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Benrahla DE, Mohan S, Trickovic M, Castelli FA, Alloul G, Sobngwi A, Abdiche R, Kieser S, Demontant V, Trawinski E, Chollet C, Rodriguez C, Kitagishi H, Fenaille F, Trajkovski M, Motterlini R, Foresti R. An orally active carbon monoxide-releasing molecule enhances beneficial gut microbial species to combat obesity in mice. Redox Biol 2024; 72:103153. [PMID: 38608580 PMCID: PMC11025006 DOI: 10.1016/j.redox.2024.103153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Carbon monoxide (CO), a gaseous signaling molecule, has shown promise in preventing body weight gain and metabolic dysfunction induced by high fat diet (HFD), but the mechanisms underlying these effects are largely unknown. An essential component in response to HFD is the gut microbiome, which is significantly altered during obesity and represents a target for developing new therapeutic interventions to fight metabolic diseases. Here, we show that CO delivered to the gut by oral administration with a CO-releasing molecule (CORM-401) accumulates in faeces and enriches a variety of microbial species that were perturbed by a HFD regimen. Notably, Akkermansia muciniphila, which exerts salutary metabolic effects in mice and humans, was strongly depleted by HFD but was the most abundant gut species detected after CORM-401 treatment. Analysis of bacterial transcripts revealed a restoration of microbial functional activity, with partial or full recovery of the Krebs cycle, β-oxidation, respiratory chain and glycolysis. Mice treated with CORM-401 exhibited normalization of several plasma and fecal metabolites that were disrupted by HFD and are dependent on Akkermansia muciniphila's metabolic activity, including indoles and tryptophan derivatives. Finally, CORM-401 treatment led to an improvement in gut morphology as well as reduction of inflammatory markers in colon and cecum and restoration of metabolic profiles in these tissues. Our findings provide therapeutic insights on the efficacy of CO as a potential prebiotic to combat obesity, identifying the gut microbiota as a crucial target for CO-mediated pharmacological activities against metabolic disorders.
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Affiliation(s)
| | - Shruti Mohan
- University Paris-Est Créteil, INSERM, IMRB, F-94010, Créteil, France
| | - Matija Trickovic
- Department of Cell Physiology and Metabolism, Centre Medical Universitaire (CMU), Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Ghida Alloul
- University Paris-Est Créteil, INSERM, IMRB, F-94010, Créteil, France
| | - Arielle Sobngwi
- University Paris-Est Créteil, INSERM, IMRB, F-94010, Créteil, France
| | - Rosa Abdiche
- University Paris-Est Créteil, INSERM, IMRB, F-94010, Créteil, France
| | - Silas Kieser
- Department of Cell Physiology and Metabolism, Centre Medical Universitaire (CMU), Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Elisabeth Trawinski
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Céline Chollet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Christophe Rodriguez
- University Paris-Est Créteil, INSERM, IMRB, F-94010, Créteil, France; NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France; Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est Créteil, Créteil, France
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, 610-0321, Japan
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Mirko Trajkovski
- Department of Cell Physiology and Metabolism, Centre Medical Universitaire (CMU), Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Roberta Foresti
- University Paris-Est Créteil, INSERM, IMRB, F-94010, 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:S1198-743X(24)00146-0. [PMID: 38527613 DOI: 10.1016/j.cmi.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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Martin A, Jauvain M, Bergsten E, Demontant V, Lehours P, Barau C, Levy M, Rodriguez C, Sobhani I, Amiot A. Gastric microbiota in patients with gastric MALT lymphoma according to Helicobacter pylori infection. Clin Res Hepatol Gastroenterol 2024; 48:102247. [PMID: 37981222 DOI: 10.1016/j.clinre.2023.102247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Gastric Mucosa Associated Lymphoid Tissue lymphoma (GML) development is triggered by Helicobacter pylori (H. pylori) infection. Little is known about the impact of H. pylori infection on gastric microbiota. METHODS The gastric microbiota was retrospectively investigated using 16S rRNA gene sequencing in 32 patients with untreated GML (10 H. pylori-positive and 22 H. pylori-negative), 23 with remitted and 18 refractory GML and 35 controls. Differences in microbial diversity, bacterial composition and taxonomic repartition were assessed. RESULTS There was no change in diversity and bacterial composition between GML and control patients taking into account H. pylori status. Differential taxa analysis identified specific changes associated with H. pylori-negative GML: the abundances of Actinobacillus, Lactobacillus and Chryseobacterium were increased while the abundances of Veillonella, Atopobium, Leptotrichia, Catonella, Filifactor and Escherichia_Shigella were increased in control patients. In patients with remitted GML, the genera Haemophilus and Moraxella were significantly more abundant than in refractory patients, while Atopobium and Actinomyces were significantly more abundant in refractory patients. CONCLUSION Detailed analysis of the gastric microbiota revealed significant changes in the bacterial composition of the gastric mucosa in patients with GML that may have a role in gastric lymphomagenesis but not any new pathobionts.
