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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [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: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Gnaien M, Maufrais C, Rebai Y, Kallel A, Ma L, Hamouda S, Khalsi F, Meftah K, Smaoui H, Khemiri M, Hadj Fredj S, Bachellier-Bassi S, Najjar I, Messaoud T, Boussetta K, Kallel K, Mardassi H, d’Enfert C, Bougnoux ME, Znaidi S. A gain-of-function mutation in zinc cluster transcription factor Rob1 drives Candida albicans adaptive growth in the cystic fibrosis lung environment. PLoS Pathog 2024; 20:e1012154. [PMID: 38603707 PMCID: PMC11037546 DOI: 10.1371/journal.ppat.1012154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/23/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Candida albicans chronically colonizes the respiratory tract of patients with Cystic Fibrosis (CF). It competes with CF-associated pathogens (e.g. Pseudomonas aeruginosa) and contributes to disease severity. We hypothesize that C. albicans undergoes specific adaptation mechanisms that explain its persistence in the CF lung environment. To identify the underlying genetic and phenotypic determinants, we serially recovered 146 C. albicans clinical isolates over a period of 30 months from the sputum of 25 antifungal-naive CF patients. Multilocus sequence typing analyses revealed that most patients were individually colonized with genetically close strains, facilitating comparative analyses between serial isolates. We strikingly observed differential ability to filament and form monospecies and dual-species biofilms with P. aeruginosa among 18 serial isolates sharing the same diploid sequence type, recovered within one year from a pediatric patient. Whole genome sequencing revealed that their genomes were highly heterozygous and similar to each other, displaying a highly clonal subpopulation structure. Data mining identified 34 non-synonymous heterozygous SNPs in 19 open reading frames differentiating the hyperfilamentous and strong biofilm-former strains from the remaining isolates. Among these, we detected a glycine-to-glutamate substitution at position 299 (G299E) in the deduced amino acid sequence of the zinc cluster transcription factor ROB1 (ROB1G299E), encoding a major regulator of filamentous growth and biofilm formation. Introduction of the G299E heterozygous mutation in a co-isolated weak biofilm-former CF strain was sufficient to confer hyperfilamentous growth, increased expression of hyphal-specific genes, increased monospecies biofilm formation and increased survival in dual-species biofilms formed with P. aeruginosa, indicating that ROB1G299E is a gain-of-function mutation. Disruption of ROB1 in a hyperfilamentous isolate carrying the ROB1G299E allele abolished hyperfilamentation and biofilm formation. Our study links a single heterozygous mutation to the ability of C. albicans to better survive during the interaction with other CF-associated microbes and illuminates how adaptive traits emerge in microbial pathogens to persistently colonize and/or infect the CF-patient airways.
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Affiliation(s)
- Mayssa Gnaien
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR16IPT01), Tunis, Tunisia
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, INRAE USC2019A, Département Mycologie, Unité Biologie et Pathogénicité Fongiques, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Yasmine Rebai
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR16IPT01), Tunis, Tunisia
| | - Aicha Kallel
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR16IPT01), Tunis, Tunisia
- Hôpital La Rabta, Laboratoire de Parasitologie et de Mycologie, UR17SP03, Tunis, Tunisia
| | - Laurence Ma
- Institut Pasteur, Université Paris Cité, Biomics core facility, Centre de Ressources et Recherche Technologique (C2RT), Paris, France
| | - Samia Hamouda
- Hôpital d’Enfants Béchir Hamza de Tunis, Tunis, Tunisia
| | - Fatma Khalsi
- Hôpital d’Enfants Béchir Hamza de Tunis, Tunis, Tunisia
| | | | - Hanen Smaoui
- Hôpital d’Enfants Béchir Hamza de Tunis, Tunis, Tunisia
| | - Monia Khemiri
- Hôpital d’Enfants Béchir Hamza de Tunis, Tunis, Tunisia
| | | | - Sophie Bachellier-Bassi
- Institut Pasteur, Université Paris Cité, INRAE USC2019A, Département Mycologie, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Imène Najjar
- Institut Pasteur, Université Paris Cité, Biomics core facility, Centre de Ressources et Recherche Technologique (C2RT), Paris, France
| | | | | | - Kalthoum Kallel
- Hôpital La Rabta, Laboratoire de Parasitologie et de Mycologie, UR17SP03, Tunis, Tunisia
| | - Helmi Mardassi
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR16IPT01), Tunis, Tunisia
| | - Christophe d’Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019A, Département Mycologie, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Marie-Elisabeth Bougnoux
- Institut Pasteur, Université Paris Cité, INRAE USC2019A, Département Mycologie, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Sadri Znaidi
- Institut Pasteur de Tunis, University of Tunis El Manar, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR16IPT01), Tunis, Tunisia
- Institut Pasteur, Université Paris Cité, INRAE USC2019A, Département Mycologie, Unité Biologie et Pathogénicité Fongiques, Paris, France
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Lussac-Sorton F, Charpentier É, Imbert S, Lefranc M, Bui S, Fayon M, Berger P, Enaud R, Delhaes L. The gut-lung axis in the CFTR modulator era. Front Cell Infect Microbiol 2023; 13:1271117. [PMID: 37780857 PMCID: PMC10540301 DOI: 10.3389/fcimb.2023.1271117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
The advent of CFTR modulators represents a turning point in the history of cystic fibrosis (CF) management, changing profoundly the disease's clinical course by improving mucosal hydration. Assessing changes in airway and digestive tract microbiomes is of great interest to better understand the mechanisms and to predict disease evolution. Bacterial and fungal dysbiosis have been well documented in patients with CF; yet the impact of CFTR modulators on microbial communities has only been partially deciphered to date. In this review, we aim to summarize the current state of knowledge regarding the impact of CFTR modulators on both pulmonary and digestive microbiomes. Our analysis also covers the inter-organ connections between lung and gut communities, in order to highlight the gut-lung axis involvement in CF pathophysiology and its evolution in the era of novel modulators therapies.
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Affiliation(s)
- Florian Lussac-Sorton
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
| | - Éléna Charpentier
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
| | - Sébastien Imbert
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Maxime Lefranc
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Stéphanie Bui
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Raphaël Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
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Hong G, Daniel SG, Lee JJ, Bittinger K, Glaser L, Mattei LM, Dorgan DJ, Hadjiliadis D, Kawut SM, Collman RG. Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis. J Cyst Fibros 2023; 22:636-643. [PMID: 36822979 PMCID: PMC10440372 DOI: 10.1016/j.jcf.2023.02.003] [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: 10/12/2022] [Revised: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics. METHODS We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated. RESULTS Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences. CONCLUSION The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.
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Affiliation(s)
- Gina Hong
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Daniel J Dorgan
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Denis Hadjiliadis
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Steven M Kawut
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Ronald G Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
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Boutin S, Nurjadi D. The lung microbiome in cystic fibrosis: A gap of knowledge still to be filled. J Cyst Fibros 2023; 22:595-596. [PMID: 37487763 DOI: 10.1016/j.jcf.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023]
Affiliation(s)
- Sébastien Boutin
- University of Lübeck, Department of Infectious Diseases and Microbiology, Lübeck, Germany; Airway Research Center North (ARCN), German center for Lung Research (DZL), Lübeck, Germany.
