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Gorostidi-Aicua M, Reparaz I, Otaegui-Chivite A, García K, Romarate L, Álvarez de Arcaya A, Mendiburu I, Arruti M, Castillo-Triviño T, Moles L, Otaegui D. Bacteria-Fungi Interactions in Multiple Sclerosis. Microorganisms 2024; 12:872. [PMID: 38792701 PMCID: PMC11124083 DOI: 10.3390/microorganisms12050872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus Torulaspora and the bacterial family Enterobacteriaceae were observed in pwMS, whereas beneficial bacterial taxa, such as Prevotelladaceae and Dialister, were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi-bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management.
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Affiliation(s)
- Miriam Gorostidi-Aicua
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Iraia Reparaz
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Ane Otaegui-Chivite
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Koldo García
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Leire Romarate
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Amaya Álvarez de Arcaya
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Araba, 01009 Vitoria-Gasteiz, Spain;
| | - Idoia Mendiburu
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Maialen Arruti
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Tamara Castillo-Triviño
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Laura Moles
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - David Otaegui
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
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O'Dea AL, Feng R, Glaser LJ, Kubrak C, Rubenstein RC, Dorgan DJ, Hadjiliadis D, Kawut SM, Hong G. The Clinical Association between Aspergillus fumigatus and Respiratory Outcomes in Adolescents and Adults with Cystic Fibrosis. Ann Am Thorac Soc 2023; 20:984-992. [PMID: 36800434 DOI: 10.1513/annalsats.202210-852oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/17/2023] [Indexed: 02/19/2023] Open
Abstract
Rationale: The clinical significance of Aspergillus fumigatus (Af) detection in the absence of allergic bronchopulmonary aspergillosis in cystic fibrosis (CF) airways remains unclear. Yet, some clinicians initiate antifungal therapy for Af-positive respiratory cultures out of concern for infection in people with CF. Objectives: To determine the association between the presence of Af and respiratory outcomes in individuals with CF. Methods: We conducted a prospective longitudinal cohort study of 206 adults and adolescents (age 14 yr and older) with CF and collected sputum for selective fungus culture. We assessed clinical outcome measurements, including patient-reported outcomes (measured by the Cystic Fibrosis Questionnaire-Revised), spirometry, and number of pulmonary exacerbations (PEx) for a 1-year period. We used mixed-effects linear models to determine the association between positive Af culture results, defined as Af detection in sputum culture at the study visit, with both respiratory domain score and forced expiratory volume in 1 second (FEV1) percent predicted, adjusted for confounders. Mixed-effects Poisson regression models were employed to examine the association between positive Af culture results and PEx events. We explored the association between Af history, defined as Af detection at baseline or within 2 years of enrollment, and respiratory outcomes. Results: Af prevalence was 10.3% (95% confidence interval [CI], 6.8, 15.7) at baseline. Forty-eight (23.3%; 95% CI, 17.7, 29.7) participants had at least one Af-positive culture result during the study period. Positive Af culture result was not associated with lower respiratory domain score. However, Af history was associated with a 6.48-point lower respiratory domain score, reflective of worse respiratory quality of life (95% CI, -11.96, -0.99; P = 0.02). Positive Af culture result was associated with a 2.54% lower FEV1 percent predicted (95% CI, -4.64, -0.44; P = 0.02) and a 1.71-fold increase in severe PEx incidence (95% CI, 1.05, 2.76; P = 0.03). Conclusions: Positive Af culture result was not associated with lower patient-reported, respiratory-related quality of life. Yet, positive Af culture result was associated with both lower FEV1 percent predicted and increased frequency of severe PEx warranting intravenous antibiotics in adolescents and adults with CF. Future studies are required to better understand the direct role of Af in lung disease progression in CF.
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Affiliation(s)
- Anna L O'Dea
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
| | - Rui Feng
- Center for Clinical Epidemiology and Biostatistics, and
| | - Laurel J Glaser
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Christina Kubrak
- Division of Allergy and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in Saint Louis, St. Louis, Missouri; and
| | - Ronald C Rubenstein
- Division of Allergy and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in Saint Louis, St. Louis, Missouri; and
| | - Daniel J Dorgan
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
| | - Denis Hadjiliadis
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Steven M Kawut
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
- Center for Clinical Epidemiology and Biostatistics, and
| | - Gina Hong
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine
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Kristensen M, de Koff EM, Chu ML, Groendijk S, Tramper-Stranders GA, de Winter-de Groot KM, Janssens HM, Tiddens HA, van Westreenen M, Sanders EAM, Arets BHGM, van der Ent CK, Prevaes SMPJ, Bogaert D. 16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients. Microbiol Spectr 2023; 11:e0405722. [PMID: 37199622 PMCID: PMC10269535 DOI: 10.1128/spectrum.04057-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.
