respiratory Unit, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Angelo Sala
- grid.4708.b0000 0004 1757 2822Department of Pharmaceutical Sciences-DISFARM, University of Milan, 20122 Milan, Italy
| | - Francesco Blasi
- grid.414818.00000 0004 1757 8749Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
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5
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Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A, Mathur R. Age and the aging process significantly alter the small bowel microbiome. Cell Rep 2021; 36:109765. [PMID: 34592155 DOI: 10.1016/j.celrep.2021.109765] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/22/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
Gut microbial diversity decreases with aging, but existing studies have used stool samples, which do not represent the entire gut. We analyzed the duodenal microbiome in 251 subjects aged 18-35 (n = 32), 36-50 (n = 41), 51-65 (n = 96), and 66-80 (n = 82). Decreased duodenal microbial diversity in older subjects is associated with combinations of chronological age, number of concomitant diseases, and number of medications used, and also correlated with increasing coliform numbers (p < 0.0001). Relative abundance (RA) of phylum Proteobacteria increases in older subjects, with increased RA of family Enterobacteriaceae and coliform genera Escherichia and Klebsiella, and is associated with alterations in the RA of other duodenal microbial taxa and decreased microbial diversity. Increased RA of specific genera are associated with chronological age only (Escherichia, Lactobacillus, and Enterococcus), number of medications only (Klebsiella), or number of concomitant diseases only (Clostridium and Bilophila). These findings indicate the small intestinal microbiome changes significantly with age and the aging process.
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Affiliation(s)
- Gabriela Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA; Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, CA, USA
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Christine Chang
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Ava Hosseini
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Jiajing Wang
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA; Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, CA, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai, Los Angeles, CA, USA.
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6
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Gramegna A, Aliberti S, Terranova L, Oriano M, Contarini M, Blasi F. Prevalence and serotyping of S. pneumoniae in a large vaccine-naive cohort of adults with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2021; 40:2443-2446. [PMID: 33937933 DOI: 10.1007/s10096-021-04263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
We conducted a prospective, observational study at the Adult CF Center, Ospedale Policlinico, Milano, Italy, from March 2017 to September 2019 to assess the prevalence and serotypes of Streptococcus pneumoniae (SP) in adults with CF naive to pneumococcal vaccination. Spontaneous sputum samples from 129 patients were analyzed for SP DNA and serotyped. SP was found in 24 subjects (19%) and the most common serotypes were 19F (16%), 4 (6%), and 9VA (3%). Higher FEV1 and non-pseudomonas infection significantly associate with SP on sputum. These results define a subgroup of patients that might deserve implementation of microbiological techniques directed to pneumococcal detection.
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Affiliation(s)
- Andrea Gramegna
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy. .,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy.
| | - Leonardo Terranova
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Martina Oriano
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Martina Contarini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
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7
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Weiser R, Rye PD, Mahenthiralingam E. Implementation of microbiota analysis in clinical trials for cystic fibrosis lung infection: Experience from the OligoG phase 2b clinical trials. J Microbiol Methods 2021; 181:106133. [PMID: 33421446 DOI: 10.1016/j.mimet.2021.106133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 11/28/2022]
Abstract
Culture-independent microbiota analysis is widely used in research and being increasingly used in translational studies. However, methods for standardisation and application of these analyses in clinical trials are limited. Here we report the microbiota analysis that accompanied two phase 2b clinical trials of the novel, non-antibiotic therapy OligoG CF-5/20 for cystic fibrosis (CF) lung infection. Standardised protocols (DNA extraction, PCR, qPCR and 16S rRNA gene sequencing analysis) were developed for application to the Pseudomonas aeruginosa (NCT02157922) and Burkholderia cepacia complex (NCT02453789) clinical trials involving 45 and 13 adult trial participants, respectively. Microbiota analysis identified that paired sputum samples from an individual participant, taken within 2 h of each other, had reproducible bacterial diversity profiles. Although culture microbiology had identified patients as either colonised by P. aeruginosa or B. cepacia complex species at recruitment, microbiota analysis revealed patient lung infection communities were not always dominated by these key CF pathogens. Microbiota profiles were patient-specific and remained stable over the course of both clinical trials (6 sampling points over the course of 140 days). Within the Burkholderia trial, participants were infected with B. cenocepacia (n = 4), B. multivorans (n = 6), or an undetermined species (n = 3). Colonisation with either B. cenocepacia or B. multivorans influenced the overall bacterial community structure in sputum. Overall, we have shown that sputum microbiota in adults with CF is stable over a 2 h time-frame, suggesting collection of a single sample on a collection day is sufficient to capture the microbiota diversity. Despite the uniform pathogen culture-positivity status at recruitment, trial participants were highly heterogeneous in their lung microbiota. Understanding the microbiota profiles of individuals with CF ahead of future clinical trials would be beneficial in the context of patient stratification and trial design.
