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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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2
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Fan Y, Wu L, Zhai B. The mycobiome: interactions with host and implications in diseases. Curr Opin Microbiol 2023; 75:102361. [PMID: 37527562 DOI: 10.1016/j.mib.2023.102361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, our understanding of the composition and function of the human mucosal surface-associated fungal community (i.e. the mycobiome) has rapidly expanded. Fungi colonize at various sites of the mucosal surface at birth and play important roles in the development and homeostasis of immune system throughout adulthood. Here, we review the recent research progresses in the human mycobiome at different body sites, including the gastrointestinal (GI) tract, the respiratory tract, the urogenital tract, the oral cavity, the skin surface, and the tumor tissues. Researchers have made extensive effort in characterizing the interactions between mycobiome and immune system, especially in the GI tract. We discuss the mycobiome dysbiosis and its implications to the progression of diseases such as inflammatory bowel diseases, alcoholic liver diseases, systemic infections, cancers, and so on, indicating the potential of mycobiome-targeting intervention strategy for life-threatening diseases.
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Affiliation(s)
- Yani Fan
- Clinical laboratory, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, Guangdong Province, China; Maternal-Fetal Medicine Institute, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lijuan Wu
- Clinical laboratory, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, Guangdong Province, China; Maternal-Fetal Medicine Institute, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, China.
| | - Bing Zhai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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3
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Murante D, Demers EG, Kurbessoian T, Ruzic M, Ashare A, Stajich JE, Hogan DA. Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung. mBio 2023; 14:e0117123. [PMID: 37432019 PMCID: PMC10470810 DOI: 10.1128/mbio.01171-23] [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: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 07/12/2023] Open
Abstract
The genetic disease cystic fibrosis (CF) frequently leads to chronic lung infections by bacteria and fungi. We identified three individuals with CF with persistent lung infections dominated by Clavispora (Candida) lusitaniae. Whole-genome sequencing analysis of multiple isolates from each infection found evidence for selection for mutants in the gene MRS4 in all three distinct lung-associated populations. In each population, we found one or two unfixed, non-synonymous mutations in MRS4 relative to the reference allele found in multiple environmental and clinical isolates including the type strain. Genetic and phenotypic analyses found that all evolved alleles led to loss of function (LOF) of Mrs4, a mitochondrial iron transporter. RNA-seq analyses found that Mrs4 variants with decreased activity led to increased expression of genes involved in iron acquisition mechanisms in both low iron and replete iron conditions. Furthermore, surface iron reductase activity and intracellular iron were much higher in strains with Mrs4 LOF variants. Parallel studies found that a subpopulation of a CF-associated Exophiala dermatitidis infection also had a non-synonymous LOF mutation in MRS4. Together, these data suggest that MRS4 mutations may be beneficial during chronic CF lung infections in diverse fungi, perhaps, for the purposes of adaptation to an iron-restricted environment with chronic infections. IMPORTANCE The identification of MRS4 mutations in Clavispora (Candida) lusitaniae and Exophiala dermatitidis in individuals with cystic fibrosis (CF) highlights a possible adaptive mechanism for fungi during chronic CF lung infections. The findings of this study suggest that loss of function of the mitochondrial iron transporter Mrs4 can lead to increased activity of iron acquisition mechanisms, which may be advantageous for fungi in iron-restricted environments during chronic infections. This study provides valuable information for researchers working toward a better understanding of the pathogenesis of chronic lung infections and more effective therapies to treat them.
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Affiliation(s)
- Daniel Murante
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Elora G. Demers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Tania Kurbessoian
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Marina Ruzic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Medicine, Dartmouth Health, Lebanon, New Hampshire, USA
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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4
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Kurbessoian T, Murante D, Crocker A, Hogan DA, Stajich JE. In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment. G3 (BETHESDA, MD.) 2023; 13:jkad126. [PMID: 37293838 PMCID: PMC10484061 DOI: 10.1093/g3journal/jkad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/26/2022] [Accepted: 05/18/2023] [Indexed: 06/10/2023]
Abstract
Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject 2 years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism and insertion-deletion variant analyses of 23 isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the reference genome strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition, and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, and growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.
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Affiliation(s)
- Tania Kurbessoian
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Daniel Murante
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Alex Crocker
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
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5
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Anderson FM, Visser ND, Amses KR, Hodgins-Davis A, Weber AM, Metzner KM, McFadden MJ, Mills RE, O'Meara MJ, James TY, O'Meara TR. Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease. PLoS Biol 2023; 21:e3001822. [PMID: 37205709 DOI: 10.1371/journal.pbio.3001822] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Candida albicans is a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen. C. albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is unclear how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we examined 910 commensal isolates from 35 healthy donors to identify host niche-specific adaptations. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverse C. albicans strains. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterized ZMS1 transcription factor that was sufficient to drive hyper invasion into agar. We found that SC5314 was significantly different from the majority of both commensal and bloodstream isolates in its ability to induce host cell death. However, our commensal strains retained the capacity to cause disease in the Galleria model of systemic infection, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity of C. albicans and suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.
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Affiliation(s)
- Faith M Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Noelle D Visser
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kevin R Amses
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea Hodgins-Davis
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Katura M Metzner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Michael J McFadden
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Timothy Y James
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Teresa R O'Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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6
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MacAlpine J, Robbins N, Cowen LE. Bacterial-fungal interactions and their impact on microbial pathogenesis. Mol Ecol 2023; 32:2565-2581. [PMID: 35231147 PMCID: PMC11032213 DOI: 10.1111/mec.16411] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 02/18/2022] [Indexed: 11/27/2022]
Abstract
Microbial communities of the human microbiota exhibit diverse effects on human health and disease. Microbial homeostasis is important for normal physiological functions and changes to the microbiota are associated with many human diseases including diabetes, cancer, and colitis. In addition, there are many microorganisms that are either commensal or acquired from environmental reservoirs that can cause diverse pathologies. Importantly, the balance between health and disease is intricately connected to how members of the microbiota interact and affect one another's growth and pathogenicity. However, the mechanisms that govern these interactions are only beginning to be understood. In this review, we outline bacterial-fungal interactions in the human body, including examining the mechanisms by which bacteria govern fungal growth and virulence, as well as how fungi regulate bacterial pathogenesis. We summarize advances in the understanding of chemical, physical, and protein-based interactions, and their role in exacerbating or impeding human disease. We focus on the three fungal species responsible for the majority of systemic fungal infections in humans: Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. We conclude by summarizing recent studies that have mined microbes for novel antimicrobials and antivirulence factors, highlighting the potential of the human microbiota as a rich resource for small molecule discovery.
