1
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Dai RC, Guan J, Ning YT, Kudinha T, Zhang W, Chen XF, Zhang G, Xu YC, Xiao M. Complete Genome Sequence of Candida mucifera from an Otitis Media Patient. Mycopathologia 2024; 189:78. [PMID: 39222187 DOI: 10.1007/s11046-024-00878-7] [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: 03/31/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024]
Abstract
We describe for the first time, a high-quality genome for a rare human yeast pathogen Candida mucifera, from a patient with chronic suppurative otitis media. This pathogen exhibited reduced azole susceptibility, similar to its close relatives within the Trichomonascus ciferrii species complex.
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Affiliation(s)
- Rong-Chen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Jing Guan
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Ya-Ting Ning
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, 2800, Australia
- NSW Health Pathology, Regional and Rural, Orange Hospital, Orange, NSW, 2800, Australia
| | - Wei Zhang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Ge Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China.
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China.
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2
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Mac Aogáin M, Dicker AJ, Mertsch P, Chotirmall SH. Infection and the microbiome in bronchiectasis. Eur Respir Rev 2024; 33:240038. [PMID: 38960615 PMCID: PMC11220623 DOI: 10.1183/16000617.0038-2024] [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: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.
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Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alison J Dicker
- Respiratory Research Group, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Pontus Mertsch
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center (CPC), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
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3
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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4
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Ning YT, Dai RC, Luo ZY, Xiao M, Xu Y, Yan Q, Zhang L. Draft Genome Sequence of Candida saopaulonensis from a Very Premature Infant with Sepsis. Mycopathologia 2024; 189:32. [PMID: 38622365 PMCID: PMC11018655 DOI: 10.1007/s11046-024-00838-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
The rare fungus Candida saopaulonensis has never been reported to be associated with human infection. We report the draft genome sequence of the first clinical isolate of C. saopaulonensis, which was isolated from a very premature infant with sepsis. This is the first genome assembly reaching the near-complete chromosomal level with structural annotation for this species, opening up avenues for exploring evolutionary patterns and genetic mechanisms of pathogenesis.
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Affiliation(s)
- Ya-Ting Ning
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Rong-Chen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Zheng-Yu Luo
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, 100730, China.
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5
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James SA, Parker A, Purse C, Telatin A, Baker D, Evans R, Holmes S, Funnell SGP, Carding SR. Draft Genome Sequence of a Primate Isolate of Kazachstania pintolopesii. Mycopathologia 2023; 188:821-823. [PMID: 37589873 PMCID: PMC10564811 DOI: 10.1007/s11046-023-00772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/18/2023]
Abstract
Kazachstania pintolopesii is an opportunistic mammalian pathobiont from the K. telluris species complex. No draft genomes of this species are currently available. Here, we report the first draft genome sequence of a primate isolate of K. pintolopesii (NCYC 4417).
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Affiliation(s)
- Steve A James
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK.
| | - Aimee Parker
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Catherine Purse
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Andrea Telatin
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - David Baker
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Rhiannon Evans
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sandy Holmes
- UK Health Security Agency, Porton Down, Salisbury, UK
| | - Simon G P Funnell
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
- UK Health Security Agency, Porton Down, Salisbury, UK
| | - Simon R Carding
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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6
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Deroche L, Buyck J, Cateau E, Marchand S, Brunet K. Draft Genome Sequence of the Rhinocladiella similis Clinical Isolate CBS 149759. Mycopathologia 2023:10.1007/s11046-023-00715-3. [PMID: 37022620 DOI: 10.1007/s11046-023-00715-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/08/2023] [Indexed: 04/07/2023]
Abstract
Rhinocladiella similis is a melanized fungi involved in chromoblastomycosis. R. similis genome has never been sequenced, therefore we propose the first draft genome of R. similis.
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Affiliation(s)
- Luc Deroche
- INSERM U1070, Poitiers, France
- Université de Poitiers, Faculté de Médecine Et Pharmacie, Poitiers, France
- Service de Virologie, Département Des Agents Infectieux, CHU de Poitiers, Poitiers, France
| | - Julien Buyck
- INSERM U1070, Poitiers, France
- Université de Poitiers, Faculté de Médecine Et Pharmacie, Poitiers, France
| | - Estelle Cateau
- Université de Poitiers, Faculté de Médecine Et Pharmacie, Poitiers, France
- Service de Mycologie-Parasitologie, Département Des Agents Infectieux, CHU de Poitiers, Poitiers, France
| | - Sandrine Marchand
- INSERM U1070, Poitiers, France
- Université de Poitiers, Faculté de Médecine Et Pharmacie, Poitiers, France
- Service de Toxicologie Et de Pharmacocinétique, CHU de Poitiers, Poitiers, France
| | - Kévin Brunet
- INSERM U1070, Poitiers, France.