| | - Dennis Nurjadi
- University of Lübeck, Department of Infectious Diseases and Microbiology, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
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Caparrós-Martín JA, Saladie M, Agudelo-Romero SP, Reen FJ, Ware RS, Sly PD, Stick SM, O'Gara F. Detection of bile acids in bronchoalveolar lavage fluid defines the inflammatory and microbial landscape of the lower airways in infants with cystic fibrosis. MICROBIOME 2023; 11:132. [PMID: 37312128 DOI: 10.1186/s40168-023-01543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/05/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cystic Fibrosis (CF) is a genetic condition characterized by neutrophilic inflammation and recurrent infection of the airways. How these processes are initiated and perpetuated in CF remains largely unknown. We have demonstrated a link between the intestinal microbiota-related metabolites bile acids (BA) and inflammation in the bronchoalveolar lavage fluid (BALF) from children with stable CF lung disease. To establish if BA indicate early pathological processes in CF lung disease, we combined targeted mass spectrometry and amplicon sequencing-based microbial characterization of 121 BALF specimens collected from 12-month old infants with CF enrolled in the COMBAT-CF study, a multicentre randomized placebo-controlled clinical trial comparing azithromycin versus placebo. We evaluated whether detection of BA in BALF is associated with the establishment of the inflammatory and microbial landscape of early CF lung disease, and whether azithromycin, a motilin agonist that has been demonstrated to reduce aspiration of gastric contents, alters the odds of detecting BA in BALF. We also explored how different prophylactic antibiotics regimens impact the early life BALF microbiota. RESULTS Detection of BA in BALF was strongly associated with biomarkers of airway inflammation, more exacerbation episodes during the first year of life, increased use of oral antibiotics with prolonged treatment periods, a higher degree of structural lung damage, and distinct microbial profiles. Treatment with azithromycin, a motilin agonist, which has been reported to reduce aspiration of gastric contents, did not reduce the odds of detecting BA in BALF. Culture and molecular methods showed that azithromycin does not alter bacterial load or diversity in BALF. Conversely, penicillin-type prophylaxis reduced the odds of detecting BAs in BALF, which was associated with elevated levels of circulating biomarkers of cholestasis. We also observed that environmental factors such as penicillin-type prophylaxis or BAs detection were linked to distinct early microbial communities of the CF airways, which were associated with different inflammatory landscapes but not with structural lung damage. CONCLUSIONS Detection of BA in BALF portend early pathological events in CF lung disease. Benefits early in life associated with azithromycin are not linked to its antimicrobial properties. Video Abstract.
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Affiliation(s)
- Jose A Caparrós-Martín
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia
| | - Montserrat Saladie
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia
- Present Address: Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Reus, Spain
| | - S Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - F Jerry Reen
- School of Microbiology, University College Cork, Cork, Ireland
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Peter D Sly
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Stephen M Stick
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Fergal O'Gara
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Health Innovation Research Institute (CHIRI), Curtin University, Perth, WA, Australia.
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, T12 K8AF, Ireland.
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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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8
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O’Connor JB, Wagner BD, Harris JK, Frank DN, Clabots DE, Laguna TA. Detection and identification of fungi in the lower airway of children with and without cystic fibrosis. Front Microbiol 2023; 14:1119703. [PMID: 36846802 PMCID: PMC9948248 DOI: 10.3389/fmicb.2023.1119703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Airway infection and inflammation lead to the progression of obstructive lung disease in persons with cystic fibrosis (PWCF). However, cystic fibrosis (CF) fungal communities, known drivers of CF pathophysiology, remain poorly understood due to the shortcomings of traditional fungal culture. Our objective was to apply a novel small subunit rRNA gene (SSU-rRNA) sequencing approach to characterize the lower airway mycobiome in children with and without CF. Methods Bronchoalveolar lavage fluid (BALF) samples and relevant clinical data were collected from pediatric PWCF and disease control (DC) subjects. Total fungal load (TFL) was measured using quantitative PCR, and SSU-rRNA sequencing was used for mycobiome characterization. Results were compared across groups, and Morisita-Horn clustering was performed. Results 161 (84%) of the BALF samples collected had sufficient load for SSU-rRNA sequencing, with amplification being more common in PWCF. BALF from PWCF had increased TFL and increased neutrophilic inflammation compared to DC subjects. PWCF exhibited increased abundance of Aspergillus and Candida, while Malassezia, Cladosporium, and Pleosporales were prevalent in both groups. CF and DC samples showed no clear differences in clustering when compared to each other or to negative controls. SSU-rRNA sequencing was used to profile the mycobiome in pediatric PWCF and DC subjects. Notable differences were observed between the groups, including the abundance of Aspergillus and Candida. Discussion Fungal DNA detected in the airway could represent a combination of pathogenic fungi and environmental exposure (e.g., dust) to fungus indicative of a common background signature. Next steps will require comparisons to airway bacterial communities.
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Affiliation(s)
- John B. O’Connor
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States,*Correspondence: John B. O’Connor, ✉
| | - Brandie D. Wagner
- University of Colorado School of Medicine, Aurora, CO, United States,Colorado School of Public Health, University of Colorado Denver, Aurora, CO, United States
| | - J. Kirk Harris
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Daniel N. Frank
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Diana E. Clabots
- University of Colorado School of Medicine, Aurora, CO, United States,Department of Internal Medicine, Palmetto General Hospital, Hialeah, FL, United States
| | - Theresa A. Laguna
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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9
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Hong G. Progress and challenges in fungal lung disease in cystic fibrosis. Curr Opin Pulm Med 2022; 28:584-590. [PMID: 36101907 PMCID: PMC9547960 DOI: 10.1097/mcp.0000000000000921] [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] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review is an overview of the recent progress made for the diagnosis and understanding of fungal lung disease in people with cystic fibrosis (CF), with a focus on Aspergillus fumigatus , the most common filamentous fungus in the CF airway. Currently, the longstanding question of the clinical significance of Aspergillus fumigatus and other fungi in CF respiratory cultures, in the absence of allergy, remains. Clinical criteria and biomarkers are needed to classify fungal lung disease and determine who may warrant therapy. RECENT FINDINGS Several retrospective and prospective studies have described the prevalence of A. fumigatus and other fungi in the CF lung and factors contributing to the changes in fungal epidemiology. Selective fungus culture testing for the detection of fungi in CF sputa has been well studied, yet a standardized fungus culture protocol has yet to be defined. Culture-independent molecular studies and other fungal diagnostic testing have been conducted in the CF population, leading to efforts to better understand the clinical role of these tests. Recent works have aimed to determine whether chronic A. fumigatus colonization is associated with lung disease progression measured by FEV 1 percentage predicted, structural lung disease, lung clearance index and respiratory quality-of-life. However, the existing knowledge gaps remain: definition of a fungal respiratory infection, the association between fungal infection and clinical outcomes, and indications for antifungal therapy. SUMMARY Significant progress has been made for the detection and diagnosis of fungal lung disease. Yet, the role and impact of A. fumigatus and other fungal infections on respiratory health in people with CF remains to be determined.
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Affiliation(s)
- Gina Hong
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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10
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Salazar-Hamm PS, Montoya KN, Montoya L, Cook K, Liphardt S, Taylor JW, Cook JA, Natvig DO. Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:996574. [PMID: 37746221 PMCID: PMC10512277 DOI: 10.3389/ffunb.2022.996574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/24/2022] [Indexed: 09/26/2023]
Abstract
Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.
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Affiliation(s)
| | - Kyana N. Montoya
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Kel Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Schuyler Liphardt
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
| | - Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
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11
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Bacterial composition and colony structure of the lower respiratory tract in infants and children with recurrent wheezing: a case-control study. Ital J Pediatr 2022; 48:120. [PMID: 35854266 PMCID: PMC9297564 DOI: 10.1186/s13052-022-01279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The bacterial load of the human lower respiratory tract is at least several times lower than that of the other parts of the body. This study aimed to identify the bacterial composition and colony structure of the lower respiratory tract in infants and children with recurrent wheezing compared with those of children with a bronchial foreign body and clarify whether the length of wheezing in infants can contribute to differences in the lower respiratory tract's bacterial colony structure. METHODS We collected specimens of alveolar lavage fluid from 48 infants and children who underwent fiberoptic bronchoscopy and were divided into groups: A1 (multiple wheezing: wheezing more than three times in < 1 month), A2 (persistent wheezing: > 1 month), and B (bronchial foreign body; control group). We analyzed the bacterial community structure of alveolar lavage fluid using high-throughput sequencing. The richness and diversity of the microbial communities were assessed by α and β diversity analyses. RESULTS A total of 6,644 operational taxonomic units (OTUs) were obtained based on the Illumina Nova sequencing platform and clustered according to those that met the 97% identity threshold, followed by species annotation of the OTU sequences. In the annotation results, 2,608 (39.25%) OTUs were annotated at the genus level. At the genus level, Sphingomonas and Phyllobacterium were significantly higher in group A1 than in group B. There were significantly more Phyllobacterium in group A2 than in group B. Prevotella, Neisseria, and Haemophilus were higher in group B than in groups A1 and A2. The differences in the between-group α and β diversity analyses were statistically significant. The microbial diversity in groups A1 and A2 was significantly less than that in group B, but there was no statistical difference in bacterial community diversity between groups A1 and A2. CONCLUSION Recurrent wheezing in infants and children is more likely due to alterations in the overall bacterial microecology and disruption of host respiration and immune homeostasis than the effects of a single bacterium.
