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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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Gorostidi-Aicua M, Reparaz I, Otaegui-Chivite A, García K, Romarate L, Álvarez de Arcaya A, Mendiburu I, Arruti M, Castillo-Triviño T, Moles L, Otaegui D. Bacteria-Fungi Interactions in Multiple Sclerosis. Microorganisms 2024; 12:872. [PMID: 38792701 PMCID: PMC11124083 DOI: 10.3390/microorganisms12050872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus Torulaspora and the bacterial family Enterobacteriaceae were observed in pwMS, whereas beneficial bacterial taxa, such as Prevotelladaceae and Dialister, were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi-bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management.
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Affiliation(s)
- Miriam Gorostidi-Aicua
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Iraia Reparaz
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Ane Otaegui-Chivite
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - Koldo García
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Leire Romarate
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
| | - Amaya Álvarez de Arcaya
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Araba, 01009 Vitoria-Gasteiz, Spain;
| | - Idoia Mendiburu
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Maialen Arruti
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Tamara Castillo-Triviño
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Neurology Department, Osakidetza Basque Health Service, Hospital Universitario Donostia, 20014 San Sebastián, Spain
| | - Laura Moles
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
| | - David Otaegui
- Biogipuzkoa Health Research Institute, Neuroimmunology Group, 20014 San Sebastián, Spain; (M.G.-A.); (I.R.); (A.O.-C.); (K.G.); (L.R.); (I.M.); (M.A.); (T.C.-T.)
- Center for Biomedical Research Network in Neurodegenerative Diseases (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
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Karajacob AS, Azizan NB, Al-Maleki ARM, Goh JPE, Loke MF, Khor HM, Ho GF, Ponnampalavanar S, Tay ST. Candida species and oral mycobiota of patients clinically diagnosed with oral thrush. PLoS One 2023; 18:e0284043. [PMID: 37068057 PMCID: PMC10109505 DOI: 10.1371/journal.pone.0284043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Overgrowth of Candida yeasts in the oral cavity may result in the development of oral thrush in immunocompromised individuals. This study analyzed the diversity and richness of the oral mycobiota of patients clinically diagnosed with oral thrush (OT), follow-up of oral thrush patients after antifungal therapy (AT), and healthy controls (HC). Oral rinse and oral swab samples were collected from 38 OT patients, 21 AT patients, and 41 healthy individuals (HC). Pellet from the oral rinse and oral swab were used for the isolation of oral Candida yeasts on Brilliance Candida Agar followed by molecular speciation. ITS1 amplicon sequencing using Illumina MiSeq was performed on DNA extracted from the oral rinse pellet of 16 OT, 7 AT, and 7 HC oral rinse samples. Trimmed sequence data were taxonomically grouped and analyzed using the CLC Microbial Genomics Module workflow. Candida yeasts were isolated at significantly higher rates from oral rinse and swab samples of OT (68.4%, p < 0.001) and AT (61.9%, p = 0.012) patients, as compared to HC (26.8%). Predominance of Candida albicans specifically, was noted in OT (60.5%, p < 0.001) and AT (42.9%, p = 0.006) vs. HC (9.8%), while non-albicans Candida species was dominant in HC. Analysis of oral mycobiota from OT patients showed the presence of 8 phyla, 222 genera, and 309 fungal species. Low alpha diversity (Shannon index, p = 0.006; Chao-1 biased corrected index, p = 0.01), varied beta diversity (Bray-Curtis, p = 0.01986; Jaccard, p = 0.02766; Weighted UniFrac, p = 0.00528), and increased relative abundance of C. albicans (p = 3.18E-02) was significantly associated with the oral mycobiota of OT vs. HC. This study supported that C. albicans is the main etiological agent in oral thrush and highlights the association of fungal biodiversity with the pathophysiology of oral thrush.