- Université de Poitiers, Faculté de Médecine Et Pharmacie, Poitiers, France.
- Service de Mycologie-Parasitologie, Département Des Agents Infectieux, CHU de Poitiers, Poitiers, France.
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7
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There Is More to Wounds than Bacteria: Fungal Biofilms in Chronic Wounds. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-022-00187-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abstract
Purpose of Review
The management of chronic wounds, a debilitating condition, presents a considerable challenge to healthcare professionals and a significant burden on services. When these wounds are exposed to the external environment, they are susceptible to microbial infection, which further complicates their management and worsens clinical outcomes.
Recent Findings
Bacteria typically exist in wounds as part of a biofilm, which is often polymicrobial in nature, alongside bacteria and fungi that are described as being more virulent and tolerant towards antimicrobials and antiseptics. Despite advancing knowledge in polymicrobial biofilm wound infections with respect to bacteria, the role of fungi is largely ignored, and their influence in chronicity and clinical management is not fully appreciated or understood.
Summary
The purpose of this review is to explore the significance of fungi within chronic wound environments and, in doing so, understand the importance of interkingdom interactions in wound management.
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8
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Draft Genome Sequence of the Fluconazole-Resistant Candida palmioleophila Clinical Isolate CBS 18098. Mycopathologia 2022; 188:169-171. [PMID: 36287321 DOI: 10.1007/s11046-022-00682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/07/2022] [Indexed: 10/31/2022]
Abstract
Candida palmioleophila belongs to the Saccharomycetales. This opportunistic yeast which has been associated with invasive infections in human and animals, warrants a specific attention as it is frequently misidentified and display reduced susceptibility to fluconazole. Here, we report the first draft genome of C. palmioleophila, obtained from a clinical isolate.
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9
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Deroche L, Buyck J, Cateau E, Rammaert B, Marchand S, Brunet K. Draft Genome Sequence of Kazachstania bovina Yeast Isolated from Human Infection. Mycopathologia 2022; 187:413-415. [PMID: 35829847 DOI: 10.1007/s11046-022-00639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022]
Abstract
Kazachstania bovina is a yeast species from the K. telluris complex that has been recently involved in bloodstream infections. While yeast genomes from this complex have already been sequenced, K. bovina genome has not been published yet. Here is the first draft genome of K. bovina (CBS 16326).
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Affiliation(s)
- Luc Deroche
- INSERM U1070, Poitiers, France
- Faculté de Médecine et Pharmacie, Université de Poitiers, Poitiers, France
- Département des Agents Infectieux, Service de Virologie, CHU de Poitiers, Poitiers, France
| | - Julien Buyck
- INSERM U1070, Poitiers, France
- Faculté de Médecine et Pharmacie, Université de Poitiers, Poitiers, France
| | - Estelle Cateau
- Faculté de Médecine et Pharmacie, Université de Poitiers, Poitiers, France
- Département des Agents Infectieux, Service de Mycologie-Parasitologie, CHU de Poitiers, Poitiers, France
- Laboratoire Écologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Blandine Rammaert
- INSERM U1070, Poitiers, France
- Faculté de Médecine et Pharmacie, Université de Poitiers, Poitiers, France
- Service de Maladies Infectieuses et Tropicales, CHU de Poitiers, Poitiers, France
| | - Sandrine Marchand
- INSERM U1070, Poitiers, France
- Faculté de Médecine et Pharmacie, Université de Poitiers, Poitiers, France
- Service de Toxicologie et de Pharmacocinétique, CHU de Poitiers, Poitiers, France
| | - Kévin Brunet
- INSERM U1070, Poitiers, France.
- Faculté de Médecine et Pharmacie, Université de Poitiers, Poitiers, France.
- Département des Agents Infectieux, Service de Mycologie-Parasitologie, CHU de Poitiers, Poitiers, France.