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12
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A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease. PLoS One 2022; 17:e0267195. [PMID: 35551278 PMCID: PMC9098062 DOI: 10.1371/journal.pone.0267195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
Background Few studies have examined the stability of the pulmonary mycobiome. We report longitudinal changes in the oral and pulmonary mycobiome of participants with and without COPD in a large-scale bronchoscopy study (MicroCOPD). Methods Repeated sampling was performed in 30 participants with and 21 without COPD. We collected an oral wash (OW) and a bronchoalveolar lavage (BAL) sample from each participant at two time points. The internal transcribed spacer 1 region of the ribosomal RNA gene cluster was PCR amplified and sequenced on an Illumina HiSeq sequencer. Differences in taxonomy, alpha diversity, and beta diversity between the two time points were compared, and we examined the effect of intercurrent antibiotic use. Results Sample pairs were dominated by Candida. We observed less stability in the pulmonary taxonomy compared to the oral taxonomy, additionally emphasised by a higher Yue-Clayton measure in BAL compared to OW (0.69 vs 0.22). No apparent effect was visually seen on taxonomy from intercurrent antibiotic use or participant category. We found no systematic variation in alpha diversity by time either in BAL (p-value 0.16) or in OW (p-value 0.97), and no obvious clusters on bronchoscopy number in PCoA plots. Pairwise distance analyses showed that OW samples from repeated sampling appeared more stable compared to BAL samples using the Bray-Curtis distance metric (p-value 0.0012), but not for Jaccard. Conclusion Results from the current study propose that the pulmonary mycobiome is less stable than the oral mycobiome, and neither COPD diagnosis nor intercurrent antibiotic use seemed to influence the stability.
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:microorganisms10040810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-336-88-32 or +34-336-83-30
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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14
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Keir HR, Chalmers JD. Neutrophil extracellular traps in chronic lung disease: implications for pathogenesis and therapy. Eur Respir Rev 2022; 31:31/163/210241. [PMID: 35197267 PMCID: PMC9488971 DOI: 10.1183/16000617.0241-2021] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Neutrophilic inflammation has a key role in the pathophysiology of multiple chronic lung diseases. The formation of neutrophil extracellular traps (NETs) has emerged as a key mechanism of disease in neutrophilic lung diseases including asthma, COPD, cystic fibrosis and, most recently, bronchiectasis. NETs are large, web-like structures composed of DNA and anti-microbial proteins that are able to bind pathogens, prevent microbial dissemination and degrade bacterial virulence factors. The release of excess concentrations of proteases, antimicrobial proteins, DNA and histones, however, also leads to tissue damage, impaired mucociliary clearance, impaired bacterial killing and increased inflammation. A number of studies have linked airway NET formation with greater disease severity, increased exacerbations and overall worse disease outcomes across the spectrum of airway diseases. Treating neutrophilic inflammation has been challenging in chronic lung disease because of the delicate balance between reducing inflammation and increasing the risk of infections through immunosuppression. Novel approaches to suppressing NET formation or the associated inflammation are in development and represent an important therapeutic target. This review will discuss the relationship between NETs and the pathophysiology of cystic fibrosis, asthma, COPD and bronchiectasis, and explore the current and future development of NET-targeting therapies. NETs contribute to the pathophysiology of chronic lung disease. Immunomodulating therapies that may reduce inflammatory mediators and NET formation, without compromising bacterial clearance, offer a new treatment path for patients. https://bit.ly/3fyJC6I
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Affiliation(s)
- Holly R Keir
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, UK
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15
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Ding F, Krasilnikova AA, Leontieva MR, Stoyanova LG, Netrusov AI. Analysis of Kefir Grains from Different Regions of the Planet Using High-Throughput Sequencing. MOSCOW UNIVERSITY BIOLOGICAL SCIENCES BULLETIN 2022; 77:286-291. [PMID: 36843649 PMCID: PMC9940072 DOI: 10.3103/s0096392522040010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/23/2022] [Accepted: 11/10/2022] [Indexed: 02/22/2023]
Abstract
The taxonomic composition and spatial localization of yeast and bacteria in kefir grains (KG) obtained for study from different regions of the planet were investigated. The diversity of their microbiome has been demonstrated by high-throughput sequencing of bacterial 16S rRNA genes and the ITS1 region of the 18S-ITS1-5.8S-ITS2-28S complex of yeast rRNA. It has been established that the main representatives of the complex community of KG from different regions are lactic acid bacteria (LAB; lactobacilli, lactococci, and Leuconostoc spp. in different ratios) and different types of yeast of the genus Kazachstania (family Saccharomycetaceae). Acetic acid bacteria and a small percentage of yeast Kluyveromyces marxianus were detected in the KG from Tibet, and yeast Pichia kluyveri was detected in the KG from Ossetia.
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Affiliation(s)
- F. Ding
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia ,Shenzhen MSU-BIT University, 518172 Shenzhen, China
| | - A. A. Krasilnikova
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - M. R. Leontieva
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - L. G. Stoyanova
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - A. I. Netrusov
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia ,Faculty of Biology and Biotechnology, High School of Economics, 101000 Moscow, Russia
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16
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Yano J, Fidel PL. Methods Related to the Immunopathogenesis of Vulvovaginal Candidiasis and Associated Neutrophil Anergy. Methods Mol Biol 2022; 2542:193-218. [PMID: 36008666 DOI: 10.1007/978-1-0716-2549-1_14] [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] [Indexed: 06/15/2023]
Abstract
Vulvovaginal candidiasis (VVC) is a common mucosal disease, caused primarily by Candida albicans that affects up to 75% of women of childbearing age. The pathogenesis of VVC and recurrent VVC (RVVC) is largely understood after decades of research. In this regard, an immunopathological response involving the migration of neutrophils that become dysfunctional (anergic) in the vaginal environment leads to the symptomatic conditions. However, immunotherapeutic strategies to correct the immunopathogenesis are still elusive. Much of the mechanistic discoveries have been uncovered using the established mouse model of chronic VVC. This chapter details the methods widely used for the mouse model of experimental VVC and associated outcome measures of the immunopathologic response and resulting symptomatic condition and focuses further on assays used to demonstrate "neutrophil anergy" in the model. These methods may serve as a source or resource for further experimentation with the ultimate goal to reduce or eliminate VVC/RVVC.
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Affiliation(s)
- Junko Yano
- Louisiana State University Health, New Orleans, LA, USA
| | - Paul L Fidel
- Louisiana State University Health, New Orleans, LA, USA.
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17
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Chronic Diseases Associated with Malassezia Yeast. J Fungi (Basel) 2021; 7:jof7100855. [PMID: 34682276 PMCID: PMC8540640 DOI: 10.3390/jof7100855] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/01/2023] Open
Abstract
Malassezia are a lipid-dependent basidiomycetous yeast of the normal skin microbiome, although Malassezia DNA has been recently detected in other body sites and has been associated with certain chronic human diseases. This new perspective raises many questions. Are these yeasts truly present in the investigated body site or were they contaminated by other body sites, adjacent or not? Does this DNA contamination come from living or dead yeast? If these yeasts are alive, do they belong to the resident mycobiota or are they transient colonizers which are not permanently established within these niches? Finally, are these yeasts associated with certain chronic diseases or not? In an attempt to shed light on this knowledge gap, we critically reviewed the 31 published studies focusing on the association of Malassezia spp. with chronic human diseases, including psoriasis, atopic dermatitis (AD), chronic rhinosinusitis (CRS), asthma, cystic fibrosis (CF), HIV infection, inflammatory bowel disease (IBD), colorectal cancer (CRC), and neurodegenerative diseases.
