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Chu VT, Tsitsiklis A, Mick E, Ambroggio L, Kalantar KL, Glascock A, Osborne CM, Wagner BD, Matthay MA, DeRisi JL, Calfee CS, Mourani PM, Langelier CR. The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients. Nat Commun 2024; 15:92. [PMID: 38168095 PMCID: PMC10762195 DOI: 10.1038/s41467-023-44353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Antimicrobial resistant lower respiratory tract infections are an increasing public health threat and an important cause of global mortality. The lung microbiome can influence susceptibility of respiratory tract infections and represents an important reservoir for exchange of antimicrobial resistance genes. Studies of the gut microbiome have found an association between age and increasing antimicrobial resistance gene burden, however, corollary studies in the lung microbiome remain absent. We performed an observational study of children and adults with acute respiratory failure admitted to the intensive care unit. From tracheal aspirate RNA sequencing data, we evaluated age-related differences in detectable antimicrobial resistance gene expression in the lung microbiome. Using a multivariable logistic regression model, we find that detection of antimicrobial resistance gene expression was significantly higher in adults compared with children after adjusting for demographic and clinical characteristics. This association remained significant after additionally adjusting for lung bacterial microbiome characteristics, and when modeling age as a continuous variable. The proportion of adults expressing beta-lactam, aminoglycoside, and tetracycline antimicrobial resistance genes was higher compared to children. Together, these findings shape our understanding of the lung resistome in critically ill patients across the lifespan, which may have implications for clinical management and global public health.
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Affiliation(s)
- Victoria T Chu
- Division of Infectious Diseases & Global Health, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Alexandra Tsitsiklis
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | | | | | - Christina M Osborne
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Brandie D Wagner
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Michael A Matthay
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Peter M Mourani
- Arkansas Children's Research Institute, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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Yi XZ, Yang JH, Huang Y, Han XR, Li HM, Cen LJ, Lin ZH, Pan CX, Wang Z, Guan WJ. Differential airway resistome and its correlations with clinical characteristics in Haemophilus- or Pseudomonas-predominant microbial subtypes of bronchiectasis. Respir Res 2023; 24:264. [PMID: 37919749 PMCID: PMC10623730 DOI: 10.1186/s12931-023-02562-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023] Open
Abstract
The prevalence and clinical correlates of antibiotic resistance genes (ARGs) in bronchiectasis are not entirely clear. We aimed to profile the ARGs in sputum from adults with bronchiectasis, and explore the association with airway microbiome and disease severity and subtypes. In this longitudinal study, we prospectively collected 118 sputum samples from stable and exacerbation visits of 82 bronchiectasis patients and 19 healthy subjects. We profiled ARGs with shotgun metagenomic sequencing, and linked these to sputum microbiome and clinical characteristics, followed by validation in an international cohort. We compared ARG profiles in bronchiectasis according to disease severity, blood and sputum inflammatory subtypes. Unsupervised clustering revealed a Pseudomonas predominant subgroup (n = 16), Haemophilus predominant subgroup (n = 48), and balanced microbiome subgroup (N = 54). ARGs of multi-drug resistance were over-dominant in the Pseudomonas-predominant subgroup, while ARGs of beta-lactam resistance were most abundant in the Haemophilus-predominant subgroup. Pseudomonas-predominant subgroup yielded the highest ARG diversity and total abundance, while Haemophilus-predominant subgroup and balanced microbiota subgroup were lowest in ARG diversity and total abundance. PBP-1A, ksgA and emrB (multidrug) were most significantly enriched in Haemophilus-predominant subtype. ARGs generally correlated positively with Bronchiectasis Severity Index, fluoroquinolone use, and modified Reiff score. 68.6% of the ARG-clinical correlations could be validated in an independent international cohort. In conclusion, ARGs are differentially associated with the dominant microbiome and clinical characteristics in bronchiectasis.
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Affiliation(s)
- Xin-Zhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China
| | - Jun-Hao Yang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China
| | - Yan Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
- Department of Geriatrics, National Key Clinical Specialty, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Xiao-Rong Han
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui-Min Li
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China
| | - Lai-Jian Cen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
| | - Zhen-Hong Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
| | - Cui-Xia Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China.
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China.