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Affiliation(s)
- Maartje Kristensen
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma M. de Koff
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Mei Ling Chu
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simone Groendijk
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Karin M. de Winter-de Groot
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hettie M. Janssens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harm A. Tiddens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mireille van Westreenen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elisabeth A. M. Sanders
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bert H. G. M. Arets
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine M. P. J. Prevaes
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Debby Bogaert
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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Song Y, Kim MS, Chung J, Na HS. Simultaneous Analysis of Bacterial and Fungal Communities in Oral Samples from Intubated Patients in Intensive Care Unit. Diagnostics (Basel) 2023; 13:diagnostics13101784. [PMID: 37238268 DOI: 10.3390/diagnostics13101784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/28/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Intubated patients in intensive care units (ICUs) too frequently contract ventilator-associated pneumonia or Candida infections. Oropharyngeal microbes are believed to play an important etiologic role. This study was undertaken to determine whether next-generation sequencing (NGS) can be used to simultaneously analyze bacterial and fungal communities. Buccal samples were collected from intubated ICU patients. Primers targeting the V1-V2 region of bacterial 16S rRNA and the internal transcribed spacer 2 (ITS2) region of fungal 18S rRNA were used. V1-V2, ITS2, or mixed V1-V2/ITS2 primers were used to prepare an NGS library. Bacterial and fungal relative abundances were comparable for V1-V2, ITS2, or mixed V1-V2/ITS2 primers, respectively. A standard microbial community was used to adjust the relative abundances to theoretical abundance, and NGS and RT-PCR-adjusted relative abundances showed a high correlation. Using mixed V1-V2/ITS2 primers, bacterial and fungal abundances were simultaneously determined. The constructed microbiome network revealed novel interkingdom and intrakingdom interactions, and the simultaneous detection of bacterial and fungal communities using mixed V1-V2/ITS2 primers enabled analysis across two kingdoms. This study provides a novel approach to simultaneously determining bacterial and fungal communities using mixed V1-V2/ITS2 primers.
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Affiliation(s)
- Yuri Song
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
- Oral Genomics Research Center, Pusan National University, Yangsan 50612, Republic of Korea
| | - Myoung Soo Kim
- Department of Nursing, College of Natural Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
- Oral Genomics Research Center, Pusan National University, Yangsan 50612, Republic of Korea
- Dental Research Institute, BK21 PLUS Project, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
- Oral Genomics Research Center, Pusan National University, Yangsan 50612, Republic of Korea
- Dental Research Institute, BK21 PLUS Project, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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Smythe P, Wilkinson HN. The Skin Microbiome: Current Landscape and Future Opportunities. Int J Mol Sci 2023; 24:ijms24043950. [PMID: 36835363 PMCID: PMC9963692 DOI: 10.3390/ijms24043950] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.
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Affiliation(s)
- Paisleigh Smythe
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Holly N. Wilkinson
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
- Correspondence:
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Fungal Infection and Inflammation in Cystic Fibrosis. Pathogens 2021; 10:pathogens10050618. [PMID: 34069863 PMCID: PMC8157353 DOI: 10.3390/pathogens10050618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022] Open
Abstract
Fungi are frequently recovered from lower airway samples from people with cystic fibrosis (CF), yet the role of fungi in the progression of lung disease is debated. Recent studies suggest worsening clinical outcomes associated with airway fungal detection, although most studies to date are retrospective or observational. The presence of fungi can elicit a T helper cell type 2 (Th-2) mediated inflammatory reaction known as allergic bronchopulmonary aspergillosis (ABPA), particularly in those with a genetic atopic predisposition. In this review, we discuss the epidemiology of fungal infections in people with CF, risk factors associated with development of fungal infections, and microbiologic approaches for isolation and identification of fungi. We review the spectrum of fungal disease presentations, clinical outcomes after isolation of fungi from airway samples, and the importance of considering airway co-infections. Finally, we discuss the association between fungi and airway inflammation highlighting gaps in knowledge and future research questions that may further elucidate the role of fungus in lung disease progression.