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Affiliation(s)
| | - Nuramirah Binti Azizan
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Joanne Pei En Goh
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mun Fai Loke
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Hui Min Khor
- Department of Medicine, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Gwo Fuang Ho
- Department of Clinical Oncology, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Sasheela Ponnampalavanar
- Department of Medicine, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Sun Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
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New Tools in Laboratory Diagnosis of Invasive Fungal Infections. Fungal Biol 2022. [DOI: 10.1007/978-3-030-89664-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Resendiz-Sharpe A, Merckx R, Verweij PE, Maertens J, Lagrou K. Stable prevalence of triazole-resistance in Aspergillus fumigatus complex clinical isolates in a Belgian tertiary care center from 2016 to 2020. J Infect Chemother 2021; 27:1774-1778. [PMID: 34518094 DOI: 10.1016/j.jiac.2021.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/06/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Prevalence reports of triazole-resistance in Aspergillus fumigatus differ between countries and centers and may likewise vary over time. Continuous local surveillance programs to establish the evolving epidemiology of triazole-resistance in A. fumigatus are crucial to guide therapeutic recommendations. Here, we determined the prevalence of triazole-resistance in A. fumigatus complex culture-positive patients at the tertiary care center University Hospitals Leuven in Belgium in clinical isolates from 2016 to 2020. METHODS All A. fumigatus complex isolates cultured from UZ Leuven patients between 2016 and 2020 were screened for triazole-resistance. Confirmation of resistance to voriconazole, posaconazole and itraconazole was performed with the European Committee for Antimicrobial Susceptibility Testing (EUCAST) broth microdilution method. Mutations in the cyp51A gene in triazole-resistant isolates were determined by sequencing. Patients were classified as susceptible or resistant cases based on their isolate's susceptibility phenotype. RESULTS We screened 2494 A. fumigatus complex isolates from 1600 patients (320 ± 38 [SD] patients per year). The prevalence of triazole-resistance in patients was 8.3% (28/337), 6.7% (26/386), 7.0% (21/301), 7.1% (21/294) and 7.4% (21/282) in 2016, 2017, 2018, 2019 and 2020 respectively, with an overall triazole-resistance prevalence of 7.1% (85/1192; 95% CI 6.6-7.7%). The TR34/L98H mutation was the most prevalent (83.0%, 78/94) with most isolates displaying resistance to all triazole antifungals tested (94.8%, 74/78). CONCLUSION The prevalence of triazole-resistance in A. fumigatus has remained stable from 2016 to 2020 in our center ranging between 6.7 and 8.3%, with an overall five-year prevalence of 7.1%. The environmentally associated cyp51A gene mutations were most prevalent amongst triazole-resistant isolates and conferred resistance to all antifungals tested in 73% of the isolates.
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Affiliation(s)
| | - Rita Merckx
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands; Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
| | - Johan Maertens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Department of Laboratory Medicine and National Reference Center for Mycosis, Excellence Center for Medical Mycology (ECMM), University Hospitals Leuven, Leuven, Belgium.
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6
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Recent Advances and Novel Approaches in Laboratory-Based Diagnostic Mycology. J Fungi (Basel) 2021; 7:jof7010041. [PMID: 33440757 PMCID: PMC7827937 DOI: 10.3390/jof7010041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 12/16/2022] Open
Abstract
What was once just culture and microscopy the field of diagnostic mycology has significantly advanced in recent years and continues to incorporate novel assays and strategies to meet the changes in clinical demand. The emergence of widespread resistance to antifungal therapy has led to the development of a range of molecular tests that target mutations associated with phenotypic resistance, to complement classical susceptibility testing and initial applications of next-generation sequencing are being described. Lateral flow assays provide rapid results, with simplicity allowing the test to be performed outside specialist centres, potentially as point-of-care tests. Mycology has responded positively to an ever-diversifying patient population by rapidly identifying risk and developing diagnostic strategies to improve patient management. Nowadays, the diagnostic repertoire of the mycology laboratory employs classical, molecular and serological tests and should be keen to embrace diagnostic advancements that can improve diagnosis in this notoriously difficult field.