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Affiliation(s)
- Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
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7
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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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Murante D, Demers EG, Kurbessoian T, Ruzic M, Ashare A, Stajich JE, Hogan DA. Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535776. [PMID: 37066389 PMCID: PMC10104081 DOI: 10.1101/2023.04.05.535776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The genetic disease cystic fibrosis (CF) frequently leads to chronic lung infections by bacteria and fungi. We identified three individuals with CF with persistent lung infections dominated by Clavispora ( Candida ) lusitaniae . Whole genome sequencing analysis of multiple isolates from each infection found evidence for selection for mutants in the gene MRS4 in all three distinct lung-associated populations. In each population, we found one or two unfixed, non-synonymous mutations in MRS4 relative to the reference allele found in multiple environmental and clinical isolates including the type strain. Genetic and phenotypic analyses found that all evolved alleles led to loss of function of Mrs4, a mitochondrial iron transporter. RNA Seq analyses found that Mrs4 variants with decreased activity led to increased expression of genes involved in iron acquisition mechanisms in both low iron and replete iron conditions. Furthermore, surface iron reductase activity and intracellular iron was much higher in strains with Mrs4 loss of function variants. Parallel studies found that a subpopulation of a CF-associated Exophiala dermatiditis infection also had a non-synonymous loss of function mutation in MRS4. Together, these data suggest that MRS4 mutations may be beneficial during chronic CF lung infections in diverse fungi perhaps for the purposes of adaptation to an iron restricted environment with chronic infections.
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Affiliation(s)
- Daniel Murante
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Elora G. Demers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Tania Kurbessoian
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Marina Ruzic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
- Department of Medicine, Dartmouth Health, Lebanon, NH, USA
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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9
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Kakade P, Sircaik S, Maufrais C, Ene IV, Bennett RJ. Aneuploidy and gene dosage regulate filamentation and host colonization by Candida albicans. Proc Natl Acad Sci U S A 2023; 120:e2218163120. [PMID: 36893271 PMCID: PMC10089209 DOI: 10.1073/pnas.2218163120] [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: 10/24/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023] Open
Abstract
Aneuploidy is a frequent occurrence in fungal species where it can alter gene expression and promote adaptation to a variety of environmental cues. Multiple forms of aneuploidy have been observed in the opportunistic fungal pathogen Candida albicans, which is a common component of the human gut mycobiome but can escape this niche and cause life-threatening systemic disease. Using a barcode sequencing (Bar-seq) approach, we evaluated a set of diploid C. albicans strains and found that a strain carrying a third copy of chromosome (Chr) 7 was associated with increased fitness during both gastrointestinal (GI) colonization and systemic infection. Our analysis revealed that the presence of a Chr 7 trisomy resulted in decreased filamentation, both in vitro and during GI colonization, relative to isogenic euploid controls. A target gene approach demonstrated that NRG1, encoding a negative regulator of filamentation located on Chr 7, contributes to increased fitness of the aneuploid strain due to inhibition of filamentation in a gene dosage-dependent fashion. Together, these experiments establish how aneuploidy enables the reversible adaptation of C. albicans to its host via gene dosage-dependent regulation of morphology.
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Affiliation(s)
- Pallavi Kakade
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Shabnam Sircaik
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Corinne Maufrais
- Institut Pasteur Bioinformatic Hub, Université Paris Cité, Paris75015, France
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Richard J. Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
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10
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Genome plasticity in Candida albicans: A cutting-edge strategy for evolution, adaptation, and survival. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105256. [PMID: 35231665 DOI: 10.1016/j.meegid.2022.105256] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/12/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Candida albicans is the most implicated fungal species that grows as a commensal or opportunistic pathogen in the human host. It is associated with many life-threatening infections, especially in immunocompromised persons. The genome of Candida albicans is very flexible and can withstand a wide assortment of variations in a continuously changing environment. Thus, genome plasticity is central to its adaptation and has long been of considerable interest. C. albicans has a diploid heterozygous genome that is highly dynamic and can display variation from small to large scale chromosomal rearrangement and aneuploidy, which have implications in drug resistance, virulence, and pathogenicity. This review presents an up-to-date overview of recent genomic studies involving C. albicans. It discusses the accumulating evidence that shows how mitotic recombination events, ploidy dynamics, aneuploidy, and loss of heterozygosity (LOH) influence evolution, adaptation, and survival in C. albicans. Understanding the factors that affect the genome is crucial for a proper understanding of species and rapid development and adjustment of therapeutic strategies to mitigate their spread.
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11
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Gutierrez MW, van Tilburg Bernardes E, Changirwa D, McDonald B, Arrieta MC. "Molding" immunity-modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease. Mucosal Immunol 2022; 15:573-583. [PMID: 35474360 DOI: 10.1038/s41385-022-00515-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023]
Abstract
Fungi are important yet understudied contributors to the microbial communities of the gastrointestinal tract. Starting at birth, the intestinal mycobiome undergoes a period of dynamic maturation under the influence of microbial, host, and extrinsic influences, with profound functional implications for immune development in early life, and regulation of immune homeostasis throughout life. Candida albicans serves as a model organism for understanding the cross-talk between fungal colonization dynamics and immunity, and exemplifies unique mechanisms of fungal-immune interactions, including fungal dimorphism, though our understanding of other intestinal fungi is growing. Given the prominent role of the gut mycobiome in promoting immune homeostasis, emerging evidence points to fungal dysbiosis as an influential contributor to immune dysregulation in a variety of inflammatory and infectious diseases. Here we review current knowledge on the factors that govern host-fungi interactions in the intestinal tract and immunological outcomes in both mucosal and systemic compartments.
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Affiliation(s)
- Mackenzie W Gutierrez
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Erik van Tilburg Bernardes
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Diana Changirwa
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada.,Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Braedon McDonald
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,International Microbiome Centre, University of Calgary, Calgary, AB, Canada.,Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Immunology Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada. .,Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
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12
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Palmieri F, Koutsokera A, Bernasconi E, Junier P, von Garnier C, Ubags N. Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp. Front Med (Lausanne) 2022; 9:832510. [PMID: 35386908 PMCID: PMC8977413 DOI: 10.3389/fmed.2022.832510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- *Correspondence: Fabio Palmieri,
| | - Angela Koutsokera
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eric Bernasconi
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christophe von Garnier
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Niki Ubags,
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13
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Antimicrobial and cytotoxic activity of electrosprayed chitosan nanoparticles against endodontic pathogens and Balb/c 3T3 fibroblast cells. Sci Rep 2021; 11:24487. [PMID: 34966174 PMCID: PMC8716534 DOI: 10.1038/s41598-021-04322-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022] Open
Abstract
The aims of this study were to synthesize highly positively charged chitosan nanoparticles (Ch-Np) using the electrospraying technique, and to test their antimicrobial activity against endodontic pathogens, and cytotoxicity against fibroblast cells. Ch-Np were synthesized from low molecular weight chitosan (LMW-Ch) using the electrospraying technique, and characterized. The antimicrobial activity was evaluated against Streptococcus mutans, Enterococcus faecalis, and Candida albicans in their planktonic state using a Time-Kill Test performed by using broth micro-dilution technique, and against biofilm biomass using a microtiter plate biofilm assay. The cytotoxicity was evaluated using Balb/c 3T3 fibroblast cells with the standard MTT assay. Electrospraying of LMW-Ch produced Ch-Np with an average size of 200 nm, and a surface charge of 51.7 mV. Ch-Np completely eradicated S. mutans and E. faecalis in the planktonic state and showed fungistatic activity against C. albicans. Furthermore, it significantly reduced the biofilm biomass for all the tested microbial species [S. mutans (p = 0.006), E. faecalis (p < 0.0001), and C. albicans (p = 0.004)]. When tested for cytotoxicity using 3T3 cells, Ch-Np showed no cytotoxicity. In conclusion, the highly positively charged, colloidal dispersion of Ch-Np are effective as a biocompatible endodontic antimicrobial agent.