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Spacova I, Van Beeck W, Seys S, Devos F, Vanoirbeek J, Vanderleyden J, Ceuppens J, Petrova M, Lebeer S. Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model. Gut Microbes 2020; 11:1729-1744. [PMID: 32522072 PMCID: PMC7524350 DOI: 10.1080/19490976.2020.1766345] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Allergic asthma is a highly prevalent inflammatory disease of the lower airways, clinically characterized by airway hyperreactivity and deterioration of airway function. Immunomodulatory probiotic bacteria are increasingly being explored to prevent asthma development, alone or in combination with other treatments. In this study, wild-type and recombinant probiotic Lactobacillus rhamnosus GR-1 were tested as preventive treatment of experimental allergic asthma in mice. Recombinant L. rhamnosus GR-1 was designed to produce the major birch pollen allergen Bet v 1, to promote allergen-specific immunomodulation. Administration of wild-type and recombinant L. rhamnosus GR-1 prevented the development of airway hyperreactivity. Recombinant L. rhamnosus GR-1 also prevented elevation of airway total cell counts, lymphocyte counts and lung IL-1β levels, while wild-type L. rhamnosus GR-1 inhibited airway eosinophilia. Of note, a shift in gut microbiome composition was observed after asthma development, which correlated with the severity of airway inflammation and airway hyperreactivity. In the groups that received L. rhamnosus GR-1, this asthma-associated shift in gut microbiome composition was not observed, indicating microbiome-modulating effects of this probiotic. These data demonstrate that L. rhamnosus GR-1 can prevent airway function deterioration in allergic asthma. Bet v 1 expression by L. rhamnosus GR-1 further contributed to lower airway inflammation, although not solely through the expected reduction in T helper 2-associated responses, suggesting involvement of additional mechanisms. The beneficial effects of L. rhamnosus GR-1 correlate with increased gut microbiome resilience, which in turn is linked to protection of airway function, and thus further adds support to the existence of a gut-lung axis.
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Affiliation(s)
- Irina Spacova
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium,Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Wannes Van Beeck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sven Seys
- Allergy and Clinical Immunology Research Group, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Fien Devos
- Centre for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Jeroen Vanoirbeek
- Centre for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Jozef Vanderleyden
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Jan Ceuppens
- Allergy and Clinical Immunology Research Group, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Mariya Petrova
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium,Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium,Microbiome Insights and Probiotics Consultancy, Karlovo, Bulgaria,Mariya Petrova Microbiome insights and Probiotics Consultancy,Karlovo4300, Bulgaria
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium,Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium,CONTACT Sarah Lebeer University of Antwerp, Department of Bioscience Engineering,AntwerpB-2020, Belgium
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Roisin L, Melloul E, Woerther PL, Royer G, Decousser JW, Guillot J, Dannaoui E, Botterel F. Modulated Response of Aspergillus fumigatus and Stenotrophomonas maltophilia to Antimicrobial Agents in Polymicrobial Biofilm. Front Cell Infect Microbiol 2020; 10:574028. [PMID: 33123497 PMCID: PMC7573239 DOI: 10.3389/fcimb.2020.574028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction: The complexity of biofilms constitutes a therapeutic challenge and the antimicrobial susceptibility of fungal-bacterial biofilms remains poorly studied. The filamentous fungus Aspergillus fumigatus (Af) and the Gram-negative bacillus Stenotrophomonas maltophilia (Sm) can form biofilms and can be co-isolated from the airways of cystic fibrosis (CF) patients. We previously developed an in vitro biofilm model which highlighted the antibiosis effect of Sm on Af, which was dependent on the bacterial fitness. The aim of the present study was to investigate the in vitro susceptibility of Af and Sm in mono- or polymicrobial biofilms to five antimicrobial agents alone and in two-drug combinations. Methods: Af and Sm clinical reference strains and two strains from CF sputa were tested through a planktonic and biofilm approaches. Af, Sm, or Af-Sm susceptibilities to amphotericin B (AMB), itraconazole (ITC), voriconazole (VRC), levofloxacin (LVX), and rifampicin (RFN) were evaluated by conventional planktonic techniques, crystal violet, XTT, qPCR, and viable plate count. Results: Af planktonic cells and biofilms in formation were more susceptible to AMB, ITC, and VRC than Af mature biofilms. Af mature biofilms were susceptible to AMB, but not to ITC and VRC. Based on viable plate count, a lower concentration of LVX and RFN was required to reduce Sm cell numbers on biofilms in formation compared with mature biofilms. The antibiosis effect of Sm on Af growth was more pronounced for the association of CF strains that exhibited a higher fitness than the reference strains. In Af-Sm biofilms, the fungal susceptibility to AMB was increased compared with Af biofilms. In contrast, the bacterial susceptibility to LVX decreased in Af-Sm biofilms and was fungal biomass-dependent. The combination of AMB (64 μg/mL) with LVX or RFN (4 μg/mL) was efficient to impair Af and Sm growth in the polymicrobial biofilm. Conclusion: Sm increased the Af susceptibility to AMB, whereas Af protected Sm from LVX. Interactions between Af and Sm within biofilms modulate susceptibility to antimicrobial agents, opening the way to new antimicrobial strategies in CF patients.