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Rodrigues LS, Gazara RK, Passarelli-Araujo H, Valengo AE, Pontes PVM, Nunes-da-Fonseca R, de Souza RF, Venancio TM, Dalla-Costa LM. First Genome Sequences of Two Multidrug-Resistant Candida haemulonii var. vulnera Isolates From Pediatric Patients With Candidemia. Front Microbiol 2020; 11:1535. [PMID: 32719671 PMCID: PMC7350289 DOI: 10.3389/fmicb.2020.01535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022] Open
Abstract
Candida haemulonii is a complex formed by C. haemulonii sensu stricto, C. haemulonii var. vulnera, and C. duobushaemulonii. Members of this complex are opportunistic pathogens closely related to C. pseudohaemulonii, C. lusitaniae, and C. auris, all members of a multidrug-resistant clade. Complete genome sequences for all members of this group are available in the GenBank database, except for C. haemulonii var. vulnera. Here, we report the first draft genomes of two C. haemulonii var. vulnera (isolates K1 and K2) and comparative genome analysis of closely related fungal species. The isolates were biofilm producers and non-susceptible to amphotericin B and fluconazole. The draft genomes comprised 350 and 387 contigs and total genome sizes of 13.21 and 13.26 Mb, with 5,479 and 5,507 protein-coding genes, respectively, allowing the identification of virulence and resistance genes. Comparative analyses of orthologous genes within the multidrug-resistant clade showed a total of 4,015 core clusters, supporting the conservation of 24,654 proteins and 3,849 single-copy gene clusters. Candida haemulonii var. vulnera shared a larger number of clusters with C. haemulonii and C. auris; however, more singletons were identified in C. lusitaniae and C. auris. Additionally, a multiple sequence alignment of Erg11p proteins revealed variants likely involved in reduced susceptibility to azole and polyene antifungal agents. The data presented in this work will, therefore, be of utmost importance for researchers studying the biology of the C. haemulonii complex and related species.
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Affiliation(s)
- Luiza Souza Rodrigues
- Faculdades Pequeno Príncipe, Curitiba, Brazil.,Instituto de Pesquisas Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Rajesh Kumar Gazara
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.,Department of Electrical Engineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Paula Veronesi Marinho Pontes
- Instituto de Biodiversidade e Sustentabilidade, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | - Robson Francisco de Souza
- Laboratório de Estrutura e Evolução de Proteínas, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Libera Maria Dalla-Costa
- Faculdades Pequeno Príncipe, Curitiba, Brazil.,Instituto de Pesquisas Pelé Pequeno Príncipe, Curitiba, Brazil
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Mycobiome in the Gut: A Multiperspective Review. Mediators Inflamm 2020; 2020:9560684. [PMID: 32322167 PMCID: PMC7160717 DOI: 10.1155/2020/9560684] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/23/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022] Open
Abstract
Human gut is home to a diverse and complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi, and other microorganisms that have an undisputable role in maintaining good health for the host. Studies on the interplay between microbiota in the gut and various human diseases remain the key focus among many researchers. Nevertheless, advances in sequencing technologies and computational biology have helped us to identify a diversity of fungal community that reside in the gut known as the mycobiome. Although studies on gut mycobiome are still in its infancy, numerous sources have reported its potential role in host homeostasis and disease development. Nonetheless, the actual mechanism of its involvement remains largely unknown and underexplored. Thus, in this review, we attempt to discuss the recent advances in gut mycobiome research from multiple perspectives. This includes understanding the composition of fungal communities in the gut and the involvement of gut mycobiome in host immunity and gut-brain axis. Further, we also discuss on multibiome interactions in the gut with emphasis on fungi-bacteria interaction and the influence of diet in shaping gut mycobiome composition. This review also highlights the relation between fungal metabolites and gut mycobiota in human homeostasis and the role of gut mycobiome in various human diseases. This multiperspective review on gut mycobiome could perhaps shed new light for future studies in the mycobiome research area.
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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10
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Abstract
As we learn more and more about the classes of organisms that infect humans, we are discovering that many organisms, including pathogenic organisms, may have a complex relationship with humans in which infection seldom results in the production disease. In some cases, infection may be just one biological event that occurs during a multievent process that develops sequentially, over time, and involves genetic and environmental factors that may vary among individuals. Consequently, the role of infectious organisms in the development of human disease may not meet all of the criteria normally required to determine when an organism can be called the cause of a disease. This chapter reviews the expanding role of infections in the development of human disease. We discuss prion diseases of humans, a fascinating example of an infectious disease-causing agent that is not a living organism. We also discuss the diseases of unknown etiology for which infectious organisms may play a role. In addition, this chapter reviews some of the misconceptions and recurring errors associated with the classification of infectious diseases that have led to misdiagnoses and have impeded our understanding of the role of organisms in the development of human diseases.