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14
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McDonough LD, Mishra AA, Tosini N, Kakade P, Penumutchu S, Liang SH, Maufrais C, Zhai B, Taur Y, Belenky P, Bennett RJ, Hohl TM, Koh AY, Ene IV. Candida albicans Isolates 529L and CHN1 Exhibit Stable Colonization of the Murine Gastrointestinal Tract. mBio 2021; 12:e0287821. [PMID: 34724818 PMCID: PMC8561340 DOI: 10.1128/mbio.02878-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is a pathobiont that colonizes multiple niches in the body including the gastrointestinal (GI) tract but is also responsible for both mucosal and systemic infections. Despite its prevalence as a human commensal, the murine GI tract is generally refractory to colonization with the C. albicans reference isolate SC5314. Here, we identify two C. albicans isolates, 529L and CHN1, that stably colonize the murine GI tract in three different animal facilities under conditions where SC5314 is lost from this niche. Analysis of the bacterial microbiota did not show notable differences among mice colonized with the three C. albicans strains. We compared the genotypes and phenotypes of these three strains and identified thousands of single nucleotide polymorphisms (SNPs) and multiple phenotypic differences, including their ability to grow and filament in response to nutritional cues. Despite striking filamentation differences under laboratory conditions, however, analysis of cell morphology in the GI tract revealed that the three isolates exhibited similar filamentation properties in this in vivo niche. Notably, we found that SC5314 is more sensitive to the antimicrobial peptide CRAMP, and the use of CRAMP-deficient mice modestly increased the ability of SC5314 to colonize the GI tract relative to CHN1 and 529L. These studies provide new insights into how strain-specific differences impact C. albicans traits in the host and advance CHN1 and 529L as relevant strains to study C. albicans pathobiology in its natural host niche. IMPORTANCE Understanding how fungi colonize the GI tract is increasingly recognized as highly relevant to human health. The animal models used to study Candida albicans commensalism commonly rely on altering the host microbiome (via antibiotic treatment or defined diets) to establish successful GI colonization by the C. albicans reference isolate SC5314. Here, we characterize two C. albicans isolates that can colonize the murine GI tract without antibiotic treatment and can therefore be used as tools for studying fungal commensalism. Importantly, experiments were replicated in three different animal facilities and utilized three different mouse strains. Differential colonization between fungal isolates was not associated with alterations in the bacterial microbiome but rather with distinct responses to CRAMP, a host antimicrobial peptide. This work emphasizes the importance of C. albicans intraspecies variation as well as host antimicrobial defense mechanisms in defining the outcome of commensal interactions.
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Affiliation(s)
- Liam D. McDonough
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Animesh A. Mishra
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Nicholas Tosini
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pallavi Kakade
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Shen-Huan Liang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | | | - Bing Zhai
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ying Taur
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Richard J. Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Tobias M. Hohl
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Andrew Y. Koh
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Iuliana V. Ene
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
- Department of Mycology, Institut Pasteur, Paris, France
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15
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MacAlpine J, Daniel-Ivad M, Liu Z, Yano J, Revie NM, Todd RT, Stogios PJ, Sanchez H, O'Meara TR, Tompkins TA, Savchenko A, Selmecki A, Veri AO, Andes DR, Fidel PL, Robbins N, Nodwell J, Whitesell L, Cowen LE. A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. Nat Commun 2021; 12:6151. [PMID: 34686660 PMCID: PMC8536679 DOI: 10.1038/s41467-021-26390-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/01/2021] [Indexed: 11/23/2022] Open
Abstract
The fungus Candida albicans is an opportunistic pathogen that can exploit imbalances in microbiome composition to invade its human host, causing pathologies ranging from vaginal candidiasis to fungal sepsis. Bacteria of the genus Lactobacillus are colonizers of human mucosa and can produce compounds with bioactivity against C. albicans. Here, we show that some Lactobacillus species produce a small molecule under laboratory conditions that blocks the C. albicans yeast-to-filament transition, an important virulence trait. It remains unexplored whether the compound is produced in the context of the human host. Bioassay-guided fractionation of Lactobacillus-conditioned medium linked this activity to 1-acetyl-β-carboline (1-ABC). We use genetic approaches to show that filamentation inhibition by 1-ABC requires Yak1, a DYRK1-family kinase. Additional biochemical characterization of structurally related 1-ethoxycarbonyl-β-carboline confirms that it inhibits Yak1 and blocks C. albicans biofilm formation. Thus, our findings reveal Lactobacillus-produced 1-ABC can prevent the yeast-to-filament transition in C. albicans through inhibition of Yak1.
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Affiliation(s)
- Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Zhongle Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Junko Yano
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Sciences Center School of Dentistry, New Orleans, LA, USA
| | - Nicole M Revie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Peter J Stogios
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL, USA
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Teresa R O'Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Thomas A Tompkins
- Rosell Institute for Microbiome and Probiotics, 6100 Avenue Royalmount, Montreal, QC, Canada
| | - Alexei Savchenko
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL, USA
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Amanda O Veri
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Paul L Fidel
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Sciences Center School of Dentistry, New Orleans, LA, USA
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Justin Nodwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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16
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Magee LC, Louis M, Khan V, Micalo L, Chaudary N. Managing Fungal Infections in Cystic Fibrosis Patients: Challenges in Clinical Practice. Infect Drug Resist 2021; 14:1141-1153. [PMID: 33790585 PMCID: PMC7998013 DOI: 10.2147/idr.s267219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/25/2021] [Indexed: 12/31/2022] Open
Abstract
Cystic Fibrosis (CF) is an autosomal recessive disease characterized by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Impairment of the CFTR protein in the respiratory tract results in the formation of thick mucus, development of inflammation, destruction of bronchial tissue, and development of bacterial or fungal infections over time. CF patients are commonly colonized and/or infected with fungal organisms, Candida albicans or Aspergillus fumigatus, with prevalence rates ranging from 5% to 78% in the literature. Risk factors for acquiring fungal organisms include older age, coinfection with Pseudomonas aeruginosa, prolonged use of oral and inhaled antibiotics, and lower forced expiratory volume (FEV1). There are limited data available to differentiate between contamination, colonization, and active infection. Furthermore, the pathogenicity of colonization is variable in the literature as some studies report a decline in lung function associated with fungal colonization whereas others showed no difference. Limited data are available for the eradication of fungal colonization and the treatment of active invasive aspergillosis in adult CF patients. In this review article, we discuss the challenges in clinical practice and current literature available for laboratory findings, clinical diagnosis, and treatment options for fungal infections in adult CF patients.