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10
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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11
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Henderickx JGE, de Weerd H, Groot Jebbink LJ, van Zoeren-Grobben D, Hemels MAC, van Lingen RA, Knol J, Belzer C. The first fungi: mode of delivery determines early life fungal colonization in the intestine of preterm infants. MICROBIOME RESEARCH REPORTS 2022; 1:7. [PMID: 38089064 PMCID: PMC10714301 DOI: 10.20517/mrr.2021.03] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 01/15/2022] [Indexed: 06/26/2024]
Abstract
Aim: The role of intestinal fungi in human health and disease is becoming more evident. The mycobiota composition and diversity of preterm infants is affected by interactions with bacteria and clinical variables. In this study, we aimed to characterize the composition and the diversity of the preterm infant mycobiota and the effect of clinical variables on it in the first six postnatal weeks. Methods: Preterm infants (n = 50) and full-term infants (n = 6) admitted to Isala Women and Children's hospital (Zwolle, The Netherlands) who were born during 24-36 or 37-40 weeks of gestation, respectively, were included in this study. Feces were collected during the first six postnatal weeks (n = 109) and their mycobiota composition and diversity were characterized by ITS2 amplicon sequencing. Results: Composition analyses identified fungi and other eukaryotic kingdoms, of which Viridiplantae was most abundant. Of the fungal kingdom, Ascomycota and Basidiomycota were the first and second most prominent phyla in early life of all infants. Candida was the most abundant genus in the first six weeks of life and increased with gestational and postnatal age. Fungal phylogenetic diversity remained stable in the first six postnatal weeks. The individuality and the mode of delivery were identified as significant predictors for the variation in the mycobiota composition. Vaginally delivered infants were enriched in Candida spp., whereas infants delivered through emergency C-section were characterized by Malassezia spp. Conclusion: These results indicate that fungi and other eukaryotic kingdoms are detected in the intestine of preterm and full-term infants in the first six postnatal weeks. Similar to the microbiota, colonization of the preterm intestine with fungi is determined by clinical variables including individuality and mode of delivery.
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Affiliation(s)
- Jannie G. E. Henderickx
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Heleen de Weerd
- Danone Nutricia Research, Uppsalalaan 12, Utrecht 3584 CT, The Netherlands
| | - Liesbeth J. Groot Jebbink
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Diny van Zoeren-Grobben
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Marieke A. C. Hemels
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Richard A. van Lingen
- Isala Women and Children’s Hospital, Department of Neonatology, Dokter van Heesweg 2, Zwolle 8025 AB, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
- Danone Nutricia Research, Uppsalalaan 12, Utrecht 3584 CT, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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12
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de Jong AW, Francisco EC, de Almeida JN, Brandão IB, Pereira FM, Dias PHP, de Miranda Costa MM, de Souza Jordão RT, Vu D, Colombo AL, Hagen F. Nanopore Genome Sequencing and Variant Analysis of the Susceptible Candida auris Strain L1537/2020, Salvador, Brazil. Mycopathologia 2021; 186:883-887. [PMID: 34669105 PMCID: PMC8527438 DOI: 10.1007/s11046-021-00593-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/10/2021] [Indexed: 02/08/2023]
Abstract
Candida auris has been reported worldwide, but only in December 2020, the first strain from a COVID-19 patient in Brazil was isolated. Here, we describe the genome sequence of this susceptible C. auris strain and performed variant analysis of the genetic relatedness with strains from other geographic localities.
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Affiliation(s)
- Auke W de Jong
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, NL-3584CT, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elaine C Francisco
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, NL-3584CT, Utrecht, The Netherlands.,Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - João Nóbrega de Almeida
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Igor B Brandão
- Comissão de Controle de Infecção Hospitalar, Hospital de Bahia, Salvador, Brazil
| | | | - Pedro H Presta Dias
- Centro de Informações Estratégicas de Vigilância em Saúde da Bahia, Salvador, Brazil
| | | | | | - Duong Vu
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, NL-3584CT, Utrecht, The Netherlands
| | - Arnaldo L Colombo
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, NL-3584CT, Utrecht, The Netherlands. .,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands. .,Department of Dermatology, Jining No. 1 People's Hospital, Shandong, China.
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13
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Shiller J, Duvaux L, Vandeputte P, Lemaire C, Rougeron A, De Bernonville TD, Giraud S, Le Cam B, Bouchara JP, Gastebois A. Draft Genome Sequence of the Environmental Fungus Scedosporium dehoogii. Mycopathologia 2021; 186:889-892. [PMID: 34570289 DOI: 10.1007/s11046-021-00582-w] [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: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 11/25/2022]
Abstract
Today, the genus Scedosporium comprises at least ten species with four of them, Scedosporium apiospermum, Scedosporium boydii, Scedosporium aurantiacum and Scedosporium minutisporum capable of colonizing the lungs of patients with cystic fibrosis. Scedosporium dehoogii, which is also common in the soil, has never been reported as causing human pulmonary infections. Here we report the first genome sequence for S. dehoogii, an invaluable resource to understand the genetic bases of pathogenesis in the genus Scedosporium.