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Affiliation(s)
- Lolita Roisin
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Elise Melloul
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Paul-Louis Woerther
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France.,Unité de Bactériologie-Hygiène, Département de prévention, diagnostic et traitement des infections, Hôpital Henri Mondor, AP-HP, Créteil, France
| | - Guilhem Royer
- Unité de Bactériologie-Hygiène, Département de prévention, diagnostic et traitement des infections, Hôpital Henri Mondor, AP-HP, Créteil, France.,LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Evry, Université Paris-Saclay, CNRS, Evry, France
| | - Jean-Winoc Decousser
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France.,Unité de Bactériologie-Hygiène, Département de prévention, diagnostic et traitement des infections, Hôpital Henri Mondor, AP-HP, Créteil, France
| | - Jacques Guillot
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France.,Unité de Parasitologie-Mycologie, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Eric Dannaoui
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France.,Unité de Parasitologie-Mycologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP, Université Paris-Descartes, Paris, France
| | - Françoise Botterel
- EA 7380 Dynamyc, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France.,Unité de Parasitologie-Mycologie, Département de prévention, diagnostic et traitement des infections, Hôpital Henri Mondor, AP-HP, Créteil, France
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10
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Rick EM, Woolnough KF, Seear PJ, Fairs A, Satchwell J, Richardson M, Monteiro WR, Craner M, Bourne M, Wardlaw AJ, Pashley CH. The airway fungal microbiome in asthma. Clin Exp Allergy 2020; 50:1325-1341. [PMID: 32808353 DOI: 10.1111/cea.13722] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Fungal involvement in asthma is associated with severe disease. The full spectrum of fungal species in asthma is not well described and is derived largely from insensitive culture techniques. OBJECTIVES To use high-throughput sequencing to describe the airway mycobiota in asthmatics with and without fungal sensitization and healthy controls; to compare samples representing different airway compartments; to determine whether the mycobiota was influenced by the fungal composition of outdoor air; and to compare findings with clinically relevant outcomes. METHODS We amplified the internal transcribed spacer region 2 of the nuclear ribosomal operon to identify the fungal species present. Ninety-seven subjects were recruited and provided sputum (83 asthmatics; 14 healthy subjects), with 29 also undergoing a bronchoscopy. A subset of airway samples were compared with matched outdoor air and mouthwash samples. RESULTS Two hundred and six taxa at the species level were identified in sputum, most at low relative abundance. Aspergillus fumigatus, Candida albicans and Mycosphaerella tassiana had the highest relative abundances and were the most prevalent species across all subjects. The airway mycobiota consisted of a complex community with high diversity between individuals. Notable shifts in the balance of fungi detected in the lung were associated with asthma status, asthma duration and biomarkers of inflammation. Aspergillus tubingensis, a member of the Aspergillus niger species complex, was most prevalent from bronchoscopic protected brush samples and significantly associated with a low sputum neutrophilia. Cryptococcus pseudolongus, from the Cryptococcus humicola species complex, was more abundant from bronchoscopy samples than sputum, and differentially more abundant in asthma than health. CONCLUSIONS AND CLINICAL RELEVANCE The airway mycobiota was dominated by a relatively small number of species, but was distinct from the oropharyngeal mycobiota and air samples. Members of the A. niger and C. humicola species complexes may play unexpected roles in the pathogenesis of asthma.