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
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Chu VT, Tsitsiklis A, Mick E, Ambroggio L, Kalantar KL, Glascock A, Osborne CM, Wagner BD, Matthay MA, DeRisi JL, Calfee CS, Mourani PM, Langelier CR. The antibiotic resistance reservoir of the lung microbiome expands with age. RESEARCH SQUARE 2023:rs.3.rs-3283415. [PMID: 37790384 PMCID: PMC10543260 DOI: 10.21203/rs.3.rs-3283415/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Antimicrobial resistant lower respiratory tract infections (LRTI) are an increasing public health threat, and an important cause of global mortality. The lung microbiome influences LRTI susceptibility and represents an important reservoir for exchange of antimicrobial resistance genes (ARGs). Studies of the gut microbiome have found an association between age and increasing antimicrobial resistance gene (ARG) burden, however corollary studies in the lung microbiome remain absent, despite the respiratory tract representing one of the most clinically significant sites for drug resistant infections. We performed a prospective, multicenter observational study of 261 children and 88 adults with acute respiratory failure, ranging in age from 31 days to ≥ 89 years, admitted to intensive care units in the United States. We performed RNA sequencing on tracheal aspirates collected within 72 hours of intubation, and evaluated age-related differences in detectable ARG expression in the lung microbiome as a primary outcome. Secondary outcomes included number and classes of ARGs detected, proportion of patients with an ARG class, and composition of the lung microbiome. Multivariable logistic regression models (adults vs children) or continuous age (years) were adjusted for sex, race/ethnicity, LRTI status, and days from intubation to specimen collection. Detection of ARGs was significantly higher in adults compared with children after adjusting for sex, race/ethnicity, LRTI diagnosis, and days from intubation to specimen collection (adjusted odds ratio (aOR): 2.16, 95% confidence interval (CI): 1.10-4.22). A greater proportion of adults compared with children had beta-lactam ARGs (31% (CI: 21-41%) vs 13% (CI: 10-18%)), aminoglycoside ARGs (20% (CI: 13-30%) vs 2% (CI: 0.6-4%)), and tetracycline ARGs (14% (CI: 7-23%) vs 3% (CI: 1-5%)). Adults ≥70 years old had the highest proportion of these three ARG classes. The total bacterial abundance of the lung microbiome increased with age, and microbiome alpha diversity varied with age. Taxonomic composition of the lung microbiome, measured by Bray Curtis dissimilarity index, differed between adults and children (p = 0.003). The association between age and increased ARG detection remained significant after additionally including lung microbiome total bacterial abundance and alpha diversity in the multivariable logistic regression model (aOR: 2.38, (CI: 1.25-4.54)). Furthermore, this association remained robust when modeling age as a continuous variable (aOR: 1.02, (CI: 1.01-1.03) per year of age). Taken together, our results demonstrate that age is an independent risk factor for ARG detection in the lower respiratory tract microbiome. These data shape our understanding of the lung resistome in critically ill patients across the lifespan, which may have implications for clinical management and global public health.
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Affiliation(s)
- Victoria T. Chu
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexandra Tsitsiklis
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, CO, USA
| | | | | | - Christina M. Osborne
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, CO, USA
| | - Brandie D. Wagner
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, CO, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Michael A. Matthay
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Peter M. Mourani
- Arkansas Children’s Research Institute, Arkansas Children’s Hospital, Little Rock, AR, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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O’Connor L, Heyderman R. The challenges of defining the human nasopharyngeal resistome. Trends Microbiol 2023:S0966-842X(23)00056-2. [DOI: 10.1016/j.tim.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023]
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Pailhoriès H, Herrmann JL, Velo-Suarez L, Lamoureux C, Beauruelle C, Burgel PR, Héry-Arnaud G. Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome. Eur Respir Rev 2022; 31:31/164/210259. [PMID: 35613743 DOI: 10.1183/16000617.0259-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
The development of resistome analysis, i.e. the comprehensive analysis of antibiotic-resistance genes (ARGs), is enabling a better understanding of the mechanisms of antibiotic-resistance emergence. The respiratory microbiome is a dynamic and interactive network of bacteria, with a set of ARGs that could influence the response to antibiotics. Viruses such as bacteriophages, potential carriers of ARGs, may also form part of this respiratory resistome. Chronic respiratory diseases (CRDs) such as cystic fibrosis, severe asthma, chronic obstructive pulmonary disease and bronchiectasis, managed with long-term antibiotic therapies, lead to multidrug resistance. Antibiotic susceptibility testing provides a partial view of the bacterial response to antibiotics in the complex lung environment. Assessing the ARG network would allow personalised, targeted therapeutic strategies and suitable antibiotic stewardship in CRDs, depending on individual resistome and microbiome signatures. This review summarises the influence of pulmonary antibiotic protocols on the respiratory microbiome, detailing the variable consequences according to antibiotic class and duration of treatment. The different resistome-profiling methods are explained to clarify their respective place in antibiotic-resistance analysis in the lungs. Finally, this review details current knowledge on the respiratory resistome related to therapeutic strategies and provides insight into the application of resistome analysis to counter the emergence of multidrug-resistant respiratory pathogens.