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MalaSelect: A Selective Culture Medium for Malassezia Species. J Fungi (Basel) 2021; 7:jof7100824. [PMID: 34682245 PMCID: PMC8538348 DOI: 10.3390/jof7100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Malassezia species are fastidious and slow-growing yeasts in which isolation from polymicrobial samples is hampered by fast-growing microorganisms. Malassezia selective culture media are needed. Although cycloheximide is often used, some fungi, including the chief human commensal Candida albicans, are resistant to this compound. This study aimed to test whether the macrolide rapamycin could be used in combination with cycloheximide to develop a Malassezia-selective culture medium. Rapamycin susceptibility testing was performed via microdilution assays in modified Dixon against two M. furfur and five Candida spp. The MIC was the lowest concentration that reduced growth by a minimum of 90%. Rapamycin ± cycloheximide 500 mg/L was also added to FastFung solid, and yeast suspensions were inoculated and incubated for 72 h. Rapamycin MICs for Candida spp. ranged from 0.5 to 2 mg/L, except for C. krusei, for which the MIC was >32 mg/L. M. furfur stains were rapamycin-resistant. Rapamycin and cycloheximide supplementation of the FastFung medium effectively inhibited the growth of non-Malassezia yeast, including cycloheximide-resistant C. albicans and C. tropicalis. Based on our findings, this “MalaSelect” medium should be further evaluated on polymicrobial samples for Malassezia isolation and culture.
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Van den Bossche S, De Broe E, Coenye T, Van Braeckel E, Crabbé A. The cystic fibrosis lung microenvironment alters antibiotic activity: causes and effects. Eur Respir Rev 2021; 30:30/161/210055. [PMID: 34526313 DOI: 10.1183/16000617.0055-2021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Chronic airway colonisation by Pseudomonas aeruginosa, a hallmark of cystic fibrosis (CF) lung disease, is associated with increased morbidity and mortality and despite aggressive antibiotic treatment, P. aeruginosa is able to persist in CF airways. In vitro antibiotic susceptibility assays are poor predictors of antibiotic efficacy to treat respiratory tract infections in the CF patient population and the selection of the antibiotic(s) is often made on an empirical base. In the current review, we discuss the factors that are responsible for the discrepancies between antibiotic activity in vitro and clinical efficacy in vivo We describe how the CF lung microenvironment, shaped by host factors (such as iron, mucus, immune mediators and oxygen availability) and the microbiota, influences antibiotic activity and varies widely between patients. A better understanding of the CF microenvironment and population diversity may thus help improve in vitro antibiotic susceptibility testing and clinical decision making, in turn increasing the success rate of antibiotic treatment.
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Affiliation(s)
| | - Emma De Broe
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Eva Van Braeckel
- Dept of Respiratory Medicine, Cystic Fibrosis Reference Centre, Ghent University Hospital, Ghent, Belgium.,Dept of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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Viñado C, Girón RM, Ibáñez E, García-Ortega A, Pérez I, Polanco D, Pemán J, Solé A. Filamentous fungi in the airway of patients with cystic fibrosis: Just spectators? Rev Iberoam Micol 2021; 38:168-174. [PMID: 34535388 DOI: 10.1016/j.riam.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/17/2021] [Accepted: 03/24/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND There are important advances in the management of bacterial infection in patients with cystic fibrosis (CF), but there are many gaps in the field of fungal infections. AIMS The aim of this study was to analyse whether chronic respiratory filamentous fungal colonization had clinical impact and whether antifungal treatment can change the disease. METHODS The prospective, bicentric and descriptive study was carried out within a 3-year follow-up period, with four-month periodicity medical controls. Adult patients from two CF units of tertiary hospitals were included. Clinical, microbiological, analytical and spirometric variables were collected. Quality of life was evaluated in a subgroup, using the Spanish version of the Revised Cystic Fibrosis Quality of Life Questionnaire (CFQ-R). To statistically analyze the evolution of forced expiratory along time (volume of air blown out in 1 second -FEV1-) and the forced vital capacity (FVC), mixed linear models were carried out. RESULTS From the ninety-eight patients under study, 40 suffered chronic filamentous fungal colonization. The presence of filamentous fungi in airway was associated to an annual fall of FEV1 and FVC of 0.029 and 0.017 litres, respectively (p<0.001). In addition, worse quality of life based on CFQ-R, significant when concerning physical condition and emotional state, was also linked with the fungal colonization. Protocolized antifungal therapy, nebulized or oral, improved FEV1 in 0.023 and 0.024 litres per year, respectively (p<0.001). CONCLUSIONS Chronic filamentous fungal colonization in patients with CF is associated with a significant annual decline of lung function that persists over time. Chronic antifungal therapy slows down this progression, mainly in the patient with more advanced disease.
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Affiliation(s)
- Clara Viñado
- Servicio de Neumología del Hospital de Barbastro, Spain.
| | - Rosa María Girón
- Unidad de Fibrosis Quística del Hospital Universitario de la Princesa de Madrid, Spain
| | - Elisa Ibáñez
- Servicio de Microbiología del Hospital Universitario y Politécnico La Fe de Valencia, Spain
| | - Alberto García-Ortega
- Unidad de Fibrosis Quística y Trasplante Pulmonar del Hospital Universitario y Politécnico La Fe de Valencia, Spain
| | - Inés Pérez
- Unidad de Fibrosis Quística y Trasplante Pulmonar del Hospital Universitario y Politécnico La Fe de Valencia, Spain
| | - Dinora Polanco
- Servicio de Neumología del Hospital Universitario Arnau de Vilanova de Lleida, Spain
| | - Javier Pemán
- Servicio de Microbiología del Hospital Universitario y Politécnico La Fe de Valencia, Spain
| | - Amparo Solé
- Unidad de Fibrosis Quística y Trasplante Pulmonar del Hospital Universitario y Politécnico La Fe de Valencia, Spain
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Ding L, Liu Y, Wu X, Wu M, Luo X, Ouyang H, Xia J, Liu X, Ding T. Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients. Front Cell Infect Microbiol 2021; 11:708827. [PMID: 34589441 PMCID: PMC8475726 DOI: 10.3389/fcimb.2021.708827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.
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Affiliation(s)
- Li Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yanmin Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaorong Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Minhao Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hui Ouyang
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jinyu Xia
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Xi Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Tao Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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22
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Tiew PY, Dicker AJ, Keir HR, Poh ME, Pang SL, Mac Aogáin M, Chua BQY, Tan JL, Xu H, Koh MS, Tee A, Abisheganaden JA, Chew FT, Miller BE, Tal-Singer R, Chalmers JD, Chotirmall SH. A high-risk airway mycobiome is associated with frequent exacerbation and mortality in COPD. Eur Respir J 2021; 57:2002050. [PMID: 32972986 DOI: 10.1183/13993003.02050-2020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The chronic obstructive pulmonary disease (COPD) bacteriome associates with disease severity, exacerbations and mortality. While COPD patients are susceptible to fungal sensitisation, the role of the fungal mycobiome remains uncertain. METHODS We report the largest multicentre evaluation of the COPD airway mycobiome to date, including participants from Asia (Singapore and Malaysia) and the UK (Scotland) when stable (n=337) and during exacerbations (n=66) as well as nondiseased (healthy) controls (n=47). Longitudinal mycobiome analysis was performed during and following COPD exacerbations (n=34), and examined in terms of exacerbation frequency, 2-year mortality and occurrence of serum specific IgE (sIgE) against selected fungi. RESULTS A distinct mycobiome profile is observed in COPD compared with controls as evidenced by increased α-diversity (Shannon index; p<0.001). Significant airway mycobiome differences, including greater interfungal interaction (by co-occurrence), characterise very frequent COPD exacerbators (three or more exacerbations per year) (permutational multivariate ANOVA; adjusted p<0.001). Longitudinal analyses during exacerbations and following treatment with antibiotics and corticosteroids did not reveal any significant change in airway mycobiome profile. Unsupervised clustering resulted in two clinically distinct COPD groups: one with increased symptoms (COPD Assessment Test score) and Saccharomyces dominance, and another with very frequent exacerbations and higher mortality characterised by Aspergillus, Curvularia and Penicillium with a concomitant increase in serum sIgE levels against the same fungi. During acute exacerbations of COPD, lower fungal diversity associates with higher 2-year mortality. CONCLUSION The airway mycobiome in COPD is characterised by specific fungal genera associated with exacerbations and increased mortality.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Alison J Dicker
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Holly R Keir
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Mau Ern Poh
- Dept of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sze Lei Pang
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
| | - Branden Qi Yu Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
| | - Jiunn Liang Tan
- Dept of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Huiying Xu
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Mariko Siyue Koh
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Augustine Tee
- Dept of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | | | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore
| | | | | | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
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23
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Adivitiya, Kaushik MS, Chakraborty S, Veleri S, Kateriya S. Mucociliary Respiratory Epithelium Integrity in Molecular Defense and Susceptibility to Pulmonary Viral Infections. BIOLOGY 2021; 10:95. [PMID: 33572760 PMCID: PMC7911113 DOI: 10.3390/biology10020095] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
Abstract
Mucociliary defense, mediated by the ciliated and goblet cells, is fundamental to respiratory fitness. The concerted action of ciliary movement on the respiratory epithelial surface and the pathogen entrapment function of mucus help to maintain healthy airways. Consequently, genetic or acquired defects in lung defense elicit respiratory diseases and secondary microbial infections that inflict damage on pulmonary function and may even be fatal. Individuals living with chronic and acute respiratory diseases are more susceptible to develop severe coronavirus disease-19 (COVID-19) illness and hence should be proficiently managed. In light of the prevailing pandemic, we review the current understanding of the respiratory system and its molecular components with a major focus on the pathophysiology arising due to collapsed respiratory epithelium integrity such as abnormal ciliary movement, cilia loss and dysfunction, ciliated cell destruction, and changes in mucus rheology. The review includes protein interaction networks of coronavirus infection-manifested implications on the molecular machinery that regulates mucociliary clearance. We also provide an insight into the alteration of the transcriptional networks of genes in the nasopharynx associated with the mucociliary clearance apparatus in humans upon infection by severe acute respiratory syndrome coronavirus-2.