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Affiliation(s)
- Eva-Maria Rick
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Kerry F Woolnough
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Paul J Seear
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Abbie Fairs
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Jack Satchwell
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
| | - Matthew Richardson
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - William R Monteiro
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Michelle Craner
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Michelle Bourne
- Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Andrew J Wardlaw
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK.,Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, Glenfield Hospital, University Hospitals of Leicester, Leicester, UK
| | - Catherine H Pashley
- Department of Respiratory Sciences, Institute for Lung Health, Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, UK
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11
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Hamm PS, Taylor JW, Cook JA, Natvig DO. Decades-old studies of fungi associated with mammalian lungs and modern DNA sequencing approaches help define the nature of the lung mycobiome. PLoS Pathog 2020; 16:e1008684. [PMID: 32730326 PMCID: PMC7392203 DOI: 10.1371/journal.ppat.1008684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Paris S. Hamm
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail:
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12
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Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens. BMC Microbiol 2020; 20:113. [PMID: 32397992 PMCID: PMC7218582 DOI: 10.1186/s12866-020-01795-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Careful consideration of experimental artefacts is required in order to successfully apply high-throughput 16S ribosomal ribonucleic acid (rRNA) gene sequencing technology. Here we introduce experimental design, quality control and "denoising" approaches for sequencing low biomass specimens. RESULTS We found that bacterial biomass is a key driver of 16S rRNA gene sequencing profiles generated from bacterial mock communities and that the use of different deoxyribonucleic acid (DNA) extraction methods [DSP Virus/Pathogen Mini Kit® (Kit-QS) and ZymoBIOMICS DNA Miniprep Kit (Kit-ZB)] and storage buffers [PrimeStore® Molecular Transport medium (Primestore) and Skim-milk, Tryptone, Glucose and Glycerol (STGG)] further influence these profiles. Kit-QS better represented hard-to-lyse bacteria from bacterial mock communities compared to Kit-ZB. Primestore storage buffer yielded lower levels of background operational taxonomic units (OTUs) from low biomass bacterial mock community controls compared to STGG. In addition to bacterial mock community controls, we used technical repeats (nasopharyngeal and induced sputum processed in duplicate, triplicate or quadruplicate) to further evaluate the effect of specimen biomass and participant age at specimen collection on resultant sequencing profiles. We observed a positive correlation (r = 0.16) between specimen biomass and participant age at specimen collection: low biomass technical repeats (represented by < 500 16S rRNA gene copies/μl) were primarily collected at < 14 days of age. We found that low biomass technical repeats also produced higher alpha diversities (r = - 0.28); 16S rRNA gene profiles similar to no template controls (Primestore); and reduced sequencing reproducibility. Finally, we show that the use of statistical tools for in silico contaminant identification, as implemented through the decontam package in R, provides better representations of indigenous bacteria following decontamination. CONCLUSIONS We provide insight into experimental design, quality control steps and "denoising" approaches for 16S rRNA gene high-throughput sequencing of low biomass specimens. We highlight the need for careful assessment of DNA extraction methods and storage buffers; sequence quality and reproducibility; and in silico identification of contaminant profiles in order to avoid spurious results.
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13
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Angebault C, Payen M, Woerther PL, Rodriguez C, Botterel F. Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? PLoS One 2020; 15:e0232215. [PMID: 32343737 PMCID: PMC7188255 DOI: 10.1371/journal.pone.0232215] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota. Methods Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results. Results AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3–11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa. Conclusion Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.
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Affiliation(s)
- Cécile Angebault
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA DYNAMiC 7380, Faculté de Santé, Univ Paris-Est Créteil, Créteil, France
- EA DYNAMiC 7380, Ecole nationale vétérinaire d’Alfort, USC Anses, Maison-Alfort, France
- * E-mail:
| | - Mathilde Payen
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
| | - Paul-Louis Woerther
- EA DYNAMiC 7380, Faculté de Santé, Univ Paris-Est Créteil, Créteil, France
- Unité de Bactériologie-Hygiène, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, APHP, Créteil, France
| | - Christophe Rodriguez
- Next-Generation Sequencing Platform”Génomiques”, INSERM U955, APHP, IMRB Créteil, Créteil, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA DYNAMiC 7380, Faculté de Santé, Univ Paris-Est Créteil, Créteil, France
- EA DYNAMiC 7380, Ecole nationale vétérinaire d’Alfort, USC Anses, Maison-Alfort, France
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Shi X, Gao Z, Lin Q, Zhao L, Ma Q, Kang Y, Yu J. Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:590-602. [PMID: 32171662 PMCID: PMC7212475 DOI: 10.1016/j.gpb.2018.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/25/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
The lethal chronic airway infection of the cystic fibrosis (CF) patients is predisposed by colonization of specific CF-philic pathogens or the CF microbiomes, but key processes and reasons of the microbiome settlement in the patients are yet to be fully understood, especially their survival and metabolic dynamics from normal to diseased status under treatment. Here, we report our meta-analysis results on CF airway microbiomes based on metabolic networks reconstructed from genome information at species level. The microbiomes of CF patients appear to engage much more redox-related activities than those of controls, and by constructing a large dataset of anti-oxidative stress (anti-OS) genes, our quantitative evaluation of the anti-OS capacity of each bacterial species in the CF microbiomes confirms strong conservation of the anti-OS responses within genera and also shows that the CF pathogens have significantly higher anti-OS capacity than commensals and other typical respiratory pathogens. In addition, the anti-OS capacity of a relevant species correlates with its relative fitness for the airways of CF patients over that for the airways of controls. Moreover, the total anti-OS capacity of the respiratory microbiome of CF patients is collectively higher than that of controls, which increases with disease progression, especially after episodes of acute exacerbation and antibiotic treatment. According to these results, we propose that the increased OS in the airways of CF patients may play an important role in reshaping airway microbiomes to a more resistant status that favors the pre-infection colonization of the CF pathogens for a higher anti-OS capacity.