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Affiliation(s)
- Antoine Martin
- Department of Gastroenterology, Henri-Mondor University Hospital, Universite Paris Est Creteil, AP-HP, EA7375, 51, Avenue du Marechal de Lattre de Tassigny CRETEIL, Creteil F-94010, France
| | - Marine Jauvain
- UMR1312 Bordeaux Institute of Cancer, BRIC, Université de Bordeaux, Bordeaux 33076, France; French National Reference Center for Campylobacters and Helicobacters, Bordeaux Hospital University Center, Bordeaux, France
| | - Emma Bergsten
- Department of Gastroenterology, Henri-Mondor University Hospital, Universite Paris Est Creteil, AP-HP, EA7375, 51, Avenue du Marechal de Lattre de Tassigny CRETEIL, Creteil F-94010, France
| | - Vanessa Demontant
- Genomics Platform and Virology Unit, Henri-Mondor University Hospital, AP-HP, Institut Mondor de Recherche Biomédicale, Universite Paris Est Creteil, INSERM U955, Créteil F-94010 France
| | - Philippe Lehours
- UMR1312 Bordeaux Institute of Cancer, BRIC, Université de Bordeaux, Bordeaux 33076, France; French National Reference Center for Campylobacters and Helicobacters, Bordeaux Hospital University Center, Bordeaux, France
| | - Caroline Barau
- Plateforme de Ressources Biologique, Henri-Mondor University Hospital, AP-HP, University Paris Est Creteil, F-94010, France
| | - Michael Levy
- Department of Gastroenterology, Henri-Mondor University Hospital, Universite Paris Est Creteil, AP-HP, EA7375, 51, Avenue du Marechal de Lattre de Tassigny CRETEIL, Creteil F-94010, France
| | - Christophe Rodriguez
- Genomics Platform and Virology Unit, Henri-Mondor University Hospital, AP-HP, Institut Mondor de Recherche Biomédicale, Universite Paris Est Creteil, INSERM U955, Créteil F-94010 France
| | - Iradj Sobhani
- Department of Gastroenterology, Henri-Mondor University Hospital, Universite Paris Est Creteil, AP-HP, EA7375, 51, Avenue du Marechal de Lattre de Tassigny CRETEIL, Creteil F-94010, France
| | - Aurelien Amiot
- Department of Gastroenterology, Henri-Mondor University Hospital, Universite Paris Est Creteil, AP-HP, EA7375, 51, Avenue du Marechal de Lattre de Tassigny CRETEIL, Creteil F-94010, France.
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Bay P, Rodriguez C, Caruso S, Demontant V, Boizeau L, Soulier A, Woerther PL, Mekontso-Dessap A, Pawlotsky JM, de Prost N, Fourati S. Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in critically ill COVID-19 patients. J Med Virol 2023; 95:e29268. [PMID: 38050838 DOI: 10.1002/jmv.29268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
Severe coronavirus disease 2019 (COVID-19) is related to dysregulated immune responses. We aimed to explore the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on the immune response by nasopharyngeal transcriptomic in critically-ill patients. This prospective monocentric study included COVID-19 patients requiring intensive care unit (ICU) admission between March 2020 and 2022. Patients were classified according to VOC (ancestral, Alpha, Delta, and Omicron). Eighty-eight patients with severe COVID-19 were included after matching (on prespecified clinical criteria). Profiling of gene expression markers of innate and adaptive immune responses were investigated by respiratory transcriptomics at ICU admission. Eighty-eight patients were included in the study after matching (ancestral [n = 24], Alpha [n = 24], Delta [n = 22], and Omicron [n = 18] variants). Respiratory transcriptomic analysis revealed distinct innate and adaptive immune profiling between variants. In comparison with the ancestral variant, there was a reduced expression of neutrophil degranulation, T cell activation, cytokines signalling pathways in patients infected with Alpha and Delta variants. In contrast, there was a higher expression of neutrophil degranulation, T and B cells activation, and inflammatory interleukins pathways in patients infected with Omicron. To conclude, Omicron induced distinct immune respiratory transcriptomics signatures compared to pre-existing variants in patients with severe COVID-19, pointing to an evolving pathophysiology of severe COVID-19 in the Omicron era.
