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Angebault C, Botterel F. Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis. Mycopathologia 2024; 189:82. [PMID: 39264513 PMCID: PMC11392981 DOI: 10.1007/s11046-024-00887-6] [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: 05/10/2024] [Accepted: 08/21/2024] [Indexed: 09/13/2024]
Abstract
Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.
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Affiliation(s)
- Cécile Angebault
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France.
- Dynamyc UR 7380, USC Anses, Ecole Nationale Vétérinaire d'Alfort (ENVA), Faculté de Santé, Univ. Paris-Est Créteil (UPEC), Créteil, France.
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- Dynamyc UR 7380, USC Anses, Ecole Nationale Vétérinaire d'Alfort (ENVA), Faculté de Santé, Univ. Paris-Est Créteil (UPEC), Créteil, France
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Boyd A, El Dani M, Ajrouche R, Demontant V, Cheval J, Lacombe K, Cosson G, Rodriguez C, Pawlotsky JM, Woerther PL, Surgers L. Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case-control study in infectious diseases department. Clin Microbiol Infect 2024; 30:1154-1163. [PMID: 38527613 DOI: 10.1016/j.cmi.2024.03.016] [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: 11/21/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
OBJECTIVE Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage. METHODS We conducted a case-control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity. RESULTS Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27-44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini-Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray-Curtis dissimilarity index, p 0.42). DISCUSSION In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.
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Affiliation(s)
- Anders Boyd
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; Stichting HIV Monitoring, Amsterdam, The Netherlands; Public Health Service of Amsterdam, Infectious Diseases, Amsterdam, The Netherlands
| | - Mariam El Dani
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; Clinical and Epidemiological Research Laboratory, Faculty of Pharmacy, Lebanese University, Hadat, Lebanon
| | - Roula Ajrouche
- Clinical and Epidemiological Research Laboratory, Faculty of Pharmacy, Lebanese University, Hadat, Lebanon; Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban (INSPECT-LB), Beirut, Lebanon
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, APHP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Justine Cheval
- NGS Platform, Henri Mondor Hospital, APHP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Karine Lacombe
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; GHU APHP. Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France
| | - Guillaume Cosson
- GHU APHP. Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France
| | - Christophe Rodriguez
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique Hôpitaux de Paris (APHP), Université Paris-Est-Créteil, Créteil, France; INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Jean-Michel Pawlotsky
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique Hôpitaux de Paris (APHP), Université Paris-Est-Créteil, Créteil, France; INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Paul-Louis Woerther
- NGS Platform, Henri Mondor Hospital, APHP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France; Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique Hôpitaux de Paris (APHP), Université Paris-Est-Créteil, Créteil, France; Université Paris-Est-Créteil (UPEC), EA 7380 Dynamic, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Laure Surgers
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, Paris, France; GHU APHP. Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.