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Hovhannisyan H, Gabaldón T. Transcriptome Sequencing Approaches to Elucidate Host-Microbe Interactions in Opportunistic Human Fungal Pathogens. Curr Top Microbiol Immunol 2019; 422:193-235. [PMID: 30128828 DOI: 10.1007/82_2018_122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Infections caused by opportunistic human fungal pathogens are a source of increasing medical concern, due to their growing incidence, the emergence of novel pathogenic species, and the lack of effective diagnostics tools. Fungal pathogens are phylogenetically diverse, and their virulence mechanisms can differ widely across species. Despite extensive efforts, the molecular bases of virulence in pathogenic fungi and their interactions with the human host remain poorly understood for most species. In this context, next-generation sequencing approaches hold the promise of helping to close this knowledge gap. In particular, high-throughput transcriptome sequencing (RNA-Seq) enables monitoring the transcriptional profile of both host and microbes to elucidate their interactions and discover molecular mechanisms of virulence and host defense. Here, we provide an overview of transcriptome sequencing techniques and approaches, and survey their application in studying the interplay between humans and fungal pathogens. Finally, we discuss novel RNA-Seq approaches in studying host-pathogen interactions and their potential role in advancing the clinical diagnostics of fungal infections.
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Affiliation(s)
- Hrant Hovhannisyan
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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Resendiz Sharpe A, Lagrou K, Meis JF, Chowdhary A, Lockhart SR, Verweij PE. Triazole resistance surveillance in Aspergillus fumigatus. Med Mycol 2018. [PMID: 29538741 DOI: 10.1093/mmy/myx144] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Triazole resistance is an increasing concern in the opportunistic mold Aspergillus fumigatus. Resistance can develop through exposure to azole compounds during azole therapy or in the environment. Resistance mutations are commonly found in the Cyp51A-gene, although other known and unknown resistance mechanisms may be present. Surveillance studies show triazole resistance in six continents, although the presence of resistance remains unknown in many countries. In most countries, resistance mutations associated with the environment dominate, but it remains unclear if these resistance traits predominately migrate or arise locally. Patients with triazole-resistant aspergillus disease may fail to antifungal therapy, but only a limited number of cohort studies have been performed that show conflicting results. Treatment failure might be due to diagnostic delay or due to the limited number of alternative treatment options. The ISHAM/ECMM Aspergillus Resistance Surveillance working group was set up to facilitate surveillance studies and stimulate international collaborations. Important aims are to determine the resistance epidemiology in countries where this information is currently lacking, to gain more insight in the clinical implications of triazole resistance through a registry and to unify nomenclature through consensus definitions.
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Affiliation(s)
- Agustin Resendiz Sharpe
- Department of Laboratory Medicine, University Hospitals Leuven, and Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine, University Hospitals Leuven, and Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Disease, Canisius Wilhelmina Hospital, Nijmegen, the Netherlands.,Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, the Netherlands
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Paul E Verweij
- Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, the Netherlands.,Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
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13
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Vidal S, Brandt BW, Dettwiler M, Abril C, Bressan J, Greub G, Frey CF, Perreten V, Rodriguez-Campos S. Limited added value of fungal ITS amplicon sequencing in the study of bovine abortion. Heliyon 2018; 4:e00915. [PMID: 30426108 PMCID: PMC6222074 DOI: 10.1016/j.heliyon.2018.e00915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/28/2018] [Accepted: 10/31/2018] [Indexed: 11/29/2022] Open
Abstract
Bovine mycotic abortion is sporadic and caused by different ubiquitous and opportunistic fungi. Recently, a broad spectrum of bacterial opportunists involved in bovine abortion was revealed by 16S rRNA gene amplicon sequencing. We hypothesized that fungal organisms potentially involved in bovine abortion also might remain undetected by conventional culture. In this retrospective study, we therefore applied fungal internal transcribed spacer 2 (ITS2) region amplicon sequencing to 74 cases of bovine abortion submitted to our diagnostic service. The investigation was complemented by fungal culture and, retrospectively, by data from bacteriological, virological and parasitological analyses and histopathological examination of placentas. Fungal DNA was found in both the placentas and abomasal contents, with 92 fungal genera identified. In 18 cases, >75% of the reads belonged to one specific fungal genus: Candida (n = 7), Malassezia (n = 4), Cryptococcus (n = 3), unidentified Capnodiales (n = 3), Actinomucor (n = 1), Cystofilobasidium (n = 1), Penicillium (n = 1), Verticillum (n = 1) and Zymoseptoria (n = 1) with one case harboring two different genera. By culture, in contrast, fungal agents were detected in only 6 cases. Inflammatory and/or necrotizing lesions were found in 27/40 histologically assessed placentas. However, no lesion-associated fungal structures were detected in HE- and PAS-stained specimens. Complementary data revealed the presence of one or more non-fungal possible abortifacient: Chlamydiales, Coxiella burnetii, Leptospira spp., Campylobacter fetus subsp. fetus, Streptococcus uberis, Escherichia coli, Streptococcus pluranimalium, Bacillus licheniformis, Campylobacter fetus subsp. fetus, Serratia marcescens, Trueperella pyogenes, Schmallenbergvirus, Neospora caninum. The mycobiota revealed by sequencing did not differ between cases with or without a possible infectious etiology. Our study suggests that amplicon sequencing of the ITS2 region from DNA isolated from bovine abortion does not provide additional information or new insight into mycotic abortion and without complementary analyses may easily lead to a false interpretation of the role of fungal organisms in bovine abortion.