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Affiliation(s)
- Pierre Bay
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Stefano Caruso
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Vanessa Demontant
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Laure Boizeau
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Alexandre Soulier
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Paul L Woerther
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- EA 7380 Dynamic, Université Paris-Est-Créteil (UPEC), École Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Armand Mekontso-Dessap
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Jean-Michel Pawlotsky
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Plateforme de Génomique, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Créteil, France
| | - Nicolas de Prost
- Service de Médecine Intensive Réanimation, DMU Médecine, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- GRC CARMAS, Faculté de Santé de Créteil, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Slim Fourati
- Équipe Virus, Hépatologie, Cancer, INSERM U955, Université Paris-Est-Créteil (UPEC), Créteil, France
- Département de Microbiologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
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Kimseng H, Rossi G, Danjean M, Jimenez-Araya B, Chaligne C, Galy A, Souhail B, Bert F, Leflon V, Fihman V, Caillault A, Demontant V, Seng S, Trawinski E, N 'Debi M, Boizeau L, Jacquier H, Ronot M, Reizine E, Le Roy V, Lefort A, Rodriguez C, Lepeule R, Woerther PL. Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses. J Infect 2023; 87:365-372. [PMID: 37604210 DOI: 10.1016/j.jinf.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA. METHODS In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae, we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture. RESULTS Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p<0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing. DISCUSSION Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future.
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Affiliation(s)
- Hadrien Kimseng
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Geoffrey Rossi
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Maxime Danjean
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Bryan Jimenez-Araya
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Camille Chaligne
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Adrien Galy
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Bérénice Souhail
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Frédéric Bert
- Department of Microbiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Véronique Leflon
- Department of Microbiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Vincent Fihman
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | | | | | - Sarah Seng
- NGS Platform, IMRB Institute, Créteil, France
| | | | | | | | - Hervé Jacquier
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Maxime Ronot
- Department of Radiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Edouard Reizine
- Department of Radiology, Henri Mondor Hospital, AP-HP, Créteil, France
| | - Vincent Le Roy
- Department of Hepatology, Henri Mondor Hospital, AP-HP, Créteil, France
| | - Agnès Lefort
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France; IAME, UMR1137, Université Paris-Cité, Paris, France
| | - Christophe Rodriguez
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; INSERM U955, IMRB Institute, Créteil, France; NGS Platform, IMRB Institute, Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; NGS Platform, IMRB Institute, Créteil, France.