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Affiliation(s)
- Jason Shiller
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Ludovic Duvaux
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France.,Univ Angers, Université de Bretagne Occidentale, CHU Angers, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA3142), SFR ICAT, 49000, Angers, France
| | - Patrick Vandeputte
- Univ Angers, Université de Bretagne Occidentale, CHU Angers, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA3142), SFR ICAT, 49000, Angers, France
| | - Christophe Lemaire
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Amandine Rougeron
- Univ Angers, Université de Bretagne Occidentale, CHU Angers, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA3142), SFR ICAT, 49000, Angers, France
| | - Thomas Dugé De Bernonville
- Université François Rabelais de Tours, EA 2106, Biomolécules et Biotechnologies Végétales (EA2106), 37000, Tours, France
| | - Sandrine Giraud
- Univ Angers, Université de Bretagne Occidentale, CHU Angers, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA3142), SFR ICAT, 49000, Angers, France
| | - Bruno Le Cam
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France
| | - Jean-Philippe Bouchara
- Univ Angers, Université de Bretagne Occidentale, CHU Angers, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA3142), SFR ICAT, 49000, Angers, France
| | - Amandine Gastebois
- Univ Angers, Université de Bretagne Occidentale, CHU Angers, Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA3142), SFR ICAT, 49000, Angers, France.
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14
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Trindade M, Sithole N, Kubicki S, Thies S, Burger A. Screening Strategies for Biosurfactant Discovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:17-52. [PMID: 34518910 DOI: 10.1007/10_2021_174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isolation and screening of bacteria and fungi for the production of surface-active compounds has been the basis for the majority of the biosurfactants discovered to date. Hence, a wide variety of well-established and relatively simple methods are available for screening, mostly focused on the detection of surface or interfacial activity of the culture supernatant. However, the success of any biodiscovery effort, specifically aiming to access novelty, relies directly on the characteristics being screened for and the uniqueness of the microorganisms being screened. Therefore, given that rather few novel biosurfactant structures have been discovered during the last decade, advanced strategies are now needed to widen access to novel chemistries and properties. In addition, more modern Omics technologies should be considered to the traditional culture-based approaches for biosurfactant discovery. This chapter summarizes the screening methods and strategies typically used for the discovery of biosurfactants and highlights some of the Omics-based approaches that have resulted in the discovery of unique biosurfactants. These studies illustrate the potentially enormous diversity that has yet to be unlocked and how we can begin to tap into these biological resources.
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Affiliation(s)
- Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa.
| | - Nombuso Sithole
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Sonja Kubicki
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Anita Burger
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
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15
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Jaggi TK, Ter SK, Mac Aogáin M, Chotirmall SH. Aspergillus-Associated Endophenotypes in Bronchiectasis. Semin Respir Crit Care Med 2021; 42:556-566. [PMID: 34261180 DOI: 10.1055/s-0041-1730947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bronchiectasis is a chronic condition of global relevance resulting in permanent and irreversible structural airway damage. Bacterial infection in bronchiectasis is well studied; however, recent molecular studies identify fungi as important pathogens, either independently or in association with bacteria. Aspergillus species are established fungal pathogens in cystic fibrosis and their role is now increasingly being recognized in noncystic fibrosis bronchiectasis. While the healthy airway is constantly exposed to ubiquitously present Aspergillus conidia in the environment, anatomically damaged airways appear more prone to colonization and subsequent infection by this fungal group. Aspergilli possess diverse immunopathological mechanistic capabilities and when coupled with innate immune defects in a susceptible host, such as that observed in bronchiectasis, it may promote a range of clinical manifestations including sensitization, allergic bronchopulmonary aspergillosis, Aspergillus bronchitis, and/or invasive aspergillosis. How such clinical states influence "endophenotypes" in bronchiectasis is therefore of importance, as each Aspergillus-associated disease state has overlapping features with bronchiectasis itself, and can evolve, depending on underlying host immunity from one type into another. Concurrent Aspergillus infection complicates the clinical course and exacerbations in bronchiectasis and therefore dedicated research to better understand the Aspergillus-host interaction in the bronchiectasis airway is now warranted.