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Affiliation(s)
- Sara Vidal
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Bernd W. Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, the Netherlands
| | - Martina Dettwiler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Carlos Abril
- Institute of Virology and Immunology, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Jenny Bressan
- Department of Neurology, Bern University Hospital and University of Bern, Freiburgstrasse, CH-3010 Bern, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland
| | - Caroline F. Frey
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Sabrina Rodriguez-Campos
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
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14
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Garcia-Rubio R, Monzon S, Alcazar-Fuoli L, Cuesta I, Mellado E. Genome-Wide Comparative Analysis of Aspergillus fumigatus Strains: The Reference Genome as a Matter of Concern. Genes (Basel) 2018; 9:E363. [PMID: 30029559 PMCID: PMC6071029 DOI: 10.3390/genes9070363] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/11/2022] Open
Abstract
Aspergillus fumigatus is a ubiquitous saprophytic mold and a major pathogen in immunocompromised patients. The effectiveness of triazole compounds, the A. fumigatus first line treatment, is being threatened by a rapid and global emergence of azole resistance. Whole genome sequencing (WGS) has emerged as an invaluable tool for the analysis of genetic differences between A. fumigatus strains, their genetic background, and antifungal resistance development. Although WGS analyses can provide a valuable amount of novel information, there are some limitations that should be considered. These analyses, based on genome-wide comparative data and single nucleotide variant (SNV) calling, are dependent on the quality of sequencing, assembling, the variant calling criteria, as well as on the suitable selection of the reference genome, which must be genetically close to the genomes included in the analysis. In this study, 28 A. fumigatus genomes sequenced in-house and 73 available in public data bases have been analyzed. All genomes were distributed in four clusters and showed a variable number of SNVs depending on the genome used as reference (Af293 or A1163). Each reference genome belonged to a different cluster. The results highlighted the importance of choosing the most suitable A. fumigatus reference genome to avoid misleading conclusions.
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Affiliation(s)
- Rocio Garcia-Rubio
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain.
| | - Sara Monzon
- Bioinformatics Unit, Common Scientific Technical Units, ISCIII, Majadahonda, 28220 Madrid, Spain.
| | - Laura Alcazar-Fuoli
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain.
| | - Isabel Cuesta
- Bioinformatics Unit, Common Scientific Technical Units, ISCIII, Majadahonda, 28220 Madrid, Spain.
| | - Emilia Mellado
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain.
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15
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Tibpromma S, Hyde KD, Bhat JD, Mortimer PE, Xu J, Promputtha I, Doilom M, Yang JB, Tang AMC, Karunarathna SC. Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand. MycoKeys 2018. [DOI: 10.3897/mycokeys.32.23670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The authors established the taxonomic status of endophytic fungi associated with leaves of Pandanaceae collected from southern Thailand. Morphotypes were initially identified based on their characteristics in culture and species level identification was done based on both morphological characteristics and phylogenetic analyses of DNA sequence data. Twenty-two isolates from healthy leaves were categorised into eight morphotypes. Appropriate universal primers were used to amplify specific gene regions and phylogenetic analyses were performed to identify these endophytes and established relationships with extant fungi. The authors identified both ascomycete and basidiomycete species, including one new genus, seven new species and nine known species. Morphological descriptions, colour plates and phylogenies are given for each taxon.