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6
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Faury H, Le Guen R, Demontant V, Rodriguez C, Souhail B, Galy A, Jolivet S, Lepeule R, Decousser JW, Fihman V, Woerther PL, Royer G. Ampicillin-susceptible Enterococcus faecium infections: clinical features, causal clades, and contribution of MALDI-TOF to early detection. Microbiol Spectr 2023; 11:e0454522. [PMID: 37747184 PMCID: PMC10581188 DOI: 10.1128/spectrum.04545-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/28/2023] [Indexed: 09/26/2023] Open
Abstract
Enterococcus faecium, a common resident of the human gastrointestinal tract, is also a major pathogen. Prompt initiation of appropriate treatment is essential to improve patient outcome in disseminated E. faecium infections. However, ampicillin resistance is frequent in this species, rendering treatment difficult. We used a comprehensive approach, including clinical data review, whole-genome sequencing, and mass spectrometry, to characterize ampicillin-susceptible (EFM-S) and ampicillin-resistant (EFM-R) isolates. We included all patients with culture-confirmed E. faecium infection attending our hospital over a 16-month period. A comparison of 32 patients infected with EFM-S strains and 251 patients infected with EFM-R strains revealed that EFM-R isolates were strongly associated with a longer hospital stay, history of prior hospitalization, and the carriage of multidrug-resistant organisms. An analysis of the genomes of 26 EFM-S and 26 EFM-R isolates from paired patients revealed a population structure almost perfectly matching ampicillin susceptibility, with resistant isolates in clade A1, and susceptible isolates in clades A2 and B. The clade B and A2 isolates mostly came from digestive or biliary tract samples, whereas clade A1 isolates were mostly obtained from urine and blood. Finally, we built a custom database for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which differentiated between clade B and clade A1/A2 strains with high-positive and high-negative predictive values (95.6% and 100%, respectively). This study provides important new insight into the clinical features and clades associated with EFM-S and EFM-R isolates. In combination with MALDI-TOF MS, these data could facilitate the rapid initiation of the most appropriate treatment.IMPORTANCEEnterococcus faecium is an important human pathogen in which the prevalence of ampicillin resistance is high. However, little is known about the clinical characteristics of patients infected with ampicillin-resistant and ampicillin-susceptible strains. Indeed, current knowledge is based on genus-wide studies of Enterococcus or studies of very small numbers of susceptible isolates, precluding robust conclusions. Our data highlight specific clinical features related to the epidemiology of EFM-S and EFM-R strains, such as length of hospital stay, history of prior hospitalization, carriage of multidrug-resistant organisms, and type of sample from which the isolate was obtained. The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with a custom-built database may make it possible to distinguish clade B isolates, which are typically susceptible to ampicillin, from clade A1/A2 isolates (A1 being typically resistant), thereby facilitating the management of these infections.
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Affiliation(s)
- Hélène Faury
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
- Equipe Opérationnelle d’Hygiène, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Ronan Le Guen
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
- Equipe Opérationnelle d’Hygiène, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Vanessa Demontant
- Plateforme de Séquençage Haut-Débit, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Christophe Rodriguez
- Plateforme de Séquençage Haut-Débit, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Bérénice Souhail
- Unité Transversale de Traitement des Infections (U2TI), Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Adrien Galy
- Unité Transversale de Traitement des Infections (U2TI), Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Sarah Jolivet
- Unité de Prévention du Risque Infectieux, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Raphaël Lepeule
- Unité Transversale de Traitement des Infections (U2TI), Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Jean-Winoc Decousser
- Equipe Opérationnelle d’Hygiène, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
- EA 7380, Université Paris-Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Vincent Fihman
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Paul-Louis Woerther
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
- Plateforme de Séquençage Haut-Débit, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
- EA 7380, Université Paris-Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Guilhem Royer
- Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, AP-HP, Hôpital Henri Mondor, Créteil, France
- EA 7380, Université Paris-Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
- EERA Unit "Ecology and Evolution of Antibiotic Resistance", Institut Pasteur-Assistance Publique/Hôpitaux de Paris-Université Paris-Saclay, Paris, France
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7
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Rodriguez C, Boizeau L, Soulier A, N'Debi M, Demontant V, Trawinski E, Seng S, Fontaine H, Woerther PL, Marchand S, Fourati S, Chevaliez S, Cappy P, Pol S, Pawlotsky JM. Unknown Circovirus in Immunosuppressed Patient with Hepatitis, France, 2022. Emerg Infect Dis 2023; 29:1051-1054. [PMID: 37081594 PMCID: PMC10124635 DOI: 10.3201/eid2905.221485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Hepatitis of undetermined origin can be caused by a wide variety of pathogens, sometimes emerging pathogens. We report the discovery, by means of routine shotgun metagenomics, of a new virus belonging to the family Circoviridae, genus Circovirus, in a patient in France who had acute hepatitis of unknown origin.