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Affiliation(s)
- Adivitiya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Manish Singh Kaushik
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Soura Chakraborty
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Shobi Veleri
- Drug Safety Division, ICMR-National Institute of Nutrition, Hyderabad 500007, India;
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
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24
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Abdillah A, Khelaifia S, Raoult D, Bittar F, Ranque S. Comparison of Three Skin Sampling Methods and Two Media for Culturing Malassezia Yeast. J Fungi (Basel) 2020; 6:jof6040350. [PMID: 33316902 PMCID: PMC7770598 DOI: 10.3390/jof6040350] [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: 10/05/2020] [Revised: 11/19/2020] [Accepted: 11/27/2020] [Indexed: 11/22/2022] Open
Abstract
Malassezia is a lipid-dependent commensal yeast of the human skin. The different culture media and skin sampling methods used to grow these fastidious yeasts are a source of heterogeneity in culture-based epidemiological study results. This study aimed to compare the performances of three methods of skin sampling, and two culture media for the detection of Malassezia yeasts by culture from the human skin. Three skin sampling methods, namely sterile gauze, dry swab, and TranswabTM with transport medium, were applied on 10 healthy volunteers at 5 distinct body sites. Each sample was further inoculated onto either the novel FastFung medium or the reference Dixon agar for the detection of Malassezia spp. by culture. At least one colony of Malassezia spp. grew on 93/300 (31%) of the cultures, corresponding to 150 samplings. The positive culture rate was 67%, 18%, and 15% (P < 10−3), for samples collected with sterile gauze, TranswabTM, and dry swab, respectively. The positive culture rate was 62% and 38% (P < 0.003) by using the FastFung and the Dixon media, respectively. Our results showed that sterile gauze rubbing skin sampling followed by inoculation on FastFung medium should be implemented in the routine clinical laboratory procedure for Malassezia spp. cultivation.
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Affiliation(s)
- Abdourahim Abdillah
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 19-21 Boulevard Jean Moulin, 13005 Marseille, France;
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.K.); (D.R.); (F.B.)
| | - Saber Khelaifia
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.K.); (D.R.); (F.B.)
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.K.); (D.R.); (F.B.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, MEPHI: Microbes, Evolution, Phylogénie et Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Fadi Bittar
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.K.); (D.R.); (F.B.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, MEPHI: Microbes, Evolution, Phylogénie et Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Stéphane Ranque
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 19-21 Boulevard Jean Moulin, 13005 Marseille, France;
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.K.); (D.R.); (F.B.)
- Correspondence:
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25
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Abstract
Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing. Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing. A better understanding of the ecological dynamics of this ecosystem may enable clinicians to harness these interactions and thereby improve treatment outcomes. Like all ecosystems, the CF lung microbial community develops through a series of stages, each of which may present with distinct microbial communities that generate unique host-microbe and microbe-microbe interactions, metabolic profiles, and clinical phenotypes. While insightful models have been developed to explain some of these stages and interactions, there is no unifying model to describe how these infections develop and persist. Here, we review current perspectives on the ecology of the CF airway and present the CF Ecological Succession (CFES) model that aims to capture the spatial and temporal complexity of CF lung infection, address current challenges in disease management, and inform the development of ecologically driven therapeutic strategies.
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26
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The Domestic Environment and the Lung Mycobiome. Microorganisms 2020; 8:microorganisms8111717. [PMID: 33147738 PMCID: PMC7693370 DOI: 10.3390/microorganisms8111717] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from the houses (ENV) of 20 of them (44.4%). Additionally, five bronchoscopes (BS) were also analyzed and negative controls were included for every procedure. All samples were processed for DNA extraction and cultures, which were performed in Sabouraud Dextrose and Potato Dextrose Agar. The fungal Internal Transcribed Spacer (ITS2) was sequenced by the Solexa/Illumina system and sequences were analyzed by QIIME 1.8.0 and compared with the UNITE Database for identification. The similarity between the two fungal communities (BAL and ENV) for a specific patient was assessed via the percentage of coincidence in the detection of specific operational taxonomic units (OTUs), and about 75% of co-occurrence was detected between the mycobiome of the LRT and the houses. Cultures confirmed the presence of the core mycobiome species. However, the low rate of isolation from BAL suggests that most of its mycobiome corresponds to non-culturable cells. This likely depends on the patient’s immune system activity and inflammatory status.
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27
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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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28
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Zhang D, Wang Y, Shen S, Hou Y, Chen Y, Wang T. The mycobiota of the human body: a spark can start a prairie fire. Gut Microbes 2020; 11:655-679. [PMID: 32150513 PMCID: PMC7524315 DOI: 10.1080/19490976.2020.1731287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mycobiota are inseparable from human health, shaking up the unique position held by bacteria among microorganisms. What is surprising is that this seemingly small species can trigger huge changes in the human body. Dysbiosis and invasion of mycobiota are confirmed to cause disease in different parts of the body. Meanwhile, our body also produces corresponding immune changes upon mycobiota infection. Several recent studies have made a connection between intestinal mycobiota and the human immune system. In this review, we focus on questions related to mycobiota, starting with an introduction of select species, then we summarize the typical diseases caused by mycobiota in different parts of the human body. Moreover, we constructed a framework for the human anti-fungal immune system based on genetics and immunology. Finally, the progression of fungal detection methods is also reviewed.
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Affiliation(s)
- Di Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Sunan Shen
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yayi Hou
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yugen Chen
- Department of Colorectal Surgery, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China,CONTACT Tingting Wang The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing210093, China
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29
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Houston CJ, Taggart CC, Downey DG. The role of inflammation in cystic fibrosis pulmonary exacerbations. Expert Rev Respir Med 2020; 14:889-903. [PMID: 32544353 DOI: 10.1080/17476348.2020.1778469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Cystic Fibrosis pulmonary exacerbations are critical events in the lives of people with CF that have deleterious effects on lung function, quality of life, and life expectancy. There are significant unmet needs in the management of exacerbations. We review here the associated inflammatory changes that underlie these events and are of interest for the development of biomarkers of exacerbation. AREAS COVERED Inflammatory responses in CF are abnormal and contribute to a sustained proinflammatory lung microenvironment, abundant in proinflammatory mediators and deficient in counter-regulatory mediators that terminate and resolve inflammation. There is increasing interest in these inflammatory pathways to discover novel biomarkers for pulmonary exacerbation management. In this review, we explore the inflammatory changes occurring during intravenous antibiotic therapy for exacerbation and how they may be applied as biomarkers to guide exacerbation therapy. A literature search was conducted using the PubMed database in February 2020. EXPERT OPINION Heterogeneity in inflammatory responses to treatment of a pulmonary exacerbation, a disease process with complex pathophysiology, limits the clinical utility of individual biomarkers. Biomarker panels may be a more successful strategy to capture informative changes within the CF population to improve pulmonary exacerbation management and outcomes.