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Affiliation(s)
- Xing Shi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100190, China
| | - Zhancheng Gao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Qiang Lin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Qin Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science and Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100190, China.
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15
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Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep 2020; 10:3589. [PMID: 32108159 PMCID: PMC7046743 DOI: 10.1038/s41598-020-60015-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.
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Affiliation(s)
- Perrine Soret
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | - Louise-Eva Vandenborght
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- Genoscreen Society, 59000, Lille, France
| | - Florence Francis
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Noémie Coron
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France
| | - Raphael Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Marta Avalos
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | | | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Rodolphe Thiebaut
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France.
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France.
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France.
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France.
- University and CHU of Lille, F-59000, Lille, France.
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Martín-Gómez MT. Taking a look on fungi in cystic fibrosis: More questions than answers. Rev Iberoam Micol 2020; 37:17-23. [PMID: 31928888 DOI: 10.1016/j.riam.2019.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) is one of the most frequent recessive inherited diseases in western countries. Advances in medical care have led to a substantial increase in the life expectancy of CF patients. Survival beyond adolescence has permitted to see fungi not only as late colonizers, but also as potential pathogens responsible of allergic reactions and chronic infections related to lung function deterioration. The role of fungi, nevertheless, has been overlooked until recently. As a result, a number of questions on their epidemiology, clinical significance, or diagnosis, among others, remain unanswered. Besides more in depth studies about the extent of the deleterious effect of fungi on the CF host, new technologies may provide the key to understand its pathogenic role, its interaction with other microbial components of the respiratory microbiota, and should pave the way to define subsets of patients at risk who would benefit from specific therapy. This review is intended to provide a quick overview on what we know about the presence of fungi in the CF airway and its repercussion in the host, and to point out some of the many knowledge gaps needed to understand and advance in the management of fungi in the airway of CF subjects.
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Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia 2020; 185:207-231. [PMID: 31894501 PMCID: PMC7223441 DOI: 10.1007/s11046-019-00413-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Karlyn Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kenny J X Lau
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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18
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Fungal Infections and ABPA. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gangneux JP, Guegan H, Vandenborght LE, Buffet-Bataillon S, Enaud R, Delhaes L. A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing. Mycoses 2019; 62:1096-1099. [PMID: 31498487 DOI: 10.1111/myc.12999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022]
Abstract
Although substantial efforts have been made to investigate about the composition of the microbiota, fungi that constitute the mycobiota play a pivotal role in maintaining microbial communities and physiological processes in the body. Here, we conducted an international survey focusing on laboratory's current procedures regarding their goals and practices of mycobiota characterisation using NGS. A questionnaire was proposed to laboratories affiliated to working groups from ECMM (NGS study group) and ESCMID (ESGHAMI and EFISG study groups). Twenty-six questionnaires from 18 countries were received. The use of NGS to characterise the mycobiota was not in routine for most of the laboratories (N = 23, 82%), and the main reason of using NGS was primary to understand the pathophysiology of a dysbiosis (N = 20), to contribute to a diagnosis (N = 16) or to implement a therapeutic strategy (N = 12). Other reported reasons were to evaluate the exposome (environmental studies) (N = 10) or to investigate epidemics (N = 8). Sputum is the main sample studied, and cystic fibrosis represents a major disease studied via the analysis of pulmonary microbiota. No consensus has emerged for the choice of the targets with 18S, ITS1 and ITS2 used alternatively among the laboratories. Other answers are detailed in the manuscript. We report a photography of mycobiota analysis that may become a major tool in the near future. We can draw some conclusions on the diversity of approaches within the answers of the 27 laboratories and underline the need for standardisation.
