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1. Mycosands: Fungal diversity and abundance in beach sand and recreational waters & mdash; Relevance to human health

Author

Betil Özhak, R.O. Rusu, Nina Gunde-Cimerman, Anna Prigitano, Aleksandra Barac, M.A. Efstratiou, A.M. Tortorano, Michelle Bull, Aurora Gitto, Esther Segal, Belinda Chapman, João Brandão, Willem J. G. Melchers, Wim G. Meijer, Dilara Ogunc, Andra-Cristina Bostanaru, Mümtaz Güran, H. Guégan, Jean-Pierre Gangneux, Sevtap Arikan-Akdagli, Laszlo Irinyi, Marlou Tehupeiory-Kooreman, Lena Klingspor, Jayne H. Stephens, Ana Sampaio, Cristina Veríssimo, Nilgun Cerikcioglu, M. Novak Babič, M. Kataržytė, C.I. Gonçalves, Aristea Velegraki, G.C. Wunderlich, Stéphane Ranque, Raquel Sabino, E. Jonikaitė, Mihai Mares, Wieland Meyer, M. Frenkel, S. Brito, Susana Silva, J. Meletiadis, Valentin Nastasa, Çağrı Ergin, Universidade de Lisboa = University of Lisbon (ULISBOA), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Hacettepe University = Hacettepe Üniversitesi, Clinical Centre of Serbia, University of the Aegean, Pamukkale University, Kfar Saba and Sackler School of Medicine, University College Dublin [Dublin] (UCD), University of Trás-os-Montes and Alto Douro [Portugal] (UTAD), Centre for Infectious Disease and Microbiology (CIDM), The Westmead Institute for Medical Research, The University of Sydney, Klaipėda University [Lituanie] (KU), Karolinska Institutet [Stockholm], Radboud University Medical Center [Nijmegen], Università degli Studi di Milano = University of Milan (UNIMI), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Universidade de Lisboa (ULISBOA), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Università degli Studi di Milano [Milano] (UNIMI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
fungal detection, 010504 meteorology & atmospheric sciences, Beaches, yeast, 01 natural sciences, Recreational water, Fusarium, Genus, swimming, Fungal diversity, Waste Management and Disposal, Ecology, fungus, microbiological parameters, Pollution, 6. Clean water, Água e Solo, Fungi in sand, Geography, Aspergillus, priority journal, Black Sea, Italy, Water pollution, allergenicity, seashore, Environmental Engineering, Adriatic Sea, Urban growth, Article, Agentes Microbianos e Ambiente, Mediterranean Sea, Sydney [New South Wales], Humans, human, species diversity, Beach, bathing water, microbiology, Australia, Sediment, 15. Life on land, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], microbial diversity, Water quality, Bathing, Mycobiota, [SDV]Life Sciences [q-bio], Allergenic fungus, relative abundance, coastal waters, Fresh Water, health status, 010501 environmental sciences, geography, population abundance, environmental management, Human health, Fungal Diversity, Abundance (ecology), Sand, freshwater environment, Atlantic Ocean, Candida, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], biology, dermatophyte, Fungi in Sand, fungal membrane, New South Wales, Beach sand, Water Microbiology, Allergenic fungi, Colony forming units, Baltic Sea, Fungus in sand, Bathing Beaches, Mycosis, All institutes and research themes of the Radboud University Medical Center, parasitic diseases, Environmental Chemistry, 14. Life underwater, environmental protection, 0105 earth and related environmental sciences, Infecções Sistémicas e Zoonoses, nonhuman, Arthrodermataceae, Fungi, Filobasidiella, Bathing water, biology.organism_classification, sediment, 13. Climate action, colony forming unit, Mycota, fungal disease, urban area
Abstract