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Affiliation(s)
- Hélène Pailhoriès
- Laboratoire de Bactériologie, Institut de Biologie en Santé - PBH, CHU Angers, Angers, France.,HIFIH Laboratory UPRES EA3859, SFR ICAT 4208, Angers University, Angers, France
| | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, INSERM, Infection and Inflammation, Montigny-le-Bretonneux, France.,AP-HP, Groupe Hospitalo-Universitaire Paris-Saclay, Hôpital Raymond Poincaré, Garches, France
| | - Lourdes Velo-Suarez
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France
| | - Claudie Lamoureux
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Clémence Beauruelle
- Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Pierre-Régis Burgel
- Respiratory Medicine and National Cystic Fibrosis Reference Center, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Institut Cochin, INSERM U1016, Paris, France
| | - Geneviève Héry-Arnaud
- Brest Center for Microbiota Analysis (CBAM), Brest University Hospital, Brest, France .,Dept of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
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Reece E, Bettio PHDA, Renwick J. Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10070827. [PMID: 34356747 PMCID: PMC8300716 DOI: 10.3390/antibiotics10070827] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most dominant pathogens in cystic fibrosis (CF) airway disease and contributes to significant inflammation, airway damage, and poorer disease outcomes. The CF airway is now known to be host to a complex community of microorganisms, and polymicrobial interactions have been shown to play an important role in shaping P. aeruginosa pathogenicity and resistance. P. aeruginosa can cause chronic infections that once established are almost impossible to eradicate with antibiotics. CF patients that develop chronic P. aeruginosa infection have poorer lung function, higher morbidity, and a reduced life expectancy. P. aeruginosa adapts to the CF airway and quickly develops resistance to several antibiotics. A perplexing phenomenon is the disparity between in vitro antimicrobial sensitivity testing and clinical response. Considering the CF airway is host to a diverse community of microorganisms or 'microbiome' and that these microorganisms are known to interact, the antimicrobial resistance and progression of P. aeruginosa infection is likely influenced by these microbial relationships. This review combines the literature to date on interactions between P. aeruginosa and other airway microorganisms and the influence of these interactions on P. aeruginosa tolerance to antimicrobials.
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Crofts TS, McFarland AG, Hartmann EM. Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. mSystems 2021; 6:e0052421. [PMID: 34184912 PMCID: PMC8269240 DOI: 10.1128/msystems.00524-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.
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Affiliation(s)
- Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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Yi B, Dalpke AH, Boutin S. Changes in the Cystic Fibrosis Airway Microbiome in Response to CFTR Modulator Therapy. Front Cell Infect Microbiol 2021; 11:548613. [PMID: 33816324 PMCID: PMC8010178 DOI: 10.3389/fcimb.2021.548613] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
The development of CFTR modulator therapies significantly changed the treatment scheme of people with cystic fibrosis. However, CFTR modulator therapy is still a life-long treatment, which is not able to correct the genetic defect and cure the disease. Therefore, it becomes crucial to understand the effects of such modulation of CFTR function on the airway physiology, especially on airway infections and inflammation that are currently the major life-limiting factors in people with cystic fibrosis. In this context, understanding the dynamics of airway microbiome changes in response to modulator therapy plays an essential role in developing strategies for managing airway infections. Whether and how the newly available therapies affect the airway microbiome is still at the beginning of being deciphered. We present here a brief review summarizing the latest information about microbiome alterations in light of modern cystic fibrosis modulator therapy.
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Affiliation(s)
- Buqing Yi
- Medical Faculty, Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Alexander H Dalpke
- Medical Faculty, Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany
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Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease. Microorganisms 2020; 8:microorganisms8071003. [PMID: 32635564 PMCID: PMC7409339 DOI: 10.3390/microorganisms8071003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.
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