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Affiliation(s)
- Jean-Pierre Gangneux
- CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Hélène Guegan
- CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Louise-Eva Vandenborght
- CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France
| | - Sylvie Buffet-Bataillon
- CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Raphael Enaud
- CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France
| | - Laurence Delhaes
- CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France
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20
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The Human Lung Mycobiome in Chronic Respiratory Disease: Limitations of Methods and Our Current Understanding. CURRENT FUNGAL INFECTION REPORTS 2019. [DOI: 10.1007/s12281-019-00347-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Interactions between Aspergillus fumigatus and Pulmonary Bacteria: Current State of the Field, New Data, and Future Perspective. J Fungi (Basel) 2019; 5:jof5020048. [PMID: 31212791 PMCID: PMC6617096 DOI: 10.3390/jof5020048] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Aspergillus fumigatus and Pseudomonas aeruginosa are central fungal and bacterial members of the pulmonary microbiota. The interactions between A. fumigatus and P. aeruginosa have only just begun to be explored. A balance between inhibitory and stimulatory effects on fungal growth was observed in mixed A. fumigatus-P. aeruginosa cultures. Negative interactions have been seen for homoserine-lactones, pyoverdine and pyochelin resulting from iron starvation and intracellular inhibitory reactive oxidant production. In contrast, several types of positive interactions were recognized. Dirhamnolipids resulted in the production of a thick fungal cell wall, allowing the fungus to resist stress. Phenazines and pyochelin favor iron uptake for the fungus. A. fumigatus is able to use bacterial volatiles to promote its growth. The immune response is also differentially regulated by co-infections.
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22
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Krüger W, Vielreicher S, Kapitan M, Jacobsen ID, Niemiec MJ. Fungal-Bacterial Interactions in Health and Disease. Pathogens 2019; 8:E70. [PMID: 31117285 PMCID: PMC6630686 DOI: 10.3390/pathogens8020070] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 12/28/2022] Open
Abstract
Fungi and bacteria encounter each other in various niches of the human body. There, they interact directly with one another or indirectly via the host response. In both cases, interactions can affect host health and disease. In the present review, we summarized current knowledge on fungal-bacterial interactions during their commensal and pathogenic lifestyle. We focus on distinct mucosal niches: the oral cavity, lung, gut, and vagina. In addition, we describe interactions during bloodstream and wound infections and the possible consequences for the human host.
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Affiliation(s)
- Wibke Krüger
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Sarah Vielreicher
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Mario Kapitan
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
| | - Ilse D Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
- Institute of Microbiology, Friedrich Schiller University, Jena 07743, Germany.
| | - Maria Joanna Niemiec
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
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23
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Richardson M, Bowyer P, Sabino R. The human lung and Aspergillus: You are what you breathe in? Med Mycol 2019; 57:S145-S154. [PMID: 30816978 PMCID: PMC6394755 DOI: 10.1093/mmy/myy149] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/01/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
The diversity of fungal species comprising the lung mycobiome is a reflection of exposure to environmental and endogenous filamentous fungi and yeasts. Most lung mycobiome studies have been culture-based. A few have utilized next generation sequencing (NGS). Despite the low number of published NGS studies, several themes emerge from the literature: (1) moulds and yeasts are present in the human respiratory tract, even during health; (2) the fungi present in the respiratory tract are highly variable between individuals; and (3) many diseases are accompanied by decreased diversity of fungi in the lungs. Even in patients with the same disease, different patients have been shown to harbor distinct fungal communities. Those fungal species present in any one individual may represent a patient's unique environmental exposure(s), either to species restricted to the indoor environment, for example, Penicillium, or species found in the outdoor environment such as Aspergillus, wood and vegetation colonizing fungi and plant pathogens. In addition to causing clinical fungal infections, the lung mycobiome may have inflammatory effects that can cause or worsen lung disease. Most respiratory diseases that have been studied, have been associated with decreases in fungal diversity. However, none of these diversity studies distinguish between accidental, transient fungal colonizers and true residents of the respiratory tract. Where does Aspergillus feature in the mycobiomes of the respiratory tract? Do these mycobiomes reflect the diversity of fungi in outdoor and internal environments? These intriguing questions are explored here.