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Affiliation(s)
- Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, Wales, CF10 3AX, UK.
| | - Philip D Rye
- AlgiPharma AS, Industriveien 33, N-1337, Sandvika, Norway.
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, Wales, CF10 3AX, UK.
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8
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Folino F, Fattizzo M, Ruggiero L, Oriano M, Aliberti S, Blasi F, Gaffuri M, Marchisio P, Torretta S. Nasopharyngeal Microbiota Analysis in Healthy and Otitis-prone Children: Focus on History of Spontaneous Tympanic Membrane Perforation. Pediatr Infect Dis J 2021; 40:16-21. [PMID: 33055502 DOI: 10.1097/inf.0000000000002895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Recurrent acute otitis media (RAOM) is common in children, and it may result in spontaneous tympanic membrane perforation (STMP), management of which is often challenging. In the upper respiratory tract (URT), resident microorganisms play a pivotal role in otitis media pathogenesis and prevention, as they are able to inhibit the colonization process and otopathogens growth. In particular, Dolosigranulum spp. and Corynebacterium spp. have been associated with respiratory health in several studies. This study aims at comparing both nasopharyngeal microbiota of children with RAOM versus matched controls and nasopharyngeal microbiota of children with a history of RAOM with STMP. METHOD Nasopharyngeal swabs were collected from 132 children, median age 3.51 (2.13-4.72), including 36 healthy children, 50 with RAOM without STMP, and 46 with RAOM with STMP. Bacterial DNA was subsequently extracted and 16S rRNA gene V3-V4 regions were polymerase chain reaction amplified and sequenced using Illumina MiSeq technology. RESULTS A higher relative abundance of Dolosigranulum and Corynebacterium genera was detected in the nasopharynx of healthy children (16.5% and 9.3%, respectively) in comparison with RAOM without STMP (8.9% and 4.3%, respectively) and RAOM with STMP (5.2% and 2.8%, respectively). A decreasing pattern in relative abundance of these 2 pivotal genera through disease severity was detected. In all groups, the most abundant genera were Moraxella, Streptococcus and Haemophilus, followed by Dolosigranulum and Corynebacterium. CONCLUSIONS Our study provides a characterization of the URT microbiota in otitis-prone children with and without history of recurrent STMP, suggesting that the role of Dolosigranulum and Corynebacterium in regulating the healthy URT microbiota should be further studied.
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Affiliation(s)
- Francesco Folino
- From the Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Miriam Fattizzo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pediatrics, ASST Sette Laghi, Del Ponte Hospital, Varese, Italy
| | - Luca Ruggiero
- From the Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Oriano
- From the Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Stefano Aliberti
- From the Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Blasi
- From the Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Michele Gaffuri
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Marchisio
- From the Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sara Torretta
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
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9
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Oriano M, Gramegna A, Terranova L, Sotgiu G, Sulaiman I, Ruggiero L, Saderi L, Wu B, Chalmers JD, Segal LN, Marchisio P, Blasi F, Aliberti S. Sputum neutrophil elastase associates with microbiota and Pseudomonas aeruginosa in bronchiectasis. Eur Respir J 2020; 56:13993003.00769-2020. [PMID: 32499333 DOI: 10.1183/13993003.00769-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/19/2020] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Neutrophilic inflammation is a major driver of bronchiectasis pathophysiology, and neutrophil elastase activity is the most promising biomarker evaluated in sputum to date. How active neutrophil elastase correlates with the lung microbiome in bronchiectasis is still unexplored. We aimed to understand whether active neutrophil elastase is associated with low microbial diversity and distinct microbiome characteristics. METHODS An observational, cross-sectional study was conducted at the bronchiectasis programme of the Policlinico Hospital in Milan, Italy, where adults with bronchiectasis were enrolled between March 2017 and March 2019. Active neutrophil elastase was measured on sputum collected during stable state, microbiota analysed through 16S rRNA gene sequencing, molecular assessment of respiratory pathogens carried out through real-time PCR and clinical data collected. RESULTS Among 185 patients enrolled, decreasing α-diversity, evaluated through the Shannon entropy (ρ -0.37, p<0.00001) and Pielou's evenness (ρ -0.36, p<0.00001) and richness (ρ -0.33, p<0.00001), was significantly correlated with increasing elastase. A significant difference in median levels of Shannon entropy as detected between patients with neutrophil elastase ≥20 µg·mL-1 (median 3.82, interquartile range 2.20-4.96) versus neutrophil elastase <20 µg·mL-1 (4.88, 3.68-5.80; p<0.0001). A distinct microbiome was found in these two groups, mainly characterised by enrichment with Pseudomonas in the high-elastase group and with Streptococcus in the low-elastase group. Further confirmation of the association of Pseudomonas aeruginosa with elevated active neutrophil elastase was found based on standard culture and targeted real-time PCR. CONCLUSIONS High levels of active neutrophil elastase are associated to low microbiome diversity and specifically to P. aeruginosa infection.