The goal of most studies published on sand contaminants is to gather and discuss knowledge to avoid faecal contamination of water by run-offs and tide retractions. Other life forms in the sand, however, are seldom studied but always pointed out as relevant. The Mycosands initiative was created to generate data on fungi in beach sands and waters, of both coastal and freshwater inland bathing sites. A team of medical mycologists and water quality specialists explored the sand culturable mycobiota of 91 bathing sites, and water of 67 of these, spanning fromthe Atlantic to the EasternMediterranean coasts, including the Italian lakes and the Adriatic, Baltic, and Black Seas. Sydney (Australia) was also included in the study. Thirteen countries took part in the initiative. The present study considered several fungal parameters (all fungi, several species of the genus Aspergillus and Candida and the genera themselves, plus other yeasts, allergenic fungi, dematiaceous fungi and dermatophytes). The study considered four variables that the team expected would influence the results of the analytical parameters, such as coast or inland location, urban and non-urban sites, period of the year, geographical proximity and type of sediment. The genera most frequently found were Aspergillus spp., Candida spp., Fusarium spp. and Cryptococcus spp. both in sand and in water. A site-blind median was found to be 89 Colony-Forming Units (CFU) of fungi per gram of sand in coastal and inland freshwaters, with variability between 0 and 6400 CFU/g. For freshwater sites, that number was 201.7 CFU/g (0, 6400 CFU/g (p = 0.01)) and for coastal sites was 76.7 CFU/g (0,3497.5 CFU/g). For coastalwaters and allwaters, themedianwas 0 CFU/ml (0, 1592 CFU/ml) and for freshwaters 6.7 (0, 310.0) CFU/ml (p < 0.001). The results advocate that beaches should bemonitored for fungi for safer use and better management. Highlights: Fungi are missing from water and sand health protection regulatory parameters; Both sand and water should be monitored for fungi; The median value of 89 CFU/g of all fungi may serve as a reference for sand regulation; Candida albicans, dermatophytes, endemic fungi and other fungi should be considered; Fungal analysis of water needs more data before reference values can be established. Acknowledgements: A. Abdillah, M. C. Esposto, J. Kabtani, K. Sarioglou, P. E. Verweij and F. Vieira for their collaboration in this study; the European Confederation of Medical Mycology for a seeding grant; the International Society for Human and Animal Mycology for some financial support; financial support from CESAM (UID/AMB/50017-POCI-01-0145-FEDER-007638) and CITAB (UID/AGR/04033/2019), via FCT/MCTES, from national funds (PIDDAC), cofounded by FEDER, (PT2020 Partnership Agreement and Compete 2020) and an NHMRC APP1121936 to W. Meyer; National and Kapodistrian University of Athens, Greece, Special Accounts for Research Grants (SARG K.A. 70/3/6915). info:eu-repo/semantics/publishedVersion

Published
2021

2. Scedosporium and Lomentospora: an updated overview of underrated opportunists

Author

Adela Martin-Vicente, Javier Pemán, Sandrine Giraud, Aitor Rementeria, José F. Cano-Lira, Ana Alastruey-Izquierdo, Mariana Ingrid Dutra da Silva Xisto, Jean-Philippe Bouchara, Jardel Vieira de Meirelles, Carsten Schwarz, Laszlo Irinyi, María Teresa Martín-Gómez, Anne Bernhardt, Rodrigo Rollin-Pinheiro, Kathrin Tintelnot, Aize Pellon, Fernando L. Hernando, Idoia Buldain, Stéphane Ranque, Leyre M. López-Soria, Andoni Ramirez-Garcia, Yohann Le Govic, Markus Nagl, Sharon C.-A. Chen, Eliana Barreto-Bergter, Wieland Meyer, Vladimír Havlíček, Michaela Lackner, Patrick Vandeputte, Johannes Rainer, Javier Capilla, Sybren de Hoog, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Institute of Earth and Environmental Science [Potsdam], University of Potsdam, Robert Koch Institute [Berlin] (RKI), Universitat Rovira i Virgili, Innsbruck Medical University [Austria] (IMU), Centre for Infectious Disease and Microbiology (CIDM), The Westmead Institute for Medical Research, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), University of Potsdam = Universität Potsdam, Innsbruck Medical University = Medizinische Universität Innsbruck (IMU), Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Medical Mycology

Subjects
0301 basic medicine, medicine.medical_specialty, Antifungal Agents, Virulence Factors, 030106 microbiology, Drug resistance, Opportunistic Infections, Scedosporium, Immunocompromised Host, 03 medical and health sciences, Local infection, Ascomycota, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Fungal, Epidemiology, medicine, Humans, Intensive care medicine, emergent, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Lomentospora, High rate, Ecology, business.industry, Mortality rate, Fungal genetics, General Medicine, Combined Modality Therapy, infection, 3. Good health, Molecular Typing, Infectious Diseases, Mycoses, Surgical Procedures, Operative, Host-Pathogen Interactions, fungi, business, pathogen
Abstract

International audience; Species of Scedosporium and Lomentospora are considered as emerging opportunists, affecting immunosuppressed and otherwise debilitated patients, although classically they are known from causing trauma-associated infections in healthy individuals. Clinical manifestations range from local infection to pulmonary colonization and severe invasive disease, in which mortality rates may be over 80%. These unacceptably high rates are due to the clinical status of patients, diagnostic difficulties, and to intrinsic antifungal resistance of these fungi. In consequence, several consortia have been founded to increase research efforts on these orphan fungi. The current review presents recent findings and summarizes the most relevant points, including the Scedosporium/Lomentospora taxonomy, environmental distribution, epidemiology, pathology, virulence factors, immunology, diagnostic methods, and therapeutic strategies.