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Affiliation(s)
- Lauren C Magee
- Department of Pharmacy, Virginia Commonwealth University Health System, Richmond, VA, USA
| | - Mariam Louis
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Jacksonville, FL, USA
| | - Vaneeza Khan
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Lavender Micalo
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Nauman Chaudary
- Division of Pulmonary Disease and Critical Care Medicine, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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17
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Yi B, Dalpke AH, Boutin S. Changes in the Cystic Fibrosis Airway Microbiome in Response to CFTR Modulator Therapy. Front Cell Infect Microbiol 2021; 11:548613. [PMID: 33816324 PMCID: PMC8010178 DOI: 10.3389/fcimb.2021.548613] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
The development of CFTR modulator therapies significantly changed the treatment scheme of people with cystic fibrosis. However, CFTR modulator therapy is still a life-long treatment, which is not able to correct the genetic defect and cure the disease. Therefore, it becomes crucial to understand the effects of such modulation of CFTR function on the airway physiology, especially on airway infections and inflammation that are currently the major life-limiting factors in people with cystic fibrosis. In this context, understanding the dynamics of airway microbiome changes in response to modulator therapy plays an essential role in developing strategies for managing airway infections. Whether and how the newly available therapies affect the airway microbiome is still at the beginning of being deciphered. We present here a brief review summarizing the latest information about microbiome alterations in light of modern cystic fibrosis modulator therapy.
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Affiliation(s)
- Buqing Yi
- Medical Faculty, Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Alexander H Dalpke
- Medical Faculty, Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany
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18
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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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19
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Ran Z, Liu J, Wang F, Xin C, Xiong B, Song Z. Pulmonary Micro-Ecological Changes and Potential Microbial Markers in Lung Cancer Patients. Front Oncol 2021; 10:576855. [PMID: 33537234 PMCID: PMC7848173 DOI: 10.3389/fonc.2020.576855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
The relationship between the microbiome and disease has been investigated for many years. As a highly malignant tumor, biomarkers for lung cancer are diverse. However, precision of these biomarkers has not yet been achieved. It has been confirmed that lung microecology changes in lung cancer patients compared with healthy individuals. Furthermore, the abundance of some bacterial species shows obvious changes, suggesting their potential use as a microbial marker for the detection of lung cancer. In addition, recent studies have confirmed that inflammation, immune response, virulence factors, and metabolism may be potential mechanisms linking the microbiome with carcinogenesis. In this review, microbiome studies of lung cancer, potential mechanisms, potential microbial markers, and the influence of the microbiome on the diagnosis and treatment of lung cancer are summarized, providing theoretical strategies for the diagnosis and treatment of lung cancer.
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Affiliation(s)
- Zhuonan Ran
- The Second Department of Pulmonary and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jiexing Liu
- The Second Department of Pulmonary and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fen Wang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Caiyan Xin
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Bin Xiong
- The Second Department of Pulmonary and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangyong Song
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China.,Molecular Biotechnology Platform, Public Center of Experimental Technology, Southwest Medical University, Luzhou, China
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20
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Keown K, Reid A, Moore JE, Taggart CC, Downey DG. Coinfection with Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis. Eur Respir Rev 2020; 29:29/158/200011. [PMID: 33208485 DOI: 10.1183/16000617.0011-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Cystic fibrosis (CF) lung disease is characterised by mucus stasis, chronic infection and inflammation, causing progressive structural lung disease and eventual respiratory failure. CF airways are inhabited by an ecologically diverse polymicrobial environment with vast potential for interspecies interactions, which may be a contributing factor to disease progression. Pseudomonas aeruginosa and Aspergillus fumigatus are the most common bacterial and fungal species present in CF airways respectively and coinfection results in a worse disease phenotype. METHODS In this review we examine existing expert knowledge of chronic co-infection with P. aeruginosa and A. fumigatus in CF patients. We summarise the mechanisms of interaction and evaluate the clinical and inflammatory impacts of this co-infection. RESULTS P. aeruginosa inhibits A. fumigatus through multiple mechanisms: phenazine secretion, iron competition, quorum sensing and through diffusible small molecules. A. fumigatus reciprocates inhibition through gliotoxin release and phenotypic adaptations enabling evasion of P. aeruginosa inhibition. Volatile organic compounds secreted by P. aeruginosa stimulate A. fumigatus growth, while A. fumigatus stimulates P. aeruginosa production of cytotoxic elastase. CONCLUSION A complex bi-directional relationship exists between P. aeruginosa and A. fumigatus, exhibiting both mutually antagonistic and cooperative facets. Cross-sectional data indicate a worsened disease state in coinfected patients; however, robust longitudinal studies are required to derive causality and to determine whether interspecies interaction contributes to disease progression.
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Affiliation(s)
- Karen Keown
- Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK.,Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Alastair Reid
- Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK
| | - John E Moore
- Northern Ireland Public Health Laboratory, Dept of Bacteriology, Belfast City Hospital, Belfast, UK
| | - Clifford C Taggart
- Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Damian G Downey
- Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
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21
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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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22
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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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23
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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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24
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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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25
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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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26
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The Impact of Gene Dosage and Heterozygosity on The Diploid Pathobiont Candida albicans. J Fungi (Basel) 2019; 6:jof6010010. [PMID: 31892130 PMCID: PMC7151161 DOI: 10.3390/jof6010010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
Candida albicans is a fungal species that can colonize multiple niches in the human host where it can grow either as a commensal or as an opportunistic pathogen. The genome of C. albicans has long been of considerable interest, given that it is highly plastic and can undergo a wide variety of alterations. These changes play a fundamental role in determining C. albicans traits and have been shown to enable adaptation both to the host and to antifungal drugs. C. albicans isolates contain a heterozygous diploid genome that displays variation from the level of single nucleotides to largescale rearrangements and aneuploidy. The heterozygous nature of the genome is now increasingly recognized as being central to C. albicans biology, as the relative fitness of isolates has been shown to correlate with higher levels of overall heterozygosity. Moreover, loss of heterozygosity (LOH) events can arise frequently, either at single polymorphisms or at a chromosomal level, and both can alter the behavior of C. albicans cells during infection or can modulate drug resistance. In this review, we examine genome plasticity in this pathobiont focusing on how gene dosage variation and loss of heterozygosity events can arise and how these modulate C. albicans behavior.
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27
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Abstract
Although survival of individuals with cystic fibrosis (CF) has been continuously improving for the past 40 years, respiratory failure secondary to recurrent pulmonary infections remains the leading cause of mortality in this patient population. Certain pathogens such as Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and species of the Burkholderia cepacia complex continue to be associated with poorer clinical outcomes including accelerated lung function decline and increased mortality. In addition, other organisms such as anaerobes, viruses, and fungi are increasingly recognized as potential contributors to disease progression. Culture-independent molecular methods are also being used for diagnostic purposes and to examine the interaction of microorganisms in the CF airway. Given the importance of CF airway infections, ongoing initiatives to promote understanding of the epidemiology, clinical course, and treatment options for these infections are needed.
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Affiliation(s)
- Ana C Blanchard
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Valerie J Waters
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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28
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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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29
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Li XV, Leonardi I, Iliev ID. Gut Mycobiota in Immunity and Inflammatory Disease. Immunity 2019; 50:1365-1379. [PMID: 31216461 DOI: 10.1016/j.immuni.2019.05.023] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/01/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023]
Abstract
The mammalian intestine is colonized by a wealth of microorganisms-including bacteria, viruses, protozoa, and fungi-that are all integrated into a functional trans-kingdom community. Characterization of the composition of the fungal community-the mycobiota-has advanced further than the much-needed mechanistic studies. Recent findings have revealed roles for the gut mycobiota in the regulation of host immunity and in the development and progression of human diseases of inflammatory origin. We review these findings here while placing them in the context of the current understanding of the pathways and cellular networks that induce local and systemic immune responses to fungi in the gastrointestinal tract. We discuss gaps in knowledge and argue for the importance of considering bacteria-fungal interactions as we aim to define the roles of mycobiota in immune homeostasis and immune-associated pathologies.