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Affiliation(s)
- Martina Oriano
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy.,Dept of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Andrea Gramegna
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Leonardo Terranova
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Luca Ruggiero
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Laura Saderi
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Benjamin Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Paola Marchisio
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Francesco Blasi
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Stefano Aliberti
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
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10
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Liu J, Ran Z, Wang F, Xin C, Xiong B, Song Z. Role of pulmonary microorganisms in the development of chronic obstructive pulmonary disease. Crit Rev Microbiol 2020; 47:1-12. [PMID: 33040638 DOI: 10.1080/1040841x.2020.1830748] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic obstructive respiratory disease characterized by irreversible airway limitation and persistent respiratory symptoms. The main clinical symptoms of COPD are dyspnoea, chronic cough, and sputum. COPD is often accompanied by other respiratory diseases, which can cause worsening of the disease. COPD patients with dyspnoea and aggravation of cough and sputum symptoms represent acute exacerbations of COPD (AECOPD). There is mounting evidence suggesting that dysbiosis of pulmonary microbiota participates in the disease. However, investigations of dysbiosis of pulmonary microbiota and the disease are still in initial phases. To screen, diagnose, and treat this respiratory disease, integrating data from different studies can improve our understanding of the occurrence and development of COPD and AECOPD. In this review, COPD epidemiology and the primary triggering mechanism are explored. Emerging knowledge regarding the association of inflammation, caused by pulmonary microbiome imbalance, and changes in lung microbiome flora species involved in the development of the disease are also highlighted. These data will further our understanding of the pathogenesis of COPD and AECOPD and may yield novel strategies for the use of pulmonary microbiota as a potential therapeutic intervention.
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Affiliation(s)
- Jiexing Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhuonan Ran
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Fen Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Caiyan Xin
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China
| | - Bin Xiong
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, PR China.,Molecular Biotechnology Platform, Public Center of Experimental Technology, Southwest Medical University, Luzhou, PR China
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11
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Amati F, Simonetta E, Gramegna A, Tarsia P, Contarini M, Blasi F, Aliberti S. The biology of pulmonary exacerbations in bronchiectasis. Eur Respir Rev 2019; 28:28/154/190055. [PMID: 31748420 DOI: 10.1183/16000617.0055-2019] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Bronchiectasis is a heterogeneous chronic disease. Heterogeneity characterises bronchiectasis not only in the stable state but also during exacerbations, despite evidence on clinical and biological aspects of bronchiectasis, exacerbations still remain poorly understood.Although the scientific community recognises that bacterial infection is a cornerstone in the development of bronchiectasis, there is a lack of data regarding other trigger factors for exacerbations. In addition, a huge amount of data suggest a primary role of neutrophils in the stable state and exacerbation of bronchiectasis, but the inflammatory reaction involves many other additional pathways. Cole's vicious cycle hypothesis illustrates how airway dysfunction, airway inflammation, infection and structural damage are linked. The introduction of the concept of a "vicious vortex" stresses the complexity of the relationships between the components of the cycle. In this model of disease, exacerbations work as a catalyst, accelerating the progression of disease. The roles of microbiology and inflammation need to be considered as closely linked and will need to be investigated in different ways to collect samples. Clinical and translational research is of paramount importance to achieve a better comprehension of the pathophysiology of bronchiectasis, microbiology and inflammation both in the stable state and during exacerbations.