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Nagpal S, Mande SS, Hooda H, Dutta U, Taneja B. EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale. Microbiol Spectr 2024; 12:e0415023. [PMID: 38687072 PMCID: PMC11237516 DOI: 10.1128/spectrum.04150-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/30/2024] [Indexed: 05/02/2024] Open
Abstract
Bacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon-based microbiome studies have generally paid skewed attention, that too at a rather shallow genus level resolution, to the highly abundant bacteriome, with interest now forking toward the other microorganisms, particularly fungi. Given the generally sparse abundance of other microbes in the total microbiome, simultaneous sequencing of amplicons targeting multiple microbial kingdoms could be possible even with full multiplexing. Guiding studies are currently needed for performing and monitoring multi-kingdom-amplicon sequencing and data capture at scale. Aiming to address these gaps, amplification of full-length bacterial 16S rRNA gene and entire fungal internal-transcribed spacer (ITS) region was performed for human saliva samples (n = 96, including negative and positive controls). Combined amplicon DNA libraries were prepared for nanopore sequencing using a major fraction of 16S molecules and a minor fraction of ITS amplicons. Sequencing was performed in a single run of an R10.4.1 flow cell employing the latest V14 chemistry. An approach for real-time monitoring of the species saturation using dynamic rarefaction was designed as a guiding determinant of optimal run time. Real-time saturation monitoring for both bacterial and fungal species enabled the completion of sequencing within 30 hours, utilizing less than 60% of the total nanopores. Approximately 5 million high quality (HQ) taxonomically assigned reads were generated (~4.2 million bacterial and 0.7 million fungal), providing a wider (beyond bacteriome) snapshot of human oral microbiota at species-level resolution. Among the more than 400 bacterial and 240 fungal species identified in the studied samples, the species of Streptococcus (e.g., Streptococcus mitis and Streptococcus oralis) and Candida (e.g., Candida albicans and Candida tropicalis) were observed to be the dominating microbes in the oral cavity, respectively. This conformed well with the previous reports of the human oral microbiota. EnsembleSeq provides a proof-of-concept toward the identification of both fungal and bacterial species simultaneously in a single fully multiplexed nanopore sequencing run in a time- and resource-effective manner. Details of this workflow, along with the associated codebase, are provided to enable large-scale application for a holistic species-level microbiome study. IMPORTANCE Human microbiome is a sum total of a variety of microbial genomes (including bacteria, fungi, protists, viruses, etc.) present in and on the human body. Yet, a majority of amplicon-based microbiome studies have largely remained skewed toward bacteriome as an assumed proxy of the total microbiome, primarily at a shallow genus level. Cost, time, effort, data quality/management, and importantly lack of guiding studies often limit progress in the direction of moving beyond bacteriome. Here, EnsembleSeq presents a proof-of-concept toward concomitantly capturing multiple-kingdoms of microorganisms (bacteriome and mycobiome) in a fully multiplexed (96-sample) single run of long-read amplicon sequencing. In addition, the workflow captures dynamic tracking of species-level saturation in a time- and resource-effective manner.
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Affiliation(s)
- Sunil Nagpal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- TCS Research, Tata Consultancy Services Ltd, Pune, India
| | | | - Harish Hooda
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Usha Dutta
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Bhupesh Taneja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Li Y, Lou D, Zhou X, Zhuang X, Wang C. Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge. PeerJ 2024; 12:e16931. [PMID: 38371377 PMCID: PMC10874175 DOI: 10.7717/peerj.16931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
Background Urbanization has an ecological and evolutionary effect on urban microorganisms. Microorganisms are fundamental to ecosystem functions, such as global biogeochemical cycles, biodegradation and biotransformation of pollutants, and restoration and maintenance of ecosystems. Changes in microbial communities can disrupt these essential processes, leading to imbalances within ecosystems. Studying the impact of human activities on urban microbes is critical to protecting the environment, human health, and overall urban sustainability. Methods In this study, bacterial communities in the sediments of an urban artificial river were profiled by sequencing the 16S rRNA V3-V4 region. The samples collected from the eastern side of the Jiusha River were designated as the JHE group and were marked by persistent urban sewage discharges. The samples collected on the western side of the Jiusha River were categorized as the JHW group for comparative analysis. Results The calculated alpha diversity indices indicated that the bacterial community in the JHW group exhibited greater species diversity and evenness than that of the JHE group. Proteobacteria was the most dominant phylum between the two groups, followed by Bacteroidota. The relative abundance of Proteobacteria and Bacteroidota accumulated in the JHE group was higher than in the JHW group. Therefore, the estimated biomarkers in the JHE group were divided evenly between Proteobacteria and Bacteroidota, whereas the biomarkers in the JHW group mainly belonged to Proteobacteria. The Sulfuricurvum, MND1, and Thiobacillus genus were the major contributors to differences between the two groups. In contrast to JHW, JHE exhibited higher enzyme abundances related to hydrolases, oxidoreductases, and transferases, along with a prevalence of pathways associated with carbohydrate, energy, and amino acid metabolisms. Our study highlights the impact of human-induced water pollution on microorganisms in urban environments.