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Affiliation(s)
- Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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30
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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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31
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Li E, Knight JM, Wu Y, Luong A, Rodriguez A, Kheradmand F, Corry DB. Airway mycosis in allergic airway disease. Adv Immunol 2019; 142:85-140. [PMID: 31296304 DOI: 10.1016/bs.ai.2019.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The allergic airway diseases, including chronic rhinosinusitis (CRS), asthma, allergic bronchopulmonary mycosis (ABPM) and many others, comprise a heterogeneous collection of inflammatory disorders affecting the upper and lower airways and lung parenchyma that represent the most common chronic diseases of humanity. In addition to their shared tissue tropism, the allergic airway diseases are characterized by a distinct pattern of inflammation involving the accumulation of eosinophils, type 2 macrophages, innate lymphoid cells type 2 (ILC2), IgE-secreting B cells, and T helper type 2 (Th2) cells in airway tissues, and the prominent production of type 2 cytokines including interleukin (IL-) 33, IL-4, IL-5, IL-13, and many others. These factors and related inflammatory molecules induce characteristic remodeling and other changes of the airways that include goblet cell metaplasia, enhanced mucus secretion, smooth muscle hypertrophy, tissue swelling and polyp formation that account for the major clinical manifestations of nasal obstruction, headache, hyposmia, cough, shortness of breath, chest pain, wheezing, and, in the most severe cases of lower airway disease, death due to respiratory failure or disseminated, systemic disease. The syndromic nature of the allergic airway diseases that now include many physiological variants or endotypes suggests that distinct endogenous or environmental factors underlie their expression. However, findings from different perspectives now collectively link these disorders to a single infectious source, the fungi, and a molecular pathogenesis that involves the local production of airway proteinases by these organisms. In this review, we discuss the evidence linking fungi and their proteinases to the surprisingly wide variety of chronic airway and systemic disorders and the immune pathogenesis of these conditions as they relate to environmental fungi. We further discuss the important implications these new findings have for the diagnosis and future therapy of these common conditions.
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Affiliation(s)
- Evan Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - J Morgan Knight
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States; Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, United States
| | - Yifan Wu
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Amber Luong
- Department of Otolaryngology, University of Texas Health Science at Houston, Houston, TX, United States
| | - Antony Rodriguez
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States; Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, United States; Michael E. DeBakey VA Center for Translational Research on Inflammatory Diseases, Houston, TX, United States
| | - Farrah Kheradmand
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States; Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, United States; Michael E. DeBakey VA Center for Translational Research on Inflammatory Diseases, Houston, TX, United States
| | - David B Corry
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States; Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, United States; Michael E. DeBakey VA Center for Translational Research on Inflammatory Diseases, Houston, TX, United States.
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32
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Studying fungal pathogens of humans and fungal infections: fungal diversity and diversity of approaches. Microbes Infect 2019; 21:237-245. [PMID: 31255676 DOI: 10.1016/j.micinf.2019.06.011] [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: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/26/2022]
Abstract
Seminal work by Louis Pasteur revealed the contribution of fungi - yeasts and microsporidia to agroindustry and disease in animals, respectively. More than 150 years later, the impact of fungi on human health and beyond is an ever-increasing issue, although often underestimated. Recent studies estimate that fungal infections, especially those caused by Candida, Cryptococcus and Aspergillus species, kill more than one million people annually. Indeed, these neglected infections are in general very difficult to cure and the associated mortality remains very high even when antifungal treatments exist. The development of new antifungals and diagnostic tools that are both necessary to fight fungal diseases efficiently, requires greater insights in the biology of the fungal pathogens of humans in the context of the infection, on their epidemiology, and on their role in the human mycobiota. We also need a better understanding of the host immune responses to fungal pathogens as well as the genetic basis for the increased sensitivity of some individuals to fungal infections. Here, we highlight some recent progress made in these different areas of research, in particular based on work conducted in our own laboratories. These progresses should lay the ground for better management of fungal infections, as they provide opportunities for better diagnostic, vaccination, the development of classical antifungals but also strategies for targeting virulence factors or the host.
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Shen X, Yao YF, Li JY, Li Y. [Human mycobiome and diseases]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2019; 37:314-319. [PMID: 31218869 DOI: 10.7518/hxkq.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The proportion of mycobiome is less than 1% of human microbiome. However, fungal community plays a key role in human health and diseases. With high-throughput sequencing applications, the structure and composition of mycobiome in the mouth, lung, gut, vagina, and skin have been analyzed, and the role of microbiome in diseases has been investigated. Mycobiome also influences the composition of bacteriome and includes key species that maintain the structure and function of microbial communities. Fungi also influence host immune responses. In this review, we summarized the mycobiome com-position at various sites and different diseases and the interactions between fungi-bacteria and fungi-host.
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Affiliation(s)
- Xin Shen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yu-Fei Yao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ji-Yao Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yan Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Studying fungal pathogens of humans and fungal infections: fungal diversity and diversity of approaches. Genes Immun 2019; 20:403-414. [PMID: 31019254 DOI: 10.1038/s41435-019-0071-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/24/2022]
Abstract
Seminal work by Louis Pasteur revealed the contribution of fungi-yeasts and microsporidia to agroindustry and disease in animals, respectively. More than 150 years later, the impact of fungi on human health and beyond is an ever-increasing issue, although often underestimated. Recent studies estimate that fungal infections, especially those caused by Candida, Cryptococcus and Aspergillus species, kill more than one million people annually. Indeed, these neglected infections are in general very difficult to cure and the associated mortality remains very high even when antifungal treatments exist. The development of new antifungals and diagnostic tools that are both necessary to fight fungal diseases efficiently, requires greater insights in the biology of the fungal pathogens of humans in the context of the infection, on their epidemiology, and on their role in the human mycobiota. We also need a better understanding of the host immune responses to fungal pathogens as well as the genetic basis for the increased sensitivity of some individuals to fungal infections. Here, we highlight some recent progress made in these different areas of research, in particular based on work conducted in our own laboratories. These progress should lay the ground for better management of fungal infections, as they provide opportunities for better diagnostic, vaccination, the development of classical antifungals but also strategies for targeting virulence factors or the host.
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Fourie R, Pohl CH. Beyond Antagonism: The Interaction Between Candida Species and Pseudomonas aeruginosa. J Fungi (Basel) 2019; 5:jof5020034. [PMID: 31010211 PMCID: PMC6617365 DOI: 10.3390/jof5020034] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022] Open
Abstract
There are many examples of the interaction between prokaryotes and eukaryotes. One such example is the polymicrobial colonization/infection by the various opportunistic pathogenic yeasts belonging to the genus Candida and the ubiquitous bacterium, Pseudomonas aeruginosa. Although this interaction has simplistically been characterized as antagonistic to the yeast, this review highlights the complexity of the interaction with various factors influencing both microbes. The first section deals with the interactions in vitro, looking specifically at the role of cell wall components, quorum sensing molecules, phenazines, fatty acid metabolites and competition for iron in the interaction. The second part of this review places all these interactions in the context of various infection or colonization sites, i.e., lungs, wounds, and the gastrointestinal tract. Here we see that the role of the host, as well as the methodology used to establish co-infection, are important factors, influencing the outcome of the disease. Suggested future perspectives for the study of this interaction include determining the influence of newly identified participants of the QS network of P. aeruginosa, oxylipin production by both species, as well as the genetic and phenotypic plasticity of these microbes, on the interaction and outcome of co-infection.