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Affiliation(s)
- Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Soo Kai Ter
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland.,Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Ireland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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16
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Bouchara JP, Chotirmall SH, Hagen F, Chaturvedi V. Mycopathologia 2020: Legacy and Change to Remain Relevant for Content, Creation, and Communication. Mycopathologia 2021; 186:155-162. [PMID: 33704625 PMCID: PMC7948170 DOI: 10.1007/s11046-021-00531-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The 2020 COVID-19 pandemic had a profound impact on the publishing landscape. The 'pre-peer-review' publication model is likely to become common as a lag in publishing is not acceptable in a pandemic or other time! Mycopathologia is well placed to adopt such changes with its improved editorial processes, article formats, author engagements, and published articles' access and citation. Mycopathologia had an improved journal impact factor and article downloads in 2018-2019. A limited sampling suggested a slight decrease in the total submissions in 2019 (352 articles) compared to 2018 (371 articles). However, the acceptance rate improved to 30% in 2019 from 19% in 2018. Nearly half of all submissions in 2019 were rejected before peer-review or transferred to other Springer Nature journals. The published articles were contributed from 34 different countries, with authors from China, the USA, and Brazil among the top three contributors. An enhanced editorial oversight allowed peer-reviewers to focus on fewer articles that were well-matched to their expertise, which led to lower rejection rates post-peer-review. The introduction of MycopathologiaGENOME and MycopathologiaIMAGE article types received a good reception with notable downloads and citations.
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Affiliation(s)
- Jean-Philippe Bouchara
- Host-Pathogen Interaction Study Group, EA, 3142, UNIV Angers, UNIV Brest, Université Bretagne-Loire, Rennes, France
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
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17
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Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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18
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Complete Genome Sequence of Candida theae from Hickman Line Infection in an Immunocompromised Child. Mycopathologia 2020; 185:727-729. [PMID: 32705414 DOI: 10.1007/s11046-020-00476-3] [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: 01/20/2020] [Accepted: 07/06/2020] [Indexed: 10/20/2022]
Abstract
We present the first whole-genome-sequencing data of a rare fungal species, Candida theae isolated in the context of a Hickman line infection in a patient with juvenile myelomonocytic leukaemia. To our knowledge, this is the first instance of publicly available genomic data for this species. Loci associated with antifungal resistance were referenced against its closely related members of the Candida parapsilosis complex.
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19
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
- Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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20
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Morio F, O'Brien CE, Butler G. Draft Genome Sequence of the Yeast Kazachstania telluris CBS 16338 Isolated from Forest Soil in Ireland. Mycopathologia 2020; 185:587-590. [PMID: 32356255 DOI: 10.1007/s11046-020-00449-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/15/2020] [Indexed: 11/24/2022]
Abstract
Draft genomes of several Kazachstania species, a large group of ascomycetous budding yeasts, have been recently published. However, there is none yet available for pathogenic species from the K. telluris clade, including K. telluris sensu stricto, an opportunistic yeast that has been isolated from various niches and human clinical samples. Here we provide the first draft genome sequence of the strain K. telluris CBS 16338, that we isolated from forest soil in Ireland.
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Affiliation(s)
- Florent Morio
- School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland.
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie, CHU Nantes, Nantes, France.
- Département de Parasitologie Et Mycologie Médicale, EA1155 IICiMed, Institut de Recherche en Santé 2, Université de Nantes, Nantes Atlantique Universités, Nantes, France.
| | - Caoimhe E O'Brien
- School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
| | - Geraldine Butler
- School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
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21
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Gupta AB, Gaultier NE, Aung NW, Purbojati RW, Oliveira EL, Wong A, Panicker D, Putra A, Uchida A, Drautz-Moses DI, Schuster SC. Complete Genome Sequence of Penicillium oxalicum Strain SGAir0226 Isolated from Outdoor Tropical Air in Singapore. Mycopathologia 2020; 185:591-594. [PMID: 32270395 DOI: 10.1007/s11046-019-00422-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/20/2019] [Indexed: 11/28/2022]
Abstract
Penicillium oxalicum strain SGAir0226 was isolated from a tropical air sample collected in Singapore. The complete genome was assembled from long reads obtained from single-molecule real-time sequencing and was further polished and error corrected using short read sequencing data. The assembly comprises 20 contigs with a total length of 30.7 Mb. The genome was predicted to contain 8310 protein-coding genes, 237 tRNAs and 83 rRNAs.