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Affiliation(s)
- Yishi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- Focused Photonics (Hangzhou), Inc., Hangzhou, Zhejiang, China
| | - Daoming Lou
- Hangzhou Urban Water Facilities and River Conservation Management Center, Hangzhou, Zhejiang, China
| | - Xiaofei Zhou
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Xuchao Zhuang
- Focused Photonics (Hangzhou), Inc., Hangzhou, Zhejiang, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
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Debourgogne A, Monpierre L, Sy KA, Valsecchi I, Decousser JW, Botterel F. Interactions between Bacteria and Aspergillus fumigatus in Airways: From the Mycobiome to Molecular Interactions. J Fungi (Basel) 2023; 9:900. [PMID: 37755008 PMCID: PMC10533028 DOI: 10.3390/jof9090900] [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: 07/31/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Interactions between different kingdoms of microorganisms in humans are common but not well described. A recent analysis of the mycobiome has described the presence of different fungi and their positive and/or negative interactions with bacteria and other fungi. In chronic respiratory diseases, these different microorganisms form mixed biofilms to live inside. The interactions between Gram-negative bacteria and filamentous fungi in these biofilms have attracted more attention recently. In this review, we analyse the microbiota of the respiratory tract of healthy individuals and patients with chronic respiratory disease. Additionally, we describe the regulatory mechanisms that rule the mixed biofilms of Aspergillus fumigatus and Gram-negative bacteria and the effects of this biofilm on clinical presentations.
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Affiliation(s)
- Anne Debourgogne
- UR 7300, Stress Immunité Pathogène, Université de Lorraine, 54000 Vandoeuvre les Nancy, France;
| | - Lorra Monpierre
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), 94000 Créteil, France;
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| | - Khadeeja Adam Sy
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
- Institut National de la Santé et de la Recherche Médicale (Inserm) U955, 94010 Créteil, France
| | - Isabel Valsecchi
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| | - Jean-Winoc Decousser
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
- Department of Infection Control, University Hospital Henri Mondor, Assistance Publique—Hôpitaux de Paris, 94000 Créteil, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), 94000 Créteil, France;
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
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Akter A, Lyons O, Mehra V, Isenman H, Abbate V. Radiometal chelators for infection diagnostics. FRONTIERS IN NUCLEAR MEDICINE (LAUSANNE, SWITZERLAND) 2023; 2:1058388. [PMID: 37388440 PMCID: PMC7614707 DOI: 10.3389/fnume.2022.1058388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Infection of native tissues or implanted devices is common, but clinical diagnosis is frequently difficult and currently available noninvasive tests perform poorly. Immunocompromised individuals (for example transplant recipients, or those with cancer) are at increased risk. No imaging test in clinical use can specifically identify infection, or accurately differentiate bacterial from fungal infections. Commonly used [18F]fluorodeoxyglucose (18FDG) positron emission computed tomography (PET/CT) is sensitive for infection, but limited by poor specificity because increased glucose uptake may also indicate inflammation or malignancy. Furthermore, this tracer provides no indication of the type of infective agent (bacterial, fungal, or parasitic). Imaging tools that directly and specifically target microbial pathogens are highly desirable to improve noninvasive infection diagnosis and localization. A growing field of research is exploring the utility of radiometals and their chelators (siderophores), which are small molecules that bind radiometals and form a stable complex allowing sequestration by microbes. This radiometal-chelator complex can be directed to a specific microbial target in vivo, facilitating anatomical localization by PET or single photon emission computed tomography. Additionally, bifunctional chelators can further conjugate therapeutic molecules (e.g., peptides, antibiotics, antibodies) while still bound to desired radiometals, combining specific imaging with highly targeted antimicrobial therapy. These novel therapeutics may prove a useful complement to the armamentarium in the global fight against antimicrobial resistance. This review will highlight current state of infection imaging diagnostics and their limitations, strategies to develop infection-specific diagnostics, recent advances in radiometal-based chelators for microbial infection imaging, challenges, and future directions to improve targeted diagnostics and/or therapeutics.