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8
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Fourati S, Gautier G, Chovelon M, Soulier A, N'Debi M, Demontant V, Kennel C, Rodriguez C, Pawlotsky JM. Persistent SARS-CoV-2 Alpha Variant Infection in Immunosuppressed Patient, France, February 2022. Emerg Infect Dis 2022; 28:1512-1515. [PMID: 35514025 PMCID: PMC9239896 DOI: 10.3201/eid2807.220467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe persistent circulation of SARS-CoV-2 Alpha variant in an immunosuppressed patient in France during February 2022. The virus had a new pattern of mutation accumulation. The ongoing circulation of previous variants of concern could lead to reemergence of variants with the potential to propagate future waves of infection.
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9
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Lamoureux C, Surgers L, Fihman V, Gricourt G, Demontant V, Trawinski E, N'Debi M, Gomart C, Royer G, Launay N, Le Glaunec JM, Wemmert C, La Martire G, Rossi G, Lepeule R, Pawlotsky JM, Rodriguez C, Woerther PL. Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections. Front Microbiol 2022; 13:761873. [PMID: 35464955 PMCID: PMC9020828 DOI: 10.3389/fmicb.2022.761873] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
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Affiliation(s)
- Claudie Lamoureux
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Laure Surgers
- GHU AP-HP Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Vincent Fihman
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France
| | - Guillaume Gricourt
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Elisabeth Trawinski
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Melissa N'Debi
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Camille Gomart
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Guilhem Royer
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Nathalie Launay
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jeanne-Marie Le Glaunec
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Charlotte Wemmert
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Giulia La Martire
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Geoffrey Rossi
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Raphaël Lepeule
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jean-Michel Pawlotsky
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Christophe Rodriguez
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France.,NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Paul-Louis Woerther
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France.,Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
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10
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Courbin V, Riller Q, Amegnizin JL, Gricourt G, Demontant V, Fihman V, Angebault C, Mahevas M, Gaube G, Coutte L, Pawlotsky JM, Lepeule R, Rodriguez C, Woerther PL. Case Report: Cerebral Nocardiosis Caused by Nocardia cyriacigeorgica Detected by Metagenomics in an Apparently Immunocompetent Patient. Front Immunol 2022; 13:719124. [PMID: 35185867 PMCID: PMC8852340 DOI: 10.3389/fimmu.2022.719124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/20/2022] [Indexed: 01/26/2023] Open
Abstract
We report a case of meningoencephalitis due to Nocardia cyriacigeorgica diagnosed with metagenomics, while all the standard methods were negative. This diagnosis made adaptation of antimicrobial treatment possible and led to the discovery of a rare, acquired immunodeficiency syndrome.
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Affiliation(s)
- Virginie Courbin
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Quentin Riller
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Jean-Louis Amegnizin
- Department of Radiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Guillaume Gricourt
- NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Vanessa Demontant
- NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Vincent Fihman
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA Dynamyc 7380, Université Paris Est Créteil-Ecole nationale Vétérinaire de Maisons-Alfort, Créteil, France
| | - Cecile Angebault
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA Dynamyc 7380, Université Paris Est Créteil-Ecole nationale Vétérinaire de Maisons-Alfort, Créteil, France
| | - Matthieu Mahevas
- Internal Medicine Department, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Géraldine Gaube
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Laëtitia Coutte
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Christophe Rodriguez
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,NGS Plateform, IMRB Institute, AP-HP, Henri Mondor University Hospital, Université Paris-Est, Créteil, France.,EA Dynamyc 7380, Université Paris Est Créteil-Ecole nationale Vétérinaire de Maisons-Alfort, Créteil, France
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11
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Gasmi I, Machou C, Rodrigues A, Brouillet A, Nguyen TC, Rousseau B, Guillot A, Rodriguez C, Demontant V, Ait-Ahmed Y, Calderaro J, Luciani A, Pawlotsky JM, Lafdil F. Interleukin-17 programs liver progenitor cell transformation into cancer stem cells through mir-122 downregulation with increased risk of primary liver cancer initiation. Int J Biol Sci 2022; 18:1944-1960. [PMID: 35342340 PMCID: PMC8935237 DOI: 10.7150/ijbs.70408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Chronic inflammation is a key component in the development of virtually all types of primary liver cancers. However, how chronic inflammation potentiates or even may initiate liver parenchymal cell transformation remains unclear. Cancer stem cells (CSCs) represent an exciting target for novel anticancer therapeutic strategies in several types of cancers and were also described in primary liver cancers as tumor initiating cells. Recently, we reported a key role of Interleukin (IL)-17 in Liver Progenitor Cell (LPC) accumulation in preneoplastic cirrhotic livers. In this study, we evidenced in vitro, that long-term stimulation of LPCs with IL-17 led to their transformation into CSCs. Indeed, they acquired CSC-marker expression, and self-renewal properties, showed by their increased capacity to form spheroids. The miRNome analysis revealed that long-term IL-17 treatment of LPCs led to a 90% decrease in miR-122 expression. In a model using immunodeficient mice, ectopic engraftment of LPCs in an IL-17-enriched environment led to tumor occurrence with an aggressive phenotype. Contrastingly, in a murine model of hepatocellular carcinoma induced by a unique injection of diethyl-nitrosamine associated with chronic administration of carbon tetrachloride, IL-17-deficiency or anti-IL-17 therapy protected mice from liver tumor growth. In conclusion, we showed that a chronic exposure of LPCs to IL-17 cytokine promotes their transformation into CSCs. In addition, we demonstrated that IL-17-neutralizing strategies limit CSC occurrence and liver tumor progression through miR-122 restored-expression.