Published
2018

3. Developing collaborative works for faster progress on fungal respiratory infections in cystic fibrosis

Author

Gilles Nevez, Joerg Steinmann, Laurence Delhaes, Ludovic Duvaux, Jean-Philippe Bouchara, Wieland Meyer, Ludwig Sedlacek, Maxime Fleury, Nicolas Papon, Loïc Favennec, Patrick Vandeputte, Javier Pemán, Amandine Gastebois, Françoise Botterel, Jose A. Vazquez, Stéphane Ranque, Sharon C.-A. Chen, Ana Alastruey-Izquierdo, Solène Le Gal, Craig Williams, Marie-Elisabeth Bougnoux, Carsten Schwarz, Françoise Symoens, Estrella Martin Mazuelos, Guillermo Quindós, Thomas Dugé de Bernonville, Josep Cano, Amparo Solé, Amandine Rougeron, Sandrine Giraud, María Teresa Martín-Gómez, Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), University of Sheffield [Sheffield], Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Anofel Cryptosporidium National Network, Laboratoire de Parasitologie-Mycologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service de Microbiologie, Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Parasitologie et de Mycologie [Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Appareil Digestif Environnement Nutrition (ADEN ), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Augusta University, University System of Georgia (USG), The Westmead Institute for Medical Research, Centre for Infectious Disease and Microbiology (CIDM), Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), APP1031943, National Health and Medical Research Council, 2010/IC1003, Vaincre la Mucoviscidose, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Groupe d'Etude des Interactions Hôte-Parasite (GEIHP), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Groupe d’Etude des Interactions Hôte-Pathogène, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA)

Subjects
Microbiological Techniques, 0301 basic medicine, medicine.medical_specialty, Antifungal Agents, Cystic Fibrosis, biological diagnosis, 030106 microbiology, Medizin, Context (language use), Disease, Drug resistance, Cystic fibrosis, pathogenic mechanisms, cystic fibrosis, Scedosporium, 03 medical and health sciences, fungal respiratory infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Fungal, medicine, Humans, Microbiome, Intensive care medicine, Respiratory Tract Infections, Genotyping, treatment, business.industry, Fungi, Genomics, General Medicine, medicine.disease, 3. Good health, Infectious Diseases, Mycoses, Scedosporium species, Identification (biology), business
Abstract

International audience; Cystic fibrosis (CF) is the major genetic inherited disease in Caucasian populations. The respiratory tract of CF patients displays a sticky viscous mucus, which allows for the entrapment of airborne bacteria and fungal spores and provides a suitable environment for growth of microorganisms, including numerous yeast and filamentous fungal species. As a consequence, respiratory infections are the major cause of morbidity and mortality in this clinical context. Although bacteria remain the most common agents of these infections, fungal respiratory infections have emerged as an important cause of disease. Therefore, the International Society for Human and Animal Mycology (ISHAM) has launched a working group on Fungal respiratory infections in Cystic Fibrosis (Fri-CF) in October 2006, which was subsequently approved by the European Confederation of Medical Mycology (ECMM). Meetings of this working group, comprising both clinicians and mycologists involved in the follow-up of CF patients, as well as basic scientists interested in the fungal species involved, provided the opportunity to initiate collaborative works aimed to improve our knowledge on these infections to assist clinicians in patient management. The current review highlights the outcomes of some of these collaborative works in clinical surveillance, pathogenesis and treatment, giving special emphasis to standardization of culture procedures, improvement of species identification methods including the development of nonculture-based diagnostic methods, microbiome studies and identification of new biological markers, and the description of genotyping studies aiming to differentiate transient carriage and chronic colonization of the airways. The review also reports on the breakthrough in sequencing the genomes of the main Scedosporium species as basis for a better understanding of the pathogenic mechanisms of these fungi, and discusses treatment options of infections caused by multidrug resistant microorganisms, such as Scedosporium and Lomentospora species and members of the Rasamsonia argillacea species complex.