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Affiliation(s)
- Francesco Amati
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Edoardo Simonetta
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Gramegna
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Tarsia
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Contarini
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Blasi
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy .,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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12
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Leite GGS, Morales W, Weitsman S, Celly S, Parodi G, Mathur R, Sedighi R, Barlow GM, Rezaie A, Pimentel M. Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study. BMC Microbiol 2019; 19:239. [PMID: 31675917 PMCID: PMC6824053 DOI: 10.1186/s12866-019-1617-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 10/20/2019] [Indexed: 12/16/2022] Open
Abstract
Background The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associated methodologies are ill-suited for the viscosity and low microbial biomass of small intestine samples. As part of the REIMAGINE study to examine the specific roles of the small bowel microbiome in human health and disease, this study aimed to develop and validate methodologies to optimize microbial analysis of the small intestine. Results Subjects undergoing esophagogastroduodenoscopy without colon preparation for standard of care were prospectively recruited, and ~ 2 ml samples of luminal fluid were obtained from the duodenum using a custom sterile aspiration catheter. Samples of duodenal aspirates were either untreated (DA-U, N = 127) or pretreated with dithiothreitol (DA-DTT, N = 101), then cultured on MacConkey agar for quantitation of aerobic gram-negative bacteria, typically from the class Gammaproteobacteria, and on blood agar for quantitation of anaerobic microorganisms. DA-DTT exhibited 2.86-fold greater anaerobic bacterial counts compared to DA-U (P = 0.0101), but were not statistically different on MacConkey agar. DNA isolation from DA-U (N = 112) and DA-DTT (N = 43) samples and library preparation for 16S rRNA gene sequencing were also performed using modified protocols. DA-DTT samples exhibited 3.81-fold higher DNA concentrations (P = 0.0014) and 4.18-fold higher 16S library concentrations (P < 0.0001) then DA-U samples. 16S rRNA gene sequencing revealed increases in the detected relative abundances of obligate and facultative anaerobes in DA-DTT samples, including increases in the genera Clostridium (false discovery rate (FDR) P = 4.38E-6), Enterococcus (FDR P = 2.57E-8), Fusobacterium (FDR P = 0.02) and Bacteroides (FDR P = 5.43E-9). Detected levels of Gram-negative enteropathogens from the phylum Proteobacteria, such as Klebsiella (FDR P = 2.73E-6) and Providencia (FDR P < 0.0001) (family Enterobacteriaceae) and Pseudomonas (family Pseudomonadaceae) (FDR P = 0.04), were also increased in DA-DTT samples. Conclusions This study validates novel DTT-based methodology which optimizes microbial culture and 16S rRNA gene sequencing for the study of the small bowel microbiome. The microbial analyses indicate increased isolation of facultative and obligate anaerobes from the mucus layer using these novel techniques.
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Affiliation(s)
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA. .,Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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13
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Bevivino A, Bacci G, Drevinek P, Nelson MT, Hoffman L, Mengoni A. Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration. Trends Mol Med 2019; 25:1110-1122. [PMID: 31439509 DOI: 10.1016/j.molmed.2019.07.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/14/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Despite over a decade of cystic fibrosis (CF) microbiome research, much remains to be learned about the overall composition, metabolic activities, and pathogenicity of the microbes in CF airways, limiting our understanding of the respiratory microbiome's relation to disease. Systems-level integration and modeling of host-microbiome interactions may allow us to better define the relationships between microbiological characteristics, disease status, and treatment response. In this way, modeling could pave the way for microbiome-based development of predictive models, individualized treatment plans, and novel therapeutic approaches, potentially serving as a paradigm for approaching other chronic infections. In this review, we describe the challenges facing this effort and propose research priorities for a systems biology approach to CF lung disease.
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Affiliation(s)
- Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy.
| | - Giovanni Bacci
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Pavel Drevinek
- Department of Medical Microbiology, Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Maria T Nelson
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Lucas Hoffman
- Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
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