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16
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Tibpromma S, Hyde KD, Bhat JD, Mortimer PE, Xu J, Promputtha I, Doilom M, Yang JB, Tang AMC, Karunarathna SC. Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand. MycoKeys 2018; 33:25-67. [PMID: 30532625 PMCID: PMC6283267 DOI: 10.3897/mycokeys.33.23670] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/16/2018] [Indexed: 02/01/2023] Open
Abstract
The authors established the taxonomic status of endophytic fungi associated with leaves of Pandanaceae collected from southern Thailand. Morphotypes were initially identified based on their characteristics in culture and species level identification was done based on both morphological characteristics and phylogenetic analyses of DNA sequence data. Twenty-two isolates from healthy leaves were categorised into eight morphotypes. Appropriate universal primers were used to amplify specific gene regions and phylogenetic analyses were performed to identify these endophytes and established relationships with extant fungi. The authors identified both ascomycete and basidiomycete species, including one new genus, seven new species and nine known species. Morphological descriptions, colour plates and phylogenies are given for each taxon.
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Affiliation(s)
- Saowaluck Tibpromma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People’s Republic of China
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kevin D. Hyde
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People’s Republic of China
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Jayarama D. Bhat
- Formerly, Department of Botany, Goa University, Taleigão, Goa, India
- No. 128/1-J, Azad Housing Society, Curca, Goa Velha, India
| | - Peter E. Mortimer
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People’s Republic of China
| | - Jianchu Xu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People’s Republic of China
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Environmental Science Research Centre, Faculty of Science, Chiang Mai University, 50200, Thailand
| | - Mingkwan Doilom
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People’s Republic of China
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
| | - Alvin M. C. Tang
- Division of Applied Science, College of International Education, The Hong Kong Baptist University, Hong Kong SAR, China
| | - Samantha C. Karunarathna
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, People’s Republic of China
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
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17
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Gałązka A, Grządziel J. Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques. Front Microbiol 2018; 9:76. [PMID: 29441054 PMCID: PMC5797640 DOI: 10.3389/fmicb.2018.00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/12/2018] [Indexed: 11/17/2022] Open
Abstract
Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS), reduced tillage (RT), full tillage (FT), and crop rotation (CR). Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation) and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation). The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895), genus level (P = 0.026, F = 3.313) and on the species level (P = 0.033, F = 2.718). This study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function.
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Affiliation(s)
- Anna Gałązka
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation - State Research Institute, Puławy, Poland
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18
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Biswas C, Chen SCA, Halliday C, Martinez E, Rockett RJ, Wang Q, Timms VJ, Dhakal R, Sadsad R, Kennedy KJ, Playford G, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V. Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance. J Vis Exp 2017. [PMID: 29364212 DOI: 10.3791/56714] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Candida glabrata can rapidly acquire mutations that result in drug resistance, especially to azoles and echinocandins. Identification of genetic mutations is essential, as resistance detected in vitro can often be correlated with clinical failure. We examined the feasibility of using whole genome sequencing (WGS) for genome-wide analysis of antifungal drug resistance in C. glabrata. The aim was torecognize enablers and barriers in the implementation WGS and measure its effectiveness. This paper outlines the key quality control checkpoints and essential components of WGS methodology to investigate genetic markers associated with reduced susceptibility to antifungal agents. It also estimates the accuracy of data analysis and turn-around-time of testing. Phenotypic susceptibility of 12 clinical, and one ATCC strain of C. glabrata was determined through antifungal susceptibility testing. These included three isolate pairs, from three patients, that developed rise in drug minimum inhibitory concentrations. In two pairs, the second isolate of each pair developed resistance to echinocandins. The second isolate of the third pair developed resistance to 5-flucytosine. The remaining comprised of susceptible and azole resistant isolates. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-flucytosine resistance were confirmed in resistant isolates through WGS using the next generation sequencing. Non-synonymous SNPs in antifungal resistance genes such as FKS1, FKS2, CgPDR1, CgCDR1 and FCY2 were identified. Overall, an average of 98% of the WGS reads of C. glabrata isolates mapped to the reference genome with about 75-fold read depth coverage. The turnaround time and cost were comparable to Sanger sequencing. In conclusion, WGS of C. glabrata was feasible in revealing clinically significant gene mutations involved in resistance to different antifungal drug classes without the need for multiple PCR/DNA sequencing reactions. This represents a positive step towards establishing WGS capability in the clinical laboratory for simultaneous detection of antifungal resistance conferring substitutions.