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Affiliation(s)
- Anjali Bansal Gupta
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Nicolas E Gaultier
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Ngu War Aung
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Rikky W Purbojati
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Elaine L Oliveira
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Anthony Wong
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Deepa Panicker
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Alexander Putra
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Akira Uchida
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore
| | - Stephan C Schuster
- Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore.
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22
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Palanivel M, Mac Aogáin M, Purbojati RW, Uchida A, Aung NW, Lim SBY, Putra A, Drautz-Moses DI, Seaton S, Rogers TR, Schuster SC, Chotirmall SH. Whole-Genome Sequencing of Aspergillus terreus Species Complex. Mycopathologia 2020; 185:405-408. [PMID: 32108289 DOI: 10.1007/s11046-020-00433-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/07/2020] [Indexed: 02/07/2023]
Abstract
Aspergillus terreus species complex is an opportunistic fungal pathogen increasingly implicated in invasive infection, as well as chronic respiratory disease. Currently, an understanding of A. terreus pathogenicity is impeded by a limited number of whole-genome sequences of this fungal pathogen. We here describe a high-quality whole-genome assembly of European A. terreus clinical isolate M6925, derived by single-molecule real-time sequencing with short-read polishing.
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Affiliation(s)
- Mathangi Palanivel
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ngu War Aung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Serene B Y Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Alexander Putra
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Shila Seaton
- UK NEQAS for Microbiology, Products and Services, National Infection Service, Public Health England, London, UK
| | - Thomas R Rogers
- Department of Clinical Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Stephan C Schuster
- 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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23
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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: 37] [Impact Index Per Article: 9.3] [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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24
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Navarro-Muñoz JC, de Jong AW, Gerrits van den Ende B, Haas PJ, Then ER, Mohd Tap R, Collemare J, Hagen F. The High-Quality Complete Genome Sequence of the Opportunistic Fungal Pathogen Candida vulturna CBS 14366 T. Mycopathologia 2019; 184:731-734. [PMID: 31734799 DOI: 10.1007/s11046-019-00404-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/25/2019] [Indexed: 11/26/2022]
Abstract
Candida vulturna is a new member of the Candida haemulonii species complex that recently received much attention as it includes the emerging multidrug-resistant pathogen Candida auris. Here, we describe the high-quality genome sequence of C. vulturna type strain CBS 14366T to cover all genomes of pathogenic C. haemulonii species complex members.
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Affiliation(s)
- Jorge C Navarro-Muñoz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Auke W de Jong
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | | | - Pieter-Jan Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Euníce R Then
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Ratna Mohd Tap
- Mycology Laboratory, Institute for Medical Research, National Institute of Health, Setia Alam, Kuala Lumpur, 40170, Selangor, Malaysia
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands.
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China.
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25
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Nnadi NE, Giosa D, Ayanbimpe GM, D'Alessandro E, Aiese Cigliano R, Oheri CU, Aguiyi JC, Enweani IB, Romeo O. Whole-Genome Sequencing of an Uncommon Cryptococcus neoformans MLST43 Genotype Isolated in Nigeria. Mycopathologia 2019; 184:555-557. [PMID: 31473911 DOI: 10.1007/s11046-019-00376-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/20/2019] [Indexed: 12/01/2022]
Abstract
Cryptococcosis is a human infection caused mainly by two species of the Cryptococcus genus, Cryptococcus neoformans and Cryptococcus gattii, whose populations contain several phylogenetically related haploid (VN/VG-types) and hybrid genotypes. Here, we report the whole-genome sequencing of a Nigerian C. neoformans VNII, Mat-α, strain with a rare multilocus-sequence-type (MLST) genotype (ST43).
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Affiliation(s)
- Nnaemeka Emmanuel Nnadi
- Department of Microbiology, Plateau State University, Plateau State, P.M.B 2012, Bokkos, Nigeria
| | - Domenico Giosa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, Messina, Italy
| | | | | | | | - Christian Uchechukwu Oheri
- African Centre of Excellence in Phytomedicine Research and Development (ACEPRD), University of Jos, Jos, Nigeria
| | - John Chinyereze Aguiyi
- African Centre of Excellence in Phytomedicine Research and Development (ACEPRD), University of Jos, Jos, Nigeria
| | - Ifeoma Bessie Enweani
- Department of Medical Laboratory Science, Nnamdi Azikiwe University, Nnewi Campus, Nnewi, Nigeria
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 98166, Messina, Italy.
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