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Affiliation(s)
- Claire J Houston
- Airway Innate Immunity Group (Aiir), Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast , Northern Ireland
| | - Clifford C Taggart
- Airway Innate Immunity Group (Aiir), Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast , Northern Ireland
| | - Damian G Downey
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast , Northern Ireland.,Northern Ireland Regional Adult CF Centre, Belfast Health and Social Care Trust , Belfast, UK
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30
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Niccum BA, Kastman EK, Kfoury N, Robbat A, Wolfe BE. Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function. mSystems 2020; 5:e00149-20. [PMID: 32546667 PMCID: PMC7300356 DOI: 10.1128/msystems.00149-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury).IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.
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Affiliation(s)
- Brittany A Niccum
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Erik K Kastman
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Nicole Kfoury
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Albert Robbat
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, Massachusetts, USA
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31
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Cuthbertson L, Felton I, James P, Cox MJ, Bilton D, Schelenz S, Loebinger MR, Cookson WOC, Simmonds NJ, Moffatt MF. The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis. J Cyst Fibros 2020; 20:295-302. [PMID: 32540174 PMCID: PMC8048771 DOI: 10.1016/j.jcf.2020.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 02/08/2023]
Abstract
The prevalence of fungal disease is increasing in CF and non-CF bronchiectasis. Effective management of fungal disease requires an understanding of the mycobiome. Culture methods alone are inadequate for the accurate diagnosis of fungal disease. Our study provides a framework to characterize fungal airway disease using NGS. NGS can improve detection and clinical management of fungal infections.
Background The prevalence of fungal disease in cystic fibrosis (CF) and non-CF bronchiectasis is increasing and the clinical spectrum is widening. Poor sensitivity and a lack of standard diagnostic criteria renders interpretation of culture results challenging. In order to develop effective management strategies, a more accurate and comprehensive understanding of the airways fungal microbiome is required. The study aimed to use DNA sequences from sputum to assess the load and diversity of fungi in adults with CF and non-CF bronchiectasis. Methods Next generation sequencing of the ITS2 region was used to examine fungal community composition (n = 176) by disease and underlying clinical subgroups including allergic bronchopulmonary aspergillosis, chronic necrotizing pulmonary aspergillosis, non-tuberculous mycobacteria, and fungal bronchitis. Patients with no known active fungal disease were included as disease controls. Results ITS2 sequencing greatly increased the detection of fungi from sputum. In patients with CF fungal diversity was lower, while burden was higher than those with non-CF bronchiectasis. The most common operational taxonomic unit (OTU) in patients with CF was Candida parapsilosis (20.4%), whereas in non-CF bronchiectasis sputum Candida albicans (21.8%) was most common. CF patients with overt fungal bronchitis were dominated by Aspergillus spp., Exophiala spp., Candida parapsilosis or Scedosporium spp. Conclusion This study provides a framework to more accurately characterize the extended spectrum of fungal airways diseases in adult suppurative lung diseases.
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Affiliation(s)
- Leah Cuthbertson
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Imogen Felton
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Phillip James
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Michael J Cox
- National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Diana Bilton
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Silke Schelenz
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK
| | - Michael R Loebinger
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - William O C Cookson
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK.
| | - Nicholas J Simmonds
- Royal Brompton and Harefield NHS Foundation Trust, Sydney Street, London SW3 6NP, UK; National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
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32
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McKnight MM, Qu Z, Copeland JK, Guttman DS, Walker VK. A practical assessment of nano-phosphate on soybean (Glycine max) growth and microbiome establishment. Sci Rep 2020; 10:9151. [PMID: 32499485 PMCID: PMC7272607 DOI: 10.1038/s41598-020-66005-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
The efficacy of needle-shaped nano-hydroxyapatite (nHA; Ca10(PO4)6(OH)2) as a phosphate (Pi) fertilizer was evaluated as well as its impact on soil and soybean (Glycine max) bacterial and fungal communities. Microbial communities were evaluated in soy fertilized with nHA using ITS (internal transcribed spacer) and 16S rRNA high-throughput gene sequencing. Separate greenhouse growth experiments using agriculturally relevant nHA concentrations and application methods were used to assess plant growth and yield compared with no Pi (-P), soluble Pi (+P), and bulk HA controls. Overall, nHA treatments did not show significantly increased growth, biomass, total plant phosphorus concentrations, or yield compared with no Pi controls. Soil and rhizosphere community structures in controls and nHA treatment groups were similar, with minor shifts in the nHA-containing pots comparable to bulk HA controls at equal concentrations. The implementation of nHA in an agriculturally realistic manner and the resulting poor soy growth advises that contrary to some reports under specialized conditions, this nano-fertilizer may not be a viable alternative to traditional Pi fertilizers. If nano-phosphate fertilizers are to achieve their conjectured agricultural potential, alternative nHAs, with differing morphologies, physicochemical properties, and interactions with the soil matrix could be investigated using the evaluative procedures described.
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Affiliation(s)
| | - Zhi Qu
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, 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
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, ON, Canada
- School of Environmental Studies, Queen's University, Kingston, ON, Canada
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Oral prevalence and antifungal susceptibility of Candida species in cystic fibrosis patients. Arch Oral Biol 2020; 116:104772. [PMID: 32474212 DOI: 10.1016/j.archoralbio.2020.104772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE This study aimed at assessing the oral prevalence ofCandida species in cystic fibrosis patients and the antifungal susceptibility of the isolates. DESIGN One hundred patients aged 3-20 years old were included in the study and were divided into three groups: G1 (low severity disease): 25 cystic fibrosis patients with Shwachman-Kulczycki score (SK) between 100 and 71; G2 (high severity disease): 25 cystic fibrosis patients with SK score under 40; and G3 (control): 50 healthy patients age- and gender-matched to cystic fibrosis patients. Stimulated saliva samples were collected and the oral fungal concentrations were assessed. Isolates were identified by phenotypic and genotypic tests. Antifungal susceptibilities to amphotericin B, flucytosine and fluconazole were determined by CLSI methodology. Fungal counts were compared by Kruskal Wallis and Dunn's test (5%). RESULTS A total of 68 % of Group 1, 80 % of Group 2, and 44 % of controls yielded positive Candida cultures. Oral concentrations of fungi were significantly higher in cystic fibrosis patients in relation to the control group (p < 0.0005). No significant difference was observed between low and high severity cystic fibrosis groups (p > 0.05). C. albicans was most frequently isolated species in all groups. Higher variability of Candida species was observed in the control group. C. dubliniensis and C. tropicalis were only detected among cystic fibrosis groups. All the isolates were susceptible to flucytosine and fluconazole. CONCLUSIONS Patients with cystic fibrosis were more frequently colonized by Candida species and showed higher oral fungal burden. No antifungal resistant isolates were detected.
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Françoise A, Héry-Arnaud G. The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes (Basel) 2020; 11:E536. [PMID: 32403302 PMCID: PMC7288443 DOI: 10.3390/genes11050536] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.
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Affiliation(s)
- Alice Françoise
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
| | - Geneviève Héry-Arnaud
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, 29200 Brest, France
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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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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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Enaud R, Prevel R, Ciarlo E, Beaufils F, Wieërs G, Guery B, Delhaes L. The Gut-Lung Axis in Health and Respiratory Diseases: A Place for Inter-Organ and Inter-Kingdom Crosstalks. Front Cell Infect Microbiol 2020; 10:9. [PMID: 32140452 PMCID: PMC7042389 DOI: 10.3389/fcimb.2020.00009] [Citation(s) in RCA: 347] [Impact Index Per Article: 86.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
The gut and lungs are anatomically distinct, but potential anatomic communications and complex pathways involving their respective microbiota have reinforced the existence of a gut-lung axis (GLA). Compared to the better-studied gut microbiota, the lung microbiota, only considered in recent years, represents a more discreet part of the whole microbiota associated to human hosts. While the vast majority of studies focused on the bacterial component of the microbiota in healthy and pathological conditions, recent works have highlighted the contribution of fungal and viral kingdoms at both digestive and respiratory levels. Moreover, growing evidence indicates the key role of inter-kingdom crosstalks in maintaining host homeostasis and in disease evolution. In fact, the recently emerged GLA concept involves host-microbe as well as microbe-microbe interactions, based both on localized and long-reaching effects. GLA can shape immune responses and interfere with the course of respiratory diseases. In this review, we aim to analyze how the lung and gut microbiota influence each other and may impact on respiratory diseases. Due to the limited knowledge on the human virobiota, we focused on gut and lung bacteriobiota and mycobiota, with a specific attention on inter-kingdom microbial crosstalks which are able to shape local or long-reached host responses within the GLA.