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12
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Deust A, Chobert MN, Demontant V, Gricourt G, Denaës T, Thiolat A, Ruiz I, Rodriguez C, Pawlotsky JM, Teixeira-Clerc F. Macrophage autophagy protects against hepatocellular carcinogenesis in mice. Sci Rep 2021; 11:18809. [PMID: 34552122 PMCID: PMC8458469 DOI: 10.1038/s41598-021-98203-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
Autophagy is a lysosomal degradation pathway of cellular components that regulates macrophage properties. Macrophages are critically involved in tumor growth, metastasis, angiogenesis and immune suppression. Here, we investigated whether macrophage autophagy may protect against hepatocellular carcinoma (HCC). Experiments were performed in mice with deletion of the autophagy gene Atg5 in the myeloid lineage (ATG5Mye-/- mice) and their wild-type (WT) littermates. As compared to WT, ATG5Mye-/- mice were more susceptible to diethylnitrosamine (DEN)-induced hepatocarcinogenesis, as shown by enhanced tumor number and volume. Moreover, DEN-treated ATG5Mye-/- mice exhibited compromised immune cell recruitment and activation in the liver, suggesting that macrophage autophagy invalidation altered the antitumoral immune response. RNA sequencing showed that autophagy-deficient macrophages sorted from DEN mice are characterized by an enhanced expression of immunosuppressive markers. In vitro studies demonstrated that hepatoma cells impair the autophagy flux of macrophages and stimulate their expression of programmed cell death-ligand 1 (PD-L1), a major regulator of the immune checkpoint. Moreover, pharmacological activation of autophagy reduces hepatoma cell-induced PD-L1 expression in cultured macrophages while inhibition of autophagy further increases PD-L1 expression suggesting that autophagy invalidation in macrophages induces an immunosuppressive phenotype. These results uncover macrophage autophagy as a novel protective pathway regulating liver carcinogenesis.
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Affiliation(s)
- Anthony Deust
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France
| | - Marie-Noële Chobert
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France
| | - Vanessa Demontant
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France.,Plateforme de Génomique, Hôpital Henri Mondor, Créteil, France
| | | | - Timothé Denaës
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France
| | - Allan Thiolat
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France
| | - Isaac Ruiz
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France
| | - Christophe Rodriguez
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France.,Plateforme de Génomique, Hôpital Henri Mondor, Créteil, France
| | - Jean-Michel Pawlotsky
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France.,Université Paris-Est, UMR-S955, Créteil, France.,Département de Virologie, Hôpital Henri Mondor, Créteil, France
| | - Fatima Teixeira-Clerc
- INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France. .,Université Paris-Est, UMR-S955, Créteil, France. .,INSERM U955, Institut Mondor de Recherche Biomédicale, Hôpital Henri Mondor, 94000, Créteil, France.