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Affiliation(s)
- Malcolm Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Bowyer
- Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Raquel Sabino
- Nacional Institute of Health Dr. Ricardo Jorge - URSZ- Infectious Diseases Department, Lisbon, Portugal
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24
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McTaggart LR, Copeland JK, Surendra A, Wang PW, Husain S, Coburn B, Guttman DS, Kus JV. Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis. Front Microbiol 2019; 10:512. [PMID: 30930884 PMCID: PMC6428700 DOI: 10.3389/fmicb.2019.00512] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect a wide range of fungi and applied it to analysis of the fungal microbiome (mycobiome) of the lung during fungal infection. Internal transcribed spacer 1 (ITS1) amplicon sequencing and a custom analysis pipeline detected 96% of species from three mock communities comprised of potential fungal lung pathogens with good recapitulation of the expected species distributions (Pearson correlation coefficients r = 0.63, p = 0.004; r = 0.71, p < 0.001; r = 0.62, p = 0.002). We used this pipeline to analyze mycobiomes of bronchoalveolar lavage (BAL) specimens classified as culture-negative (n = 50) or culture-positive (n = 39) for Blastomyces dermatitidis/gilchristii, the causative agent of North America blastomycosis. Detected in 91.4% of the culture-positive samples, Blastomyces dominated (>50% relative abundance) the mycobiome in 68.6% of these culture-positive samples but was absent in culture-negative samples. To overcome any bias in relative abundance due to between-sample variation in fungal biomass, an abundance-weighting calculation was used to normalize the data by accounting for sample-specific PCR cycle number and PCR product concentration data utilized during sample preparation. After normalization, there was a statistically significant greater overall abundance of ITS1 amplicon in the Blastomyces-culture-positive samples versus culture-negative samples. Moreover, the normalization revealed a greater biomass of yeast and environmental fungi in several Blastomyces-culture-positive samples than in the culture-negative samples. Successful detection of Coccidioides, Scedosporium, Phaeoacremonium, and Aspergillus in 6 additional culture-positive BALs by ITS1 amplicon sequencing demonstrates the ability of this method to detect a broad range of fungi from clinical specimens, suggesting that it may be a potentially useful adjunct to traditional fungal microbiological testing for the diagnosis of respiratory mycoses.
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Affiliation(s)
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | | | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Shahid Husain
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julianne V Kus
- Public Health Ontario, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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25
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Fungal Respiratory Infections in Cystic Fibrosis (CF): Recent Progress and Future Research Agenda. Mycopathologia 2019; 183:1-5. [PMID: 29349726 DOI: 10.1007/s11046-017-0241-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Tracy MC, Moss RB. The myriad challenges of respiratory fungal infection in cystic fibrosis. Pediatr Pulmonol 2018; 53:S75-S85. [PMID: 29992775 DOI: 10.1002/ppul.24126] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/21/2018] [Indexed: 12/27/2022]
Abstract
Fungal infection in cystic fibrosis (CF) is a recognized challenge, with many areas requiring further investigation. Consensus definitions exist for allergic bronchopulmonary aspergillus in CF, but the full scope of clinically relevant non-allergic fungal disease in CF-asymptomatic colonization, transient or chronic infection localized to endobronchial mucus plugs or airway tissue, and invasive disease-is yet to be clearly defined. Recent advances in mycological culture and non-culture identification have expanded the list of both potential pathogens and community commensals in the lower respiratory tract. Here we aim to outline the current understanding of fungal presence in the CF respiratory tract, risk factors for acquiring fungi, host-pathogen interactions that influence the role of fungi from bystander to pathogen, advances in the diagnostic approaches to isolating and identifying fungi in CF respiratory samples, challenges of classifying clinical phenotypes of CF patients with fungi, and current treatment approaches. Development and validation of biomarkers characteristic of different fungal clinical phenotypes, and controlled trials of antifungal agents in well-characterized target populations, remain central challenges to surmount and goals to be achieved.
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Affiliation(s)
- Michael C Tracy
- Center for Excellence in Pulmonary Biology, Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University Medical School, Palo Alto, California
| | - Richard B Moss
- Center for Excellence in Pulmonary Biology, Division of Pulmonary, Asthma and Sleep Medicine, Department of Pediatrics, Stanford University Medical School, Palo Alto, California
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