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Affiliation(s)
- Ruan Fourie
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein 9301, South Africa.
| | - Carolina H Pohl
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein 9301, South Africa.
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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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Pais P, Galocha M, Viana R, Cavalheiro M, Pereira D, Teixeira MC. Microevolution of the pathogenic yeasts Candida albicans and Candida glabrata during antifungal therapy and host infection. MICROBIAL CELL 2019; 6:142-159. [PMID: 30854392 PMCID: PMC6402363 DOI: 10.15698/mic2019.03.670] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infections by the pathogenic yeasts Candida albicans and Candida glabrata are among the most common fungal diseases. The success of these species as human pathogens is contingent on their ability to resist antifungal therapy and thrive within the human host. C. glabrata is especially resilient to azole antifungal treatment, while C. albicans is best known for its wide array of virulence features. The core mechanisms that underlie antifungal resistance and virulence in these pathogens has been continuously addressed, but the investigation on how such mechanisms evolve according to each environment is scarcer. This review aims to explore current knowledge on micro-evolution experiments to several treatment and host-associated conditions in C. albicans and C. glabrata. The analysis of adaptation strategies that evolve over time will allow to better understand the mechanisms by which Candida species are able to achieve stable phenotypes in real-life scenarios, which are the ones that should constitute the most interesting drug targets.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Romeu Viana
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mafalda Cavalheiro
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Diana Pereira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Miguel Cacho Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,iBB - Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
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38
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Mezouar S, Chantran Y, Michel J, Fabre A, Dubus JC, Leone M, Sereme Y, Mège JL, Ranque S, Desnues B, Chanez P, Vitte J. Microbiome and the immune system: From a healthy steady-state to allergy associated disruption. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.humic.2018.10.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Evolution of drug resistance in an antifungal-naive chronic Candida lusitaniae infection. Proc Natl Acad Sci U S A 2018; 115:12040-12045. [PMID: 30389707 PMCID: PMC6255150 DOI: 10.1073/pnas.1807698115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Management of the limited number of antimicrobials currently available requires the identification of infections that contain drug-resistant isolates and the discovery of factors that promote the evolution of drug resistance. Here, we report a single fungal infection in which we have identified numerous subpopulations that differ in their alleles of a single gene that impacts drug resistance. The diversity at this locus was markedly greater than the reported heterogeneity of alleles conferring antibiotic resistance in bacterial infections. Analysis of genomes from hundreds of Clavispora (Candida) lusitaniae isolates, through individual and pooled isolate sequencing, from a single individual with cystic fibrosis revealed at least 25 nonsynonymous mutations in MRR1, which encodes a transcription factor capable of inducing fluconazole (FLZ) resistance in Candida species. Isolates with high-activity Mrr1 variants were resistant to FLZ due to elevated expression of the MDR1-encoded efflux pump. We found that high Mrr1-regulated Mdr1 activity protected against host and bacterial factors, suggesting drug resistance can be selected for indirectly and perhaps explaining the Mrr1 heterogeneity in this individual who had no prior azole exposure. Regional analysis of C. lusitaniae populations from the upper and lower lobes of the right lung suggested intermingling of subpopulations throughout. Our retrospective characterization of sputum and lung populations by pooled sequencing found that alleles that confer FLZ resistance were a minority in each pool, possibly explaining why they were undetected before unsuccessful FLZ therapy. New susceptibility testing regimes may detect problematical drug-resistant subpopulations in heterogeneous single-species infections.
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40
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Lai GC, Tan TG, Pavelka N. The mammalian mycobiome: A complex system in a dynamic relationship with the host. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1438. [PMID: 30255552 PMCID: PMC6586165 DOI: 10.1002/wsbm.1438] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022]
Abstract
Mammalian barrier surfaces are densely populated by symbiont fungi in much the same way the former are colonized by symbiont bacteria. The fungal microbiota, otherwise known as the mycobiota, is increasingly recognized as a critical player in the maintenance of health and homeostasis of the host. Here we discuss the impact of the mycobiota on host physiology and disease, the factors influencing mycobiota composition, and the current technologies used for identifying symbiont fungal species. Understanding the tripartite interactions among the host, mycobiota, and other members of the microbiota, will help to guide the development of novel prevention and therapeutic strategies for a variety of human diseases. This article is categorized under:
Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Organismal Models
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41
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Grahl N, Dolben EL, Filkins LM, Crocker AW, Willger SD, Morrison HG, Sogin ML, Ashare A, Gifford AH, Jacobs NJ, Schwartzman JD, Hogan DA. Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA. mSphere 2018; 3:e00292-18. [PMID: 30089648 PMCID: PMC6083091 DOI: 10.1128/msphere.00292-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and with further development, may provide quick and easily interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.IMPORTANCE Here we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.
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Affiliation(s)
- Nora Grahl
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Emily L Dolben
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Laura M Filkins
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alex W Crocker
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sven D Willger
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Alix Ashare
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Alex H Gifford
- Pulmonary and Critical Care Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Nicholas J Jacobs
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joseph D Schwartzman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Deborah A Hogan
- Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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Brown SP, Blackwell HE, Hammer BK. The State of the Union Is Strong: a Review of ASM's 6th Conference on Cell-Cell Communication in Bacteria. J Bacteriol 2018; 200:e00291-18. [PMID: 29760210 PMCID: PMC6018360 DOI: 10.1128/jb.00291-18] [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: 11/20/2022] Open
Abstract
The 6th American Society for Microbiology Conference on Cell-Cell Communication in Bacteria convened from 16 to 19 October 2017 in Athens, GA. In this minireview, we highlight some of the research presented at that meeting that addresses central questions emerging in the field, including the following questions. How are cell-cell communication circuits designed to generate responses? Where are bacteria communicating? Finally, why are bacteria engaging in such behaviors?