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Affiliation(s)
- Asma Akter
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London, United Kingdom
| | - Oliver Lyons
- Vascular Endovascular and Transplant Surgery, Christchurch Public Hospital, Christchurch, New Zealand
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Varun Mehra
- Department of Hematology, King’s College Hospital NHS Foundation Trust, London, United Kingdom
| | - Heather Isenman
- Department of Infectious Diseases, General Medicine, Christchurch Hospital, Christchurch, New Zealand
| | - Vincenzo Abbate
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London, United Kingdom
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Peroumal D, Sahu SR, Kumari P, Utkalaja BG, Acharya N. Commensal Fungus Candida albicans Maintains a Long-Term Mutualistic Relationship with the Host To Modulate Gut Microbiota and Metabolism. Microbiol Spectr 2022; 10:e0246222. [PMID: 36135388 PMCID: PMC9603587 DOI: 10.1128/spectrum.02462-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/12/2022] [Indexed: 01/04/2023] Open
Abstract
Candida albicans survives as a commensal fungus in the gastrointestinal tract, and that its excessive growth causes infections in immunosuppressed individuals is widely accepted. However, any mutualistic relationship that may exist between C. albicans and the host remains undetermined. Here, we showed that a long-term feeding of C. albicans does not cause any noticeable infections in the mouse model. Our 16S and 18S ribosomal DNA (rDNA) sequence analyses suggested that C. albicans colonizes in the gut and modulates microbiome dynamics, which in turn mitigates high-fat-diet-induced uncontrolled body weight gain and metabolic hormonal imbalances. Interestingly, adding C. albicans to a nonobesogenic diet stimulated the appetite-regulated hormones and helped the mice maintain a healthy body weight. In concert, our results suggest a mutualism between C. albicans and the host, contrary to the notion that C. albicans is always an adversary and indicating it can instead be a bona fide admirable companion of the host. Finally, we discuss its potential translational implication as a probiotic, especially in obese people or people dependent on high-fat calorie intakes to manage obesity associated complications. IMPORTANCE Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. Thus, we concluded that C. albicans is not always an adversary but rather can be a bona fide admirable companion of the host. More importantly, as several genomic knockout strains of C. albicans were shown to be avirulent, such candidate strains may be explored further as preferable probiotic isolates to control obesity.
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Affiliation(s)
- Doureradjou Peroumal
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Satya Ranjan Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Premlata Kumari
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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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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Liber JA, Minier DH, Stouffer-Hopkins A, Van Wyk J, Longley R, Bonito G. Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities. PeerJ 2022; 10:e12701. [PMID: 35127279 PMCID: PMC8801177 DOI: 10.7717/peerj.12701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023] Open
Abstract
Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.
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Affiliation(s)
- Julian A. Liber
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States,Department of Biology, Duke University, Durham, North Carolina, United States
| | - Douglas H. Minier
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States
| | - Anna Stouffer-Hopkins
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States
| | - Judson Van Wyk
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
| | - Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States
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Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.
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d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
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Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
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12
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Dellière S, Dannaoui E, Fieux M, Bonfils P, Gricourt G, Demontant V, Podglajen I, Woerther PL, Angebault C, Botterel F. Analysis of Microbiota and Mycobiota in Fungal Ball Rhinosinusitis: Specific Interaction between Aspergillus fumigatus and Haemophilus influenza? J Fungi (Basel) 2021; 7:550. [PMID: 34356929 PMCID: PMC8305266 DOI: 10.3390/jof7070550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Fungal ball (FB) rhinosinusitis (RS) is the main type of non-invasive fungal RS. Despite positive direct examination (DE) of biopsies, culture remains negative in more than 60% of cases. The aim of the study was to evaluate the performance/efficacy of targeted metagenomics (TM) to analyze microbiota and mycobiota in FB and find microbial associations. Forty-five sinus biopsies from patients who underwent surgery for chronic RS were included. After DE and culture, DNA was extracted, then fungal ITS1-ITS2 and bacterial V3-V4 16S rDNA loci were sequenced (MiSeqTM Illumina). Operational taxonomic units (OTUs) were defined via QIIME and assigned to SILVA (16S) and UNITE (ITS) databases. Statistical analyses were performed using SHAMAN. Thirty-eight patients had FB and seven had non-fungal rhinosinusitis (NFRS). DE and culture of FB were positive for fungi in 97.3 and 31.6% of patients, respectively. TM analysis of the 38 FB yielded more than one fungal genus in 100% of cases, with Aspergillus in 89.5% (34/38). Haemophilus was over-represented in FB with >1000 reads/sample in 47.3% (18/38) compared to NFRS (p < 0.001). TM allowed fungal identification in biopsies with negative culture. Haemophilus was associated with FB. Pathogenesis could result from fungi-bacteria interactions in a mixed biofilm-like structure.