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Affiliation(s)
- Chayanika Biswas
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital;
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rebecca J Rockett
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rajat Dhakal
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Rosemarie Sadsad
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital
| | - Karina J Kennedy
- Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School
| | - Geoffrey Playford
- Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School; Infection Management Services, Australian National University Medical School
| | - Deborah J Marriott
- Department of Microbiology and Infectious Diseases, St. Vincent's Hospital
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital; Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney
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19
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Hamad I, Ranque S, Azhar EI, Yasir M, Jiman-Fatani AA, Tissot-Dupont H, Raoult D, Bittar F. Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota. Sci Rep 2017; 7:16788. [PMID: 29196717 PMCID: PMC5711903 DOI: 10.1038/s41598-017-17132-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
Herein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut.
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Affiliation(s)
- Ibrahim Hamad
- Aix Marseille University, CNRS 7278, IRD 198, Inserm 1095, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
- Charmo University, Charmo Research Center, 46023, Chamchamal, Sulaimani, Iraq
| | - Stéphane Ranque
- Aix Marseille University, CNRS 7278, IRD 198, Inserm 1095, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A Jiman-Fatani
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hervé Tissot-Dupont
- Aix Marseille University, CNRS 7278, IRD 198, Inserm 1095, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille University, CNRS 7278, IRD 198, Inserm 1095, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix Marseille University, CNRS 7278, IRD 198, Inserm 1095, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France.
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20
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Schneider J, Heydel T, Klasen L, Pees M, Schrödl W, Schmidt V. Characterization of Nannizziopsis guarroi with genomic and proteomic analysis in three lizard species. Med Mycol 2017; 56:610-620. [DOI: 10.1093/mmy/myx083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022] Open
Affiliation(s)
- Juliane Schneider
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
| | - Tilo Heydel
- Institute of Bacteriology and Mycology, University of Leipzig, Leipzig, Germany
| | - Linus Klasen
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
| | - Michael Pees
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
| | - Wieland Schrödl
- Institute of Bacteriology and Mycology, University of Leipzig, Leipzig, Germany
| | - Volker Schmidt
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
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21
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McCarthy MW, Denning DW, Walsh TJ. Future Research Priorities in Fungal Resistance. J Infect Dis 2017; 216:S484-S492. [PMID: 28911040 DOI: 10.1093/infdis/jix103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Improved understanding of basic mycological, pharmacological, and immunological processes has led to important advances in the diagnosis and treatment of invasive fungal infections. However, the rise of fungi that are resistant to existing antifungal agents poses a substantial threat to human health. Addressing this expanding problem is an urgent priority for the international research community. In this article, we highlight important diagnostic and therapeutic advances that address the rise of resistant fungi as well as new public health initiatives that warrant further investigation to help curb the spread of these potentially lethal organisms.
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Affiliation(s)
| | - David W Denning
- University Hospital of South Manchester, University of Manchester, Manchester Academic Health Science Centre, United Kingdom
| | - Thomas J Walsh
- Transplantation-Oncology Infectious Diseases Program, Weill Cornell Medicine, New York, New York
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22
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Kaur H, Chakrabarti A. Strategies to Reduce Mortality in Adult and Neonatal Candidemia in Developing Countries. J Fungi (Basel) 2017; 3:E41. [PMID: 29371558 PMCID: PMC5715942 DOI: 10.3390/jof3030041] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/13/2017] [Accepted: 07/16/2017] [Indexed: 02/07/2023] Open
Abstract
Candidemia, the commonest invasive fungal infection, is associated with high morbidity and mortality in developing countries, though the exact prevalence is not known due to lack of systematic epidemiological data from those countries. The limited studies report a very high incidence of candidemia and unique epidemiology with a different spectrum of Candida species. The recent global emergence of multi-drug resistant Candida auris is looming large as an important threat in hospitalized patients of developing countries. While managing candidemia cases in those countries several challenges are faced, which include poor infrastructure; compromised healthcare and infection control practices; misuse and overuse of antibiotics and steroids; lack of awareness in fungal infections; non-availability of advance diagnostic tests and antifungal drugs in many areas; poor compliance to antifungal therapy and stewardship program. Considering the above limitations, innovative strategies are required to reduce mortality due to candidemia in adults and neonates. In the present review, we have unraveled the challenges of candidemia faced by low resource countries and propose a ten part strategy to reduce mortality due candidemia.