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13
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Winter S, Lechapt E, Gricourt G, N‘debi M, Boddaert N, Moshous D, Blauwblomme T, Kossorotoff M, Fouyssac F, Chareyre J, Demontant V, Chretien F, Woerther PL, Pawlotsky JM, Blanche S, Neven B, Rodriguez C. Fatal encephalitis caused by Newcastle disease virus in a child. Acta Neuropathol 2021; 142:605-608. [PMID: 34304282 DOI: 10.1007/s00401-021-02344-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/18/2022]
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14
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Rodriguez C, Gricourt G, Ndebi M, Demontant V, Poiteau L, Burrel S, Boutolleau D, Woerther PL, Calvez V, Stroer S, Pawlotsky JM. Fatal Encephalitis Caused by Cristoli Virus, an Emerging Orthobunyavirus, France. Emerg Infect Dis 2021; 26:1287-1290. [PMID: 32441621 PMCID: PMC7258463 DOI: 10.3201/eid2606.191431] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report the discovery of a new orthobunyavirus, Cristoli virus, by means of shotgun metagenomics. The virus was identified in an immunodepressed patient with fatal encephalitis. Full-length genome sequencing revealed high-level expression of a virulence factor, possibly explaining the severity of the infection. The patient’s recent history suggests circulation in France.
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15
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Fourati S, Decousser JW, Khouider S, N'Debi M, Demontant V, Trawinski E, Gourgeon A, Gangloff C, Destras G, Bal A, Josset L, Soulier A, Costa Y, Gricourt G, Lina B, Lepeule R, Pawlotsky JM, Rodriguez C. Novel SARS-CoV-2 Variant Derived from Clade 19B, France. Emerg Infect Dis 2021; 27:1540-1543. [PMID: 33900195 PMCID: PMC8084519 DOI: 10.3201/eid2705.210324] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report a novel severe acute respiratory syndrome coronavirus 2 variant derived from clade 19B (HMN.19B variant or Henri Mondor variant). This variant is characterized by the presence of 18 amino acid substitutions, including 7–8 substitutions in the spike protein and 2 deletions. These variants actively circulate in different regions of France.
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16
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Rodriguez C, Gouilh MA, Weiss N, Stroer S, Mokhtari K, Seilhean D, Mathon B, Demontant V, N'Debi M, Gricourt G, Woerther PL, Pawlotsky JM, Stefic K, Marlet J, Dequin PF, Guillon A, Pourcher V, Boutolleau D, Vabret A, Burrel S. Fatal Measles Inclusion-Body Encephalitis in Adult with Untreated AIDS, France. Emerg Infect Dis 2021; 26:2231-2234. [PMID: 32818389 PMCID: PMC7454109 DOI: 10.3201/eid2609.200366] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We report a fatal case of measles inclusion-body encephalitis occurring in a woman from Romania with AIDS. After an extensive but unsuccessful diagnostic evaluation, a pan-pathogen shotgun metagenomic approach revealed a measles virus infection. We identified no mutations previously associated with neurovirulence.
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17
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Monnet P, Rodriguez C, Gaudin O, Cirotteau P, Papouin B, Dereure O, Tetart F, Lalevee S, Colin A, Lebrun-Vignes B, Abe E, Alvarez JC, Demontant V, Gricourt G, de Prost N, Barau C, Chosidow O, Wolkenstein P, Hue S, Ortonne N, Milpied B, Ingen-Housz-Oro S. Towards a better understanding of adult idiopathic epidermal necrolysis: a retrospective study of 19 cases. J Eur Acad Dermatol Venereol 2021; 35:1569-1576. [PMID: 33834541 DOI: 10.1111/jdv.17274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/24/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Most cases of Stevens-Johnson syndrome and toxic epidermal necrolysis are drug-induced. A small subset of cases remain with unknown aetiology (idiopathic epidermal necrolysis [IEN]). OBJECTIVE We sought to better describe adult IEN and understand the aetiology. METHODS This retrospective study was conducted in 4 centres of the French national reference centre for epidermal necrolysis. Clinical data were collected for the 19 adults hospitalized for IEN between January 2015 and December 2019. Wide toxicology analysis of blood samples was performed. Histology of IEN cases was compared with blinding to skin biopsies of drug-induced EN (DIEN, 'controls'). Available baseline skin biopsies were analysed by shotgun metagenomics and transcriptomics and compared to controls. RESULTS IEN cases represented 15.6