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Affiliation(s)
- Raphaël Enaud
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, Bordeaux, France
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, Bordeaux, France
| | - Renaud Prevel
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, Bordeaux, France
- CHU de Bordeaux, Médecine Intensive Réanimation, Bordeaux, France
| | - Eleonora Ciarlo
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabien Beaufils
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, Bordeaux, France
- CHU de Bordeaux, Service d'Explorations Fonctionnelles Respiratoires, Bordeaux, France
| | - Gregoire Wieërs
- Clinique Saint Pierre, Department of Internal Medicine, Ottignies, Belgium
| | - Benoit Guery
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, Bordeaux, France
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, Bordeaux, 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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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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Azzam SZ, Cayme GJ, Martinez LR. Polymicrobial interactions involving fungi and their importance for the environment and in human disease. Microb Pathog 2019; 140:103942. [PMID: 31881258 DOI: 10.1016/j.micpath.2019.103942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Understanding polymicrobial interactions involving fungi in the environment and the human mycobiome is necessary to address environmental and medically related problems such as drought or antimicrobial resistance. The diversity of these interactions highlights the complexity of fungi, considering how some interactions can be antagonistic, while others synergistic. Over the years, an increase in studies on the mycobiome have revealed similarities between the human and environmental hosts. More recently, studies have focused on microbial commensal relationships and identifying causative agents of human disease. The overlap of some of these interactions is impossible to ignore, indicating that there are areas for medical exploitation that need to be further investigated. This review provides the latest advances in polymicrobial interactions involving fungi and discusses the importance of the fungal lifestyle in the environment and in human disease.
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Affiliation(s)
- Seham Z Azzam
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA
| | - Ginelle J Cayme
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA
| | - Luis R Martinez
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA; Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
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Amati F, Simonetta E, Gramegna A, Tarsia P, Contarini M, Blasi F, Aliberti S. The biology of pulmonary exacerbations in bronchiectasis. Eur Respir Rev 2019; 28:28/154/190055. [PMID: 31748420 DOI: 10.1183/16000617.0055-2019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Bronchiectasis is a heterogeneous chronic disease. Heterogeneity characterises bronchiectasis not only in the stable state but also during exacerbations, despite evidence on clinical and biological aspects of bronchiectasis, exacerbations still remain poorly understood.Although the scientific community recognises that bacterial infection is a cornerstone in the development of bronchiectasis, there is a lack of data regarding other trigger factors for exacerbations. In addition, a huge amount of data suggest a primary role of neutrophils in the stable state and exacerbation of bronchiectasis, but the inflammatory reaction involves many other additional pathways. Cole's vicious cycle hypothesis illustrates how airway dysfunction, airway inflammation, infection and structural damage are linked. The introduction of the concept of a "vicious vortex" stresses the complexity of the relationships between the components of the cycle. In this model of disease, exacerbations work as a catalyst, accelerating the progression of disease. The roles of microbiology and inflammation need to be considered as closely linked and will need to be investigated in different ways to collect samples. Clinical and translational research is of paramount importance to achieve a better comprehension of the pathophysiology of bronchiectasis, microbiology and inflammation both in the stable state and during exacerbations.
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Affiliation(s)
- Francesco Amati
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Edoardo Simonetta
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Gramegna
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Tarsia
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Contarini
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Blasi
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Dept of Pathophysiology and Transplantation, University of Milan, Milan, Italy .,Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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Rosen BH, Evans TIA, Moll SR, Gray JS, Liang B, Sun X, Zhang Y, Jensen-Cody CW, Swatek AM, Zhou W, He N, Rotti PG, Tyler SR, Keiser NW, Anderson PJ, Brooks L, Li Y, Pope RM, Rajput M, Hoffman EA, Wang K, Harris JK, Parekh KR, Gibson-Corley KN, Engelhardt JF. Infection Is Not Required for Mucoinflammatory Lung Disease in CFTR-Knockout Ferrets. Am J Respir Crit Care Med 2019; 197:1308-1318. [PMID: 29327941 DOI: 10.1164/rccm.201708-1616oc] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Classical interpretation of cystic fibrosis (CF) lung disease pathogenesis suggests that infection initiates disease progression, leading to an exuberant inflammatory response, excessive mucus, and ultimately bronchiectasis. Although symptomatic antibiotic treatment controls lung infections early in disease, lifelong bacterial residence typically ensues. Processes that control the establishment of persistent bacteria in the CF lung, and the contribution of noninfectious components to disease pathogenesis, are poorly understood. OBJECTIVES To evaluate whether continuous antibiotic therapy protects the CF lung from disease using a ferret model that rapidly acquires lethal bacterial lung infections in the absence of antibiotics. METHODS CFTR (cystic fibrosis transmembrane conductance regulator)-knockout ferrets were treated with three antibiotics from birth to several years of age and lung disease was followed by quantitative computed tomography, BAL, and histopathology. Lung disease was compared with CFTR-knockout ferrets treated symptomatically with antibiotics. MEASUREMENTS AND MAIN RESULTS Bronchiectasis was quantified from computed tomography images. BAL was evaluated for cellular differential and features of inflammatory cellular activation, bacteria, fungi, and quantitative proteomics. Semiquantitative histopathology was compared across experimental groups. We demonstrate that lifelong antibiotics can protect the CF ferret lung from infections for several years. Surprisingly, CF animals still developed hallmarks of structural bronchiectasis, neutrophil-mediated inflammation, and mucus accumulation, despite the lack of infection. Quantitative proteomics of BAL from CF and non-CF pairs demonstrated a mucoinflammatory signature in the CF lung dominated by Muc5B and neutrophil chemoattractants and products. CONCLUSIONS These findings implicate mucoinflammatory processes in the CF lung as pathogenic in the absence of clinically apparent bacterial and fungal infections.
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Affiliation(s)
- Bradley H Rosen
- 1 Department of Anatomy & Cell Biology.,2 Department of Medicine
| | | | | | | | - Bo Liang
- 1 Department of Anatomy & Cell Biology
| | | | | | | | | | | | - Nan He
- 1 Department of Anatomy & Cell Biology
| | - Pavana G Rotti
- 1 Department of Anatomy & Cell Biology.,4 Department of Biomedical Engineering, College of Engineering, and
| | | | | | | | | | | | | | | | | | - Kai Wang
- 7 Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa; and
| | - J Kirk Harris
- 8 Department of Pediatrics, University of Colorado, Aurora, Colorado
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45
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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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46
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Huang C, Shi G. Smoking and microbiome in oral, airway, gut and some systemic diseases. J Transl Med 2019; 17:225. [PMID: 31307469 PMCID: PMC6632217 DOI: 10.1186/s12967-019-1971-7] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/05/2019] [Indexed: 12/24/2022] Open
Abstract
The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn’s disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.
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Affiliation(s)
- Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China. .,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China.