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Affiliation(s)
- Sarah Dellière
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Hôpitaux Universitaires Henri-Mondor, 94010 Créteil, France; (S.D.); (C.A.)
- Unité de Parasitologie-Mycologie, Hôpital Saint-Louis, Assistance Publique des Hôpitaux de Paris, Université de Paris, 75010 Paris, France
| | - Eric Dannaoui
- UR DYNAMiC 7380, Faculté de Santé, Université Paris-Est Créteil, 94010 Créteil, France; (E.D.); (P.-L.W.)
- UR DYNAMiC 7380, Ecole Nationale Vétérinaire d’Alfort, USC Anses, 94700 Maison-Alfort, France
- Unité de Parasitologie-Mycologie, Département de Microbiologie, Hôpital Européen George Pompidou, APHP, Université de Paris, 75015 Paris, France
| | - Maxime Fieux
- Département d’Otorhinolaryngologie, Hôpital Européen George Pompidou, APHP, Université de Paris, 75015 Paris, France; (M.F.); (P.B.)
- Service d’Otorhinolaryngologie, d’Otoneurochirurgie et de Chirurgie Cervico-Faciale, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69310 Pierre Bénite, France
| | - Pierre Bonfils
- Département d’Otorhinolaryngologie, Hôpital Européen George Pompidou, APHP, Université de Paris, 75015 Paris, France; (M.F.); (P.B.)
| | - Guillaume Gricourt
- Plate-Forme Genomiques, APHP-IMRB, GHU Hôpitaux Universitaires Henri-Mondor, UPEC, 94010 Créteil, France; (G.G.); (V.D.)
| | - Vanessa Demontant
- Plate-Forme Genomiques, APHP-IMRB, GHU Hôpitaux Universitaires Henri-Mondor, UPEC, 94010 Créteil, France; (G.G.); (V.D.)
| | - Isabelle Podglajen
- Unité de Bactériologie, Département de Microbiologie, Hôpital Européen George Pompidou, APHP, Université de Paris, 75015 Paris, France;
| | - Paul-Louis Woerther
- UR DYNAMiC 7380, Faculté de Santé, Université Paris-Est Créteil, 94010 Créteil, France; (E.D.); (P.-L.W.)
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Hôpitaux Universitaires Henri-Mondor, 94010 Créteil, France
| | - Cécile Angebault
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Hôpitaux Universitaires Henri-Mondor, 94010 Créteil, France; (S.D.); (C.A.)
- UR DYNAMiC 7380, Faculté de Santé, Université Paris-Est Créteil, 94010 Créteil, France; (E.D.); (P.-L.W.)
- UR DYNAMiC 7380, Ecole Nationale Vétérinaire d’Alfort, USC Anses, 94700 Maison-Alfort, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Hôpitaux Universitaires Henri-Mondor, 94010 Créteil, France; (S.D.); (C.A.)
- UR DYNAMiC 7380, Faculté de Santé, Université Paris-Est Créteil, 94010 Créteil, France; (E.D.); (P.-L.W.)
- UR DYNAMiC 7380, Ecole Nationale Vétérinaire d’Alfort, USC Anses, 94700 Maison-Alfort, France
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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