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Affiliation(s)
- Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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Brown-Jaque M, Rodriguez Oyarzun L, Cornejo-Sánchez T, Martín-Gómez MT, Gartner S, de Gracia J, Rovira S, Alvarez A, Jofre J, González-López JJ, Muniesa M. Detection of Bacteriophage Particles Containing Antibiotic Resistance Genes in the Sputum of Cystic Fibrosis Patients. Front Microbiol 2018; 9:856. [PMID: 29765367 PMCID: PMC5938348 DOI: 10.3389/fmicb.2018.00856] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/13/2018] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) is a chronic disease in which the bacterial colonization of the lung is linked to an excessive inflammatory response that leads to respiratory failure. The microbiology of CF is complex. Staphylococcus aureus is the first bacterium to colonize the lungs in 30% of pediatric CF patients, and 80% of adult patients develop a chronic Pseudomonas aeruginosa infection, but other microorganisms can also be found. The use of antibiotics is essential to treat the disease, but antibiotic performance is compromised by resistance mechanisms. Among various mechanisms of transfer of antibiotic resistance genes (ARGs), the recently been reported bacteriophages are the least explored in clinical settings. To determine the role of phages in CF as mobile genetic elements (MGEs) carrying ARGs, we evaluated their presence in 71 CF patients. 71 sputum samples taken from these patients were screened for eight ARGs (blaTEM, blaCTX-M-1-group, blaCTX-M-9-group, blaOXA-48, blaVIM, mecA, qnrA, and qnrS) in the bacteriophage DNA fraction. The phages found were also purified and observed by electron microscopy. 32.4% of CF patients harbored ARGs in phage DNA. β-lactamase genes, particularly blaVIM and blaTEM, were the most prevalent and abundant, whereas mecA, qnrA, and qnrS were very rare. Siphoviridae phage particles capable of infecting P. aeruginosa and Klebsiella pneumoniae were detected in CF sputum. Phage particles harboring ARGs were found to be abundant in the lungs of both CF patients and healthy individuals and could contribute to the colonization of multiresistant strains.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Lirain Rodriguez Oyarzun
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Thais Cornejo-Sánchez
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria T Martín-Gómez
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Silvia Gartner
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Javier de Gracia
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Sandra Rovira
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Antonio Alvarez
- Cystic Fibrosis Unit, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, CIBER of Respiratory Diseases (Ciberes CB06/06/0030), Carlos III Health Institute, Barcelona, Spain
| | - Joan Jofre
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Juan J González-López
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
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How can the cystic fibrosis respiratory microbiome influence our clinical decision-making? Curr Opin Pulm Med 2018; 23:536-543. [PMID: 28786882 DOI: 10.1097/mcp.0000000000000419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Almost 15 years have now passed since bacterial community profiling techniques were first used to analyse respiratory samples from people with cystic fibrosis. Since then, many different analytical approaches have been used to try to better understand the contribution of the cystic fibrosis lung microbiota to disease, with varying degrees of success. We examine the extent to which cystic fibrosis respiratory microbiome research has been successful in informing clinical decision-making, and highlight areas that we believe have the potential to yield important insight. RECENT FINDINGS Recent research on the cystic fibrosis lung microbiome can be broadly divided into efforts to better characterize microbiota composition, particularly relative to key clinical events, and attempts to understand the cystic fibrosis lung microbiology as an interactive microbial system. The latter, in particular, has led to the development of a number of models in which microbiome-mediated processes precipitate clinical events. SUMMARY Growing technological sophistication is enabling increasingly detailed microbiological data to be generated from cystic fibrosis respiratory samples. However, translating these data into clinically useful measures that accurately predict outcomes and guide treatments remains a formidable challenge. The development of systems biology approaches that enable the integration of complex microbiome and host-derived data provide an exciting opportunity to address this goal.
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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Fraczek MG, Chishimba L, Niven RM, Bromley M, Simpson A, Smyth L, Denning DW, Bowyer P. Corticosteroid treatment is associated with increased filamentous fungal burden in allergic fungal disease. J Allergy Clin Immunol 2017; 142:407-414. [PMID: 29122659 DOI: 10.1016/j.jaci.2017.09.039] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/06/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Allergic diseases caused by fungi are common. The best understood conditions are allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitization. Our knowledge of the fungal microbiome (mycobiome) is limited to a few studies involving healthy individuals, asthmatics, and smokers. No study has yet examined the mycobiome in fungal lung disease. OBJECTIVES The main aim of this study was to determine the mycobiome in lungs of individuals with well-characterized fungal disease. A secondary objective was to determine possible effects of treatment on the mycobiome. METHODS After bronchoscopy, ribosomal internal transcribed spacer region 1 DNA was amplified and sequenced and fungal load determined by real-time PCR. Clinical and treatment variables were correlated with the main species identified. Bronchopulmonary aspergillosis (n = 16), severe asthma with fungal sensitization (n = 16), severe asthma not sensitized to fungi (n = 9), mild asthma patients (n = 7), and 10 healthy control subjects were studied. RESULTS The mycobiome was highly varied with severe asthmatics carrying higher loads of fungus. Healthy individuals had low fungal loads, mostly poorly characterized Malasezziales. The most common fungus in asthmatics was Aspergillus fumigatus complex and this taxon accounted for the increased burden of fungus in the high-level samples. Corticosteroid treatment was significantly associated with increased fungal load (P < .01). CONCLUSIONS The mycobiome is highly variable. Highest loads of fungus are observed in severe asthmatics and the most common fungus is Aspergillus fumigatus complex. Individuals receiving steroid therapy had significantly higher levels of Aspergillus and total fungus in their bronchoalveolar lavage.
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Affiliation(s)
- Marcin G Fraczek
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom; School of Biological Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Livingstone Chishimba
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Rob M Niven
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Mike Bromley
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Angela Simpson
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Lucy Smyth
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - David W Denning
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom; National Aspergillosis Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom.
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47
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Carsin A, Romain T, Ranque S, Reynaud‐Gaubert M, Dubus J, Mège J, Vitte J. Aspergillus fumigatus in cystic fibrosis: An update on immune interactions and molecular diagnostics in allergic bronchopulmonary aspergillosis. Allergy 2017; 72:1632-1642. [PMID: 28513848 DOI: 10.1111/all.13204] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2017] [Indexed: 12/13/2022]
Abstract
A wide spectrum of pathological conditions may result from the interaction of Aspergillus fumigatus and the immune system of its human host. Allergic bronchopulmonary aspergillosis is one of the most severe A. fumigatus-related diseases due to possible evolution toward pleuropulmonary fibrosis and respiratory failure. Allergic bronchopulmonary aspergillosis occurs almost exclusively in cystic fibrosis or asthmatic patients. An estimated 8%-10% of patients with cystic fibrosis experience this condition. The diagnosis of allergic bronchopulmonary aspergillosis relies on criteria first established in 1977. Progress in the understanding of host-pathogen interactions in A. fumigatus and patients with cystic fibrosis and the ongoing validation of novel laboratory tools concur to update and improve the diagnosis of allergic bronchopulmonary aspergillosis.