Published
2018

4. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections

Author

Minh Thuy Vi Hoang, Laszlo Irinyi, Sharon C. A. Chen, Tania C. Sorrell, The ISHAM Barcoding of Medical Fungi Working Group, Wieland Meyer, Michael Arabatzis, Ian Arthur, Jose F. Cano-Lira, Gianluigi Cardinali, Laura Rosio Castañón, Sharon Chen, Wen Chen, Ariya Chindamporn, Arnaldo L. Colombo, Marie Desnos-Ollivier, Wilhelm de Beer, Sybren de Hoog, Françoise Dromer, Dea Garcia-Hermoso, Marieka Gryzenhout, Josep Guarro, Catriona Halliday, Marijke Hendrickx, Sabine Huhndorf, C. Andre Levesque, Maria Luiza Moretti, Mauro de Medeiros Muniz, Analy Salles de Azevedo Melo, Angela Satie Nishikaku, Anne-Cécile Normand, Célia Pais, Renaud Piarroux, Stéphane Ranque, Barbara Robbertse, Vincent Robert, Conrad L. Schoch, Keith A. Seifert, Célia Maria de Almeida Soares, John L. Spouge, Dirk Stubbe, Maria Lucia Taylor, Conchita Toriello, Aristea Velegraki, Chompoonek Yurayart, Rosely Maria Zancopé-Oliveira, The University of Sydney, Centre for Infectious Disease and Microbiology (CIDM), The Westmead Institute for Medical Research, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), National Health and Medical Research Council of Australia (NH & MRC) grant (#APP1121936), Members of the Isham Barcoding of Medical Fungi Working Group : Michael Arabatzis, National and Kapodistrian University of Athens, Athens, Greece, Ian Arthur, PathWest Laboratory Medicine, Nedlands, WA, Australia, Jose F. Cano-Lira, Universitat Rovira i Virgili, Reus, Spain, Gianluigi Cardinali, Università degli Studi di Perugia, Perugia, Italy, Laura Rosio Castañón, Universidad Nacional Autónoma de México, Mexico City, Mexico, Sharon Chen, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, Wen Chen, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, Ariya Chindamporn, Chulalongkorn University, Bangkok, Thailand, Arnaldo L. Colombo, Universidade Federal de São Paulo, São Paulo, Brazil, Marie Desnos-Ollivier, Institut Pasteur, Paris, France, Wilhelm de Beer, FABI, Pretoria, South Africa, Sybren de Hoog, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands, Françoise Dromer, Institut Pasteur, Paris, France, Dea Garcia-Hermoso, Institut Pasteur, Paris, France, Marieka Gryzenhout, University of the Free State, Bloemfontein, South Africa, Josep Guarro, Universitat Rovira i Virgili, Reus, Spain, Catriona Halliday, University of Sydney/Westmead Hospital, Sydney, NSW, Australia, Marijke Hendrickx, BCCM/IHEM, Scientific Institute of Public Health, Brussels, Belgium, Sabine Huhndorf, The Field Museum, Chicago, IL, United States, Laszlo Irinyi, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, C. Andre Levesque, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, Wieland Meyer, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, Maria Luiza Moretti, University of Campinas, Campinas, Brazil, Mauro de Medeiros Muniz, Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil, Analy Salles de Azevedo Melo, Universidade Federal de São Paulo, São Paulo, Brazil, Angela Satie Nishikaku, Universidade Federal de São Paulo, São Paulo, Brazil, Anne-Cécile Normand, Aix-Marseille University, Marseille, France, Célia Pais, University of Minho, Braga, Portugal, Renaud Piarroux, Aix-Marseille University, Marseille, France, Stéphane Ranque, Aix-Marseille University, Marseille, France, Barbara Robbertse, National Center for Biotechnology Information, Bethesda, MD, United States, Vincent Robert, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands, Conrad L. Schoch, National Center for Biotechnology Information, Bethesda, MD, United States, Keith A. Seifert, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, Célia Maria de Almeida Soares, Universidade Federal de Goiás, Goiânia, Brazil, Tania C. Sorrell, Westmead Hospital, University of Sydney, Sydney, NSW, Australia, John L. Spouge, National Center for Biotechnology Information, Bethesda, MD, United States, Dirk Stubbe, BCCM/IHEM, Scientific Institute of Public Health, Brussels, Belgium, Maria Lucia Taylor, Universidad Nacional Autónoma de México, Mexico City, Mexico, Conchita Toriello, Universidad Nacional Autónoma de México, Mexico City, Mexico, Aristea Velegraki, National and Kapodistrian University of Athens, Athens, Greece, Chompoonek Yurayart, Kasetsart University, Bangkok, Thailand, Rosely Maria Zancopé-Oliveira, Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil., Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Westerdijk Fungal Biodiversity Institute - Medical Mycology, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Software and Databasing