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Affiliation(s)
- Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
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23
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McGee CF, Byrne H, Irvine A, Wilson J. Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus. Mycologia 2017; 109:475-484. [PMID: 28759322 DOI: 10.1080/00275514.2017.1349498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Commercial cultivation of the button mushroom Agaricus bisporus is performed through the inoculation of a semipasteurized composted material. Pasteurization of the compost material prior to inoculation results in a substrate with a fungal community that becomes dominated by A. bisporus. However, little is known about the composition and activity in the wider fungal community beyond the presence of A. bisporus in compost throughout the mushroom cropping process. In this study, the fungal cropping compost community was characterized by sequencing nuc rDNA ITS1-5.8S-ITS2 amplified from extractable DNA and RNA. The fungal community generated from DNA extracts identified a diverse community containing 211 unique species, although only 51 were identified from cDNA. Agaricus bisporus was found to dominate in the DNA-derived fungal community for the duration of the cropping process. However, analysis of cDNA extracts found A. bisporus to dominate only up to the first crop flush, after which activity decreased sharply and a much broader fungal community became active. This study has highlighted the diverse fungal community that is present in mushroom compost during cropping.
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Affiliation(s)
- C F McGee
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
| | - H Byrne
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
| | - A Irvine
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
| | - J Wilson
- a Monaghan Mushrooms R&D Department , Group Headquarters , Tyholland , County Monaghan , Ireland
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Kamińska D, Gajecka M. Is the role of human female reproductive tract microbiota underestimated? Benef Microbes 2017; 8:327-343. [PMID: 28504576 DOI: 10.3920/bm2015.0174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An issue that is currently undergoing extensive study is the influence of human vaginal microbiota (VMB) on the health status of women and their neonates. Healthy women are mainly colonised with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners; however, other bacteria may be elements of the VMB, particularly in women with bacterial vaginosis. The implementation of culture-independent molecular methods in VMB characterisation, especially next-generation sequencing, have provided new information regarding bacterial diversity in the vagina, revealing a large number of novel, fastidious, and/or uncultivated bacterial species. These molecular studies have contributed new insights regarding the role of bacterial community composition. In this study, we discuss recent findings regarding the reproductive tract microbiome. Not only bacteria but also viruses and fungi constitute important components of the reproductive tract microbiome. We focus on aspects related to the impact of the maternal microbiome on foetal development, as well as the establishment of the neonatal microbiomes, including the placenta microbiome, and the haematogenous source of intrauterine infection. We also discuss whether the role of the vaginal microbiome is currently understood and appreciated.
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Affiliation(s)
- D Kamińska
- 1 Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Swiecickiego 4, 60-781 Poznan, Poland
| | - M Gajecka
- 1 Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Swiecickiego 4, 60-781 Poznan, Poland.,2 Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
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Characterization of Metarhizium viride Mycosis in Veiled Chameleons (Chamaeleo calyptratus), Panther Chameleons (Furcifer pardalis), and Inland Bearded Dragons (Pogona vitticeps). J Clin Microbiol 2016; 55:832-843. [PMID: 28003420 DOI: 10.1128/jcm.02206-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022] Open
Abstract
Metarhizium viride has been associated with fatal systemic mycoses in chameleons, but subsequent data on mycoses caused by this fungus in reptiles are lacking. The aim of this investigation was therefore to obtain information on the presence of M. viride in reptiles kept as pets in captivity and its association with clinical signs and pathological findings as well as improvement of diagnostic procedures. Beside 18S ribosomal DNA (rDNA) (small subunit [SSU]) and internal transcribed spacer region 1 (ITS-1), a fragment of the large subunit (LSU) of 28S rDNA, including domain 1 (D1) and D2, was sequenced for the identification of the fungus and phylogenetic analysis. Cultural isolation and histopathological examinations as well as the pattern of antifungal drug resistance, determined by using agar diffusion testing, were additionally used for comparison of the isolates. In total, 20 isolates from eight inland bearded dragons (Pogona vitticeps), six veiled chameleons (Chamaeleo calyptratus), and six panther chameleons (Furcifer pardalis) were examined. Most of the lizards suffered from fungal glossitis, stomatitis, and pharyngitis or died due to visceral mycosis. Treatment with different antifungal drugs according to resistance patterns in all three different lizard species was unsuccessful. Sequence analysis resulted in four different genotypes of M. viride based on differences in the LSU fragment, whereas the SSU and ITS-1 were identical in all isolates. Sequence analysis of the SSU fragment revealed the first presentation of a valid large fragment of the SSU of M. viride According to statistical analysis, genotypes did not correlate with differences in pathogenicity, antifungal susceptibility, or species specificity.
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