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Affiliation(s)
- A. Carsin
- Aix‐Marseille Univ APHM Hôpital Timone Enfants Pneumo‐pédiatrie Centre de Ressources et de Compétences en Mucoviscidose Marseille France
- Aix‐Marseille Univ INSERM UMR 1067 CNRS UMR 7333 Marseille France
| | - T. Romain
- Aix‐Marseille Univ APHM Hôpital de La Conception Laboratoire d'Immunologie Marseille France
| | - S. Ranque
- Aix‐Marseille Univ APHM Hôpital Timone Laboratoire de Parasitologie Marseille France
- Aix‐Marseille Univ INSERM U1095 CNRS U7278 IRD 198 URMITE Marseille France
| | - M. Reynaud‐Gaubert
- Aix‐Marseille Univ INSERM U1095 CNRS U7278 IRD 198 URMITE Marseille France
- Aix‐Marseille Univ APHM Hôpital Nord Centre de Ressources et de Compétences en Mucoviscidose Marseille France
| | - J.‐C. Dubus
- Aix‐Marseille Univ APHM Hôpital Timone Enfants Pneumo‐pédiatrie Centre de Ressources et de Compétences en Mucoviscidose Marseille France
- Aix‐Marseille Univ INSERM U1095 CNRS U7278 IRD 198 URMITE Marseille France
| | - J.‐L. Mège
- Aix‐Marseille Univ APHM Hôpital de La Conception Laboratoire d'Immunologie Marseille France
- Aix‐Marseille Univ INSERM U1095 CNRS U7278 IRD 198 URMITE Marseille France
| | - J. Vitte
- Aix‐Marseille Univ INSERM UMR 1067 CNRS UMR 7333 Marseille France
- Aix‐Marseille Univ APHM Hôpital de La Conception Laboratoire d'Immunologie Marseille France
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48
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Bergeron AC, Seman BG, Hammond JH, Archambault LS, Hogan DA, Wheeler RT. Candida albicans and Pseudomonas aeruginosa Interact To Enhance Virulence of Mucosal Infection in Transparent Zebrafish. Infect Immun 2017; 85:e00475-17. [PMID: 28847848 PMCID: PMC5649025 DOI: 10.1128/iai.00475-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/10/2017] [Indexed: 01/02/2023] Open
Abstract
Polymicrobial infections often include both fungi and bacteria and can complicate patient treatment and resolution of infection. Cross-kingdom interactions among bacteria, fungi, and/or the immune system during infection can enhance or block virulence mechanisms and influence disease progression. The fungus Candida albicans and the bacterium Pseudomonas aeruginosa are coisolated in the context of polymicrobial infection at a variety of sites throughout the body, including mucosal tissues such as the lung. In vitro, C. albicans and P. aeruginosa have a bidirectional and largely antagonistic relationship. Their interactions in vivo remain poorly understood, specifically regarding host responses in mediating infection. In this study, we examine trikingdom interactions using a transparent juvenile zebrafish to model mucosal lung infection and show that C. albicans and P. aeruginosa are synergistically virulent. We find that high C. albicans burden, fungal epithelial invasion, swimbladder edema, and epithelial extrusion events serve as predictive factors for mortality in our infection model. Longitudinal analyses of fungal, bacterial, and immune dynamics during coinfection suggest that enhanced morbidity is associated with exacerbated C. albicans pathogenesis and elevated inflammation. The P. aeruginosa quorum-sensing-deficient ΔlasR mutant also enhances C. albicans pathogenicity in coinfection and induces extrusion of the swimbladder. Together, these observations suggest that C. albicans-P. aeruginosa cross talk in vivo can benefit both organisms to the detriment of the host.
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Affiliation(s)
- Audrey C Bergeron
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Brittany G Seman
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - John H Hammond
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Linda S Archambault
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Robert T Wheeler
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, Maine, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
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49
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Abstract
Fungi and mammals share a co-evolutionary history and are involved in a complex web of interactions. Studies focused on commensal bacteria suggest that pathological changes in the microbiota, historically known as dysbiosis, are at the root of many inflammatory diseases of non-infectious origin. However, the importance of dysbiosis in the fungal community - the mycobiota - was only recently acknowledged to have a pathological role, as novel findings have suggested that mycobiota disruption can have detrimental effects on host immunity. Fungal dysbiosis and homeostasis are dynamic processes that are probably more common than actual fungal infections, and therefore constantly shape the immune response. In this Review, we summarize specific mycobiota patterns that are associated with fungal dysbiosis, and discuss how mucosal immunity has evolved to distinguish fungal infections from dysbiosis and how it responds to these different conditions. We propose that gut microbiota dysbiosis is a collective feature of complex interactions between prokaryotic and eukaryotic microbial communities that can affect immunity and that can influence health and disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
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50
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Hampe IAI, Friedman J, Edgerton M, Morschhäuser J. An acquired mechanism of antifungal drug resistance simultaneously enables Candida albicans to escape from intrinsic host defenses. PLoS Pathog 2017; 13:e1006655. [PMID: 28953977 PMCID: PMC5633205 DOI: 10.1371/journal.ppat.1006655] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/09/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022] Open
Abstract
The opportunistic fungal pathogen Candida albicans frequently produces genetically altered variants to adapt to environmental changes and new host niches in the course of its life-long association with the human host. Gain-of-function mutations in zinc cluster transcription factors, which result in the constitutive upregulation of their target genes, are a common cause of acquired resistance to the widely used antifungal drug fluconazole, especially during long-term therapy of oropharyngeal candidiasis. In this study, we investigated if C. albicans also can develop resistance to the antimicrobial peptide histatin 5, which is secreted in the saliva of humans to protect the oral mucosa from pathogenic microbes. As histatin 5 has been shown to be transported out of C. albicans cells by the Flu1 efflux pump, we screened a library of C. albicans strains that contain artificially activated forms of all zinc cluster transcription factors of this fungus for increased FLU1 expression. We found that a hyperactive Mrr1, which confers fluconazole resistance by upregulating the multidrug efflux pump MDR1 and other genes, also causes FLU1 overexpression. Similarly to the artificially activated Mrr1, naturally occurring gain-of-function mutations in this transcription factor also caused FLU1 upregulation and increased histatin 5 resistance. Surprisingly, however, Mrr1-mediated histatin 5 resistance was mainly caused by the upregulation of MDR1 instead of FLU1, revealing a previously unrecognized function of the Mdr1 efflux pump. Fluconazole-resistant clinical C. albicans isolates with different Mrr1 gain-of-function mutations were less efficiently killed by histatin 5, and this phenotype was reverted when MRR1 was deleted. Therefore, antimycotic therapy can promote the evolution of strains that, as a consequence of drug resistance mutations, simultaneously have acquired increased resistance against an innate host defense mechanism and are thereby better adapted to certain host niches. The yeast Candida albicans is part of the normal microflora of most healthy persons, but it can also cause symptomatic infections when host defenses are compromised. C. albicans frequently generates genetically altered variants that are better adapted to changes in its environment during colonization and infection. We investigated if C. albicans can evolve resistance to histatin 5 (Hst 5), an antimicrobial peptide that is produced in the saliva of humans and protects the oral cavity against this pathogen. We found that activated forms of the transcription factor Mrr1 reduce the susceptibility of C. albicans to killing by Hst 5, a phenotype that was partially caused by Mrr1-mediated overexpression of the multidrug efflux pump MDR1. Gain-of-function (GOF) mutations in Mrr1 are a frequent cause of resistance to the antifungal drug fluconazole, especially during long-term treatment of oropharyngeal candidiasis in AIDS patients, but they may also reduce the fitness of the fungus in the absence of the drug. Fluconazole-resistant clinical C. albicans isolates containing GOF mutations in Mrr1 displayed enhanced Hst 5 resistance, demonstrating that antimycotic therapy can promote the evolution of strains that simultaneously have acquired increased resistance against an innate host defense mechanism and are thereby better adapted to specific host niches.
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Affiliation(s)
- Irene A. I. Hampe
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Justin Friedman
- Department of Oral Biology, University at Buffalo, Buffalo, New York, United States of America
| | - Mira Edgerton
- Department of Oral Biology, University at Buffalo, Buffalo, New York, United States of America
| | - Joachim Morschhäuser
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- * E-mail:
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