Subjects
Microbiology (medical), invasive fungal diseases, lcsh:QR1-502, ISHAM Barcoding Database, Computational biology, Biology, Barcode, Microbiology, DNA barcoding, lcsh:Microbiology, law.invention, dual barcoding system, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Internal transcribed spacer, Original Research, 030304 developmental biology, Molecular identification, internal transcribed spacer region, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, 030306 microbiology, Fungal DNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, fungal DNA barcoding, Clinical Practice, translational elongation factor 1α, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, identification, Identification (biology), Translational elongation
Abstract

International audience; Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.

Published
2019

5. Concern regarding the alleged spread of hypervirulent lymphogranuloma venereum Chlamydia trachomatis strain in Europe

Author

Helena M. B. Seth-Smith, Bart Versteeg, Cécile Bébéar, Henry J. C. de Vries, Juan C. Galán, Ian Carter, David A. Lewis, Servaas A. Morré, Adrian Egli, Bertille de Barbeyrac, Sylvia M. Bruisten, Olivia Peuchant, Nicholas R. Thomson, Jen Kok, Daniel Goldenberger, Angèle Bénard, Clinical Microbiology, Hospital for Infectious Diseases, Applied Microbiology Research, Department of Biomedicine, University of Basel (Unibas), CIBER de Epidemiología y Salud Pública, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Western Sydney Sexual Health Centre, University of Sydney, USC 3671 Infections humaines à mycoplasmes et Chlamydiae, Institut National de la Recherche Agronomique (INRA), Université de Bordeaux (UB), The Wellcome Trust Sanger Institute [Cambridge], Centre for Infectious Disease and Microbiology (CIDM), The Westmead Institute for Medical Research, Department of Infectious Diseases, Public Health Service Amsterdam, STI Outpatient Clinic, Amsterdam Infection and Immunity Institute (AI&II), Academic Medical Centre, University of Amsterdam, Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Amsterdam Medical Center, Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research Institute GROW, Maastricht University, London School of Hygiene and Tropical Medicine (LSHTM), Department of Dermatology, Academic Medical Center, AII - Infectious diseases, APH - Global Health, Medical Microbiology and Infection Prevention, APH - Methodology, Dermatology, RS: GROW - R4 - Reproductive and Perinatal Medicine, Institute for Public Health Genomics, University of Amsterdam [Amsterdam] (UvA), and Maastricht University [Maastricht]

Subjects
0301 basic medicine, bacterial outer membrane proteins, Epidemiology, OUTBREAK, genotype, [SDV]Life Sciences [q-bio], 030106 microbiology, Chlamydia trachomatis, VARIANTS, urologic and male genital diseases, medicine.disease_cause, 03 medical and health sciences, male homosexuality, Virology, Genotype, Humans, Medicine, Homosexuality, Male, lymphogranuloma venereum, business.industry, Strain (biology), Lymphogranuloma venereum, Public Health, Environmental and Occupational Health, Outbreak, bacterial infections and mycoses, medicine.disease, female genital diseases and pregnancy complications, 3. Good health, Europe, 030104 developmental biology, Bacterial Outer Membrane Proteins, Lymphogranuloma Venereum, bacteria, business, Male Homosexuality
Abstract

A recent surveillance and outbreak report published in Eurosurveillance by Petrovay et al. on the ‘Emergence of the lymphogranuloma venereum L2c genovariant, Hungary, 2012 to 2016’ [1] provides an observation of the first European cases of a genotype of Chlamydia trachomatis associated with severe haemorrhagic proctitis. The authors of this paper diagnosed the strains as lymphogranuloma venereum (LGV)- associated and performed partial sequencing of the ompA gene (ca 1,070 bp), which is a standard typing method for C. trachomatis. The ompA gene sequence obtained was compared with those from reference isolates, and reported to be 100% concordant with the ompA sequence belonging to an L2-D recombinant strain described in 2011 [2]. This strain was named ‘L2c’, as it was found to possess a chimeric genome, not because it has a novel ompA-genotype. We would like to point out that the ompA gene sequence of this L2-D recombinant strain, and by implication those of the Hungarian isolates, is identical to that of archetypal L2 strains, for example the reference strain L2/434 [3].