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47
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Vandeplassche E, Tavernier S, Coenye T, Crabbé A. Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens. Eur Respir Rev 2019; 28:28/152/190041. [PMID: 31285289 PMCID: PMC9488708 DOI: 10.1183/16000617.0041-2019] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022] Open
Abstract
The lungs of patients with cystic fibrosis (CF) are colonised by a microbial community comprised of pathogenic species, such as Pseudomonas aeruginosa and Staphylococcus aureus, and microorganisms that are typically not associated with worse clinical outcomes (considered as commensals). Antibiotics directed at CF pathogens are often not effective and a discrepancy is observed between activity of these agents in vitro and in the patient. This review describes how interspecies interactions within the lung microbiome might influence the outcome of antibiotic treatment targeted at common CF pathogens. Protective mechanisms by members of the microbiome such as antibiotic degradation (indirect pathogenicity), alterations of the cell wall, production of matrix components decreasing antibiotic penetration, and changes in metabolism are discussed. Interspecies interactions that increase bacterial susceptibility are also addressed. Furthermore, we discuss how experimental conditions, such as culture media, oxygen levels, incorporation of host–pathogen interactions, and microbial community composition may influence the outcome of microbial interaction studies related to antibiotic activity. Hereby, the importance to create in vitro conditions reflective of the CF lung microenvironment is highlighted. Understanding the role of the CF lung microbiome in antibiotic efficacy may help find novel therapeutic and diagnostic approaches to better tackle chronic lung infections in this patient population. Interspecies interactions in the lung microbiome may influence the outcome of antibiotic treatment targeted at cystic fibrosis pathogenshttp://bit.ly/2WQp0iQ
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Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Sarah Tavernier
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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48
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Ethanol Stimulates Trehalose Production through a SpoT-DksA-AlgU-Dependent Pathway in Pseudomonas aeruginosa. J Bacteriol 2019; 201:JB.00794-18. [PMID: 30936375 DOI: 10.1128/jb.00794-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/26/2019] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas aeruginosa frequently resides among ethanol-producing microbes, making its response to the microbially produced concentrations of ethanol relevant to understanding its biology. Our transcriptome analysis found that genes involved in trehalose metabolism were induced by low concentrations of ethanol, and biochemical assays showed that levels of intracellular trehalose increased significantly upon growth with ethanol. The increase in trehalose was dependent on the TreYZ pathway but not other trehalose-metabolic enzymes (TreS or TreA). The sigma factor AlgU (AlgT), a homolog of RpoE in other species, was required for increased expression of the treZ gene and trehalose levels, but induction was not controlled by the well-characterized proteolysis of its anti-sigma factor, MucA. Growth with ethanol led to increased SpoT-dependent (p)ppGpp accumulation, which stimulates AlgU-dependent transcription of treZ and other AlgU-regulated genes through DksA, a (p)ppGpp and RNA polymerase binding protein. Ethanol stimulation of trehalose also required acylhomoserine lactone (AHL)-mediated quorum sensing (QS), as induction was not observed in a ΔlasR ΔrhlR strain. A network analysis using a model, eADAGE, built from publicly available P. aeruginosa transcriptome data sets (J. Tan, G. Doing, K. A. Lewis, C. E. Price, et al., Cell Syst 5:63-71, 2017, https://doi.org/10.1016/j.cels.2017.06.003) provided strong support for our model in which treZ and coregulated genes are controlled by both AlgU- and AHL-mediated QS. Consistent with (p)ppGpp- and AHL-mediated quorum-sensing regulation, ethanol, even when added at the time of culture inoculation, stimulated treZ transcript levels and trehalose production in cells from post-exponential-phase cultures but not in cells from exponential-phase cultures. These data highlight the integration of growth and cell density cues in the P. aeruginosa transcriptional response to ethanol.IMPORTANCE Pseudomonas aeruginosa is often found with bacteria and fungi that produce fermentation products, including ethanol. At concentrations similar to those produced by environmental microbes, we found that ethanol stimulated expression of trehalose-biosynthetic genes and cellular levels of trehalose, a disaccharide that protects against environmental stresses. The induction of trehalose by ethanol required the alternative sigma factor AlgU through DksA- and SpoT-dependent (p)ppGpp. Trehalose accumulation also required AHL quorum sensing and occurred only in post-exponential-phase cultures. This work highlights how cells integrate cell density and growth cues in their responses to products made by other microbes and reveals a new role for (p)ppGpp in the regulation of AlgU activity.
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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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50
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Schwarz C, Vandeputte P, Rougeron A, Giraud S, Dugé de Bernonville T, Duvaux L, Gastebois A, Alastruey-Izquierdo A, Martín-Gomez MT, Mazuelos EM, Sole A, Cano J, Pemán J, Quindos G, Botterel F, Bougnoux ME, Chen S, Delhaès L, Favennec L, Ranque S, Sedlacek L, Steinmann J, Vazquez J, Williams C, Meyer W, Le Gal S, Nevez G, Fleury M, Papon N, Symoens F, Bouchara JP. Developing collaborative works for faster progress on fungal respiratory infections in cystic fibrosis. Med Mycol 2018. [PMID: 29538733 DOI: 10.1093/mmy/myx106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is the major genetic inherited disease in Caucasian populations. The respiratory tract of CF patients displays a sticky viscous mucus, which allows for the entrapment of airborne bacteria and fungal spores and provides a suitable environment for growth of microorganisms, including numerous yeast and filamentous fungal species. As a consequence, respiratory infections are the major cause of morbidity and mortality in this clinical context. Although bacteria remain the most common agents of these infections, fungal respiratory infections have emerged as an important cause of disease. Therefore, the International Society for Human and Animal Mycology (ISHAM) has launched a working group on Fungal respiratory infections in Cystic Fibrosis (Fri-CF) in October 2006, which was subsequently approved by the European Confederation of Medical Mycology (ECMM). Meetings of this working group, comprising both clinicians and mycologists involved in the follow-up of CF patients, as well as basic scientists interested in the fungal species involved, provided the opportunity to initiate collaborative works aimed to improve our knowledge on these infections to assist clinicians in patient management. The current review highlights the outcomes of some of these collaborative works in clinical surveillance, pathogenesis and treatment, giving special emphasis to standardization of culture procedures, improvement of species identification methods including the development of nonculture-based diagnostic methods, microbiome studies and identification of new biological markers, and the description of genotyping studies aiming to differentiate transient carriage and chronic colonization of the airways. The review also reports on the breakthrough in sequencing the genomes of the main Scedosporium species as basis for a better understanding of the pathogenic mechanisms of these fungi, and discusses treatment options of infections caused by multidrug resistant microorganisms, such as Scedosporium and Lomentospora species and members of the Rasamsonia argillacea species complex.
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Affiliation(s)
- Carsten Schwarz
- Department of Pediatric Pneumology and Immunology, Cystic Fibrosis Center Berlin/Charité -Universitätsmedizin Berlin, Berlin, Germany
| | - Patrick Vandeputte
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Laboratoire de Parasitologie-Mycologie, CHU, Angers, France
| | - Amandine Rougeron
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité UMR 5234, Bordeaux, France; CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France; Laboratoire de Parasitologie-Mycologie, CHU, Bordeaux, France
| | - Sandrine Giraud
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Thomas Dugé de Bernonville
- Biomolécules et Biotechnologies Végétales (EA 2106), Département de Biologie et Physiologie Végétales, UFR Sciences et Techniques, Université François Rabelais, Tours
| | - Ludovic Duvaux
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Institut de Recherche en Horticulture et Semences (IRHS), UMR INRA 1345, Beaucouzé, France
| | - Amandine Gastebois
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Maria Teresa Martín-Gomez
- Respiratory Bacteriology Unit & Clinical Mycology Unit, Department of Microbiology, Vall D'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Amparo Sole
- Unidad de Trasplante Pulmonar y Fibrosis Quística, Hospital Universitari la Fe, Valencia, Spain
| | - Josep Cano
- Mycology Unit, Medical School/Oenology School, Universitat Rovira i Virgili, Reus, Spain
| | - Javier Pemán
- Unidad de Micología, Servicio de Microbiología, Universitari la Fe, Valencia, Spain
| | - Guillermo Quindos
- Laboratorio de Micología Médica, Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad del País Vasco, Bilbao, Spain
| | - Françoise Botterel
- Laboratoire de Parasitologie-Mycologie, CHU Henri Mondor, Créteil, France
| | | | - Sharon Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, Westmead, New South Wales, Australia
| | - Laurence Delhaès
- Center for Cardiothoracic Research of Bordeaux, Inserm U1045, Bordeaux, France
| | - Loïc Favennec
- Laboratoire de Parasitologie-Mycologie, EA 3800, CHU Charles Nicolle and Université de Rouen, Rouen, France
| | - Stéphane Ranque
- Laboratoire de Parasitologie-Mycologie, AP-HM Timone, Marseille, France
| | - Ludwig Sedlacek
- Institute of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, Hannover, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jose Vazquez
- Division of Infectious Diseases, Department of Medicine, Georgia Regents University, Augusta, GA, USA
| | - Craig Williams
- University of the West of Scotland, Institute of Healthcare Associated Infection, University Hospital Crosshouse, Kilmarnock, United Kingdom
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Solène Le Gal
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Brest, France.,Laboratoire de Parasitologie-Mycologie, CHU, Brest, France
| | - Gilles Nevez
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Brest, France.,Laboratoire de Parasitologie-Mycologie, CHU, Brest, France
| | - Maxime Fleury
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Nicolas Papon
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Françoise Symoens
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France
| | - Jean-Philippe Bouchara
- Host-Pathogen Interaction Study Group (EA 3142), UNIV Angers, UNIV Brest, Université Bretagne-Loire, Angers, France.,Laboratoire de Parasitologie-Mycologie, CHU, Angers, France
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