Published
2017

6. Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

Author

Duy Pham Thanh, Takehiro Tomita, Vitali Sintchenko, Kate S. Baker, Benjamin P Howden, Thomas R. Connor, Martin Day, Anthony M. Smith, Karen H. Keddy, Julian Parkhill, Shah M. Faruque, Jeremy D Brown, Malika Gouali, Peter Howard, Philip Ashton, Simon R. Harris, François-Xavier Weill, Timothy J. Dallman, Claire Jenkins, Sandra Zittermann, Paul Crook, Gwenda Hughes, Nicola K. Petty, Mary Valcanis, Nicholas R. Thomson, V L Gilbart, Kaisar A. Talukder, Stephen Baker, Vanessa Allen, The Wellcome Trust Sanger Institute [Cambridge], Public Health England [London], Public Health Ontario - Santé publique Ontario, The Peter Doherty Institute for Infection and Immunity [Melbourne], University of Melbourne-The Royal Melbourne Hospital, Austin Health, Monash University [Clayton], School of Biosciences [Cardiff], Cardiff University, The University of Sydney, Westmead Hospital [Sydney], Centre for Infectious Disease and Microbiology (CIDM), The Westmead Institute for Medical Research, iThree Institute, University of Technology Sydney (UTS), Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris], Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), University of the Witwatersrand [Johannesburg] (WITS), National Institute for Communicable Diseases [Johannesburg] (NICD), International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), London School of Hygiene and Tropical Medicine (LSHTM), Wellcome Trust (grant number 098051)., and Institut Pasteur [Paris] (IP)

Subjects
Male, Serotype, Azithromycin, Disease Outbreaks, Shigella flexneri, Men who have sex with men, 0302 clinical medicine, Medicine, 030212 general & internal medicine, Child, Phylogeny, Travel, 0303 health sciences, biology, Dysentery, Middle Aged, 3. Good health, Infectious Diseases, Child, Preschool, Female, Adult, Risk, Shigellosis, Sexual transmission, Adolescent, Sexually Transmitted Diseases, Microbiology, Article, Young Adult, 03 medical and health sciences, Drug Resistance, Bacterial, Humans, Aged, Dysentery, Bacillary, Molecular epidemiology, 030306 microbiology, business.industry, Infant, Newborn, Infant, Outbreak, medicine.disease, biology.organism_classification, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, United Kingdom, Cross-Sectional Studies, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract

© 2015 Elsevier Ltd. Background: Shigellosis is an acute, severe bacterial colitis that, in high-income countries, is typically associated with travel to high-risk regions (Africa, Asia, and Latin America). Since the 1970s, shigellosis has also been reported as a sexually transmitted infection in men who have sex with men (MSM), in whom transmission is an important component of shigellosis epidemiology in high-income nations. We aimed to use sophisticated subtyping and international sampling to determine factors driving shigellosis emergence in MSM linked to an outbreak in the UK. Methods: We did a large-scale, cross-sectional genomic epidemiological study of shigellosis cases collected from 29 countries between December, 1995, and June 8, 2014. Focusing on an ongoing epidemic in the UK, we collected and whole-genome sequenced clinical isolates of Shigella flexneri serotype 3a from high-risk and low-risk regions, including cases associated with travel and sex between men. We examined relationships between geographical, demographic, and clinical patient data with the isolate antimicrobial susceptibility, genetic data, and inferred evolutionary relationships. Findings: We obtained 331 clinical isolates of S flexneri serotype 3a, including 275 from low-risk regions (44 from individuals who travelled to high-risk regions), 52 from high-risk regions, and four outgroup samples (ie, closely related, but genetically distinct isolates used to determine the root of the phylogenetic tree). We identified a recently emerged lineage of S flexneri 3a that has spread intercontinentally in less than 20 years throughout regions traditionally at low risk for shigellosis via sexual transmission in MSM. The lineage had acquired multiple antimicrobial resistance determinants, and prevailing sublineages were strongly associated with resistance to the macrolide azithromycin. Eight (4%) of 206 isolates from the MSM-associated lineage were obtained from patients who had previously provided an isolate; these serial isolations indicated atypical infection patterns (eg, reinfection). Interpretation: We identified transmission-facilitating behaviours and atypical course(s) of infection as precipitating factors in shigellosis-affected MSM. The intercontinental spread of antimicrobial-resistant shigella through established transmission routes emphasises the need for new approaches to tackle the public health challenge of sexually transmitted infections in MSM. Funding: Wellcome Trust (grant number 098051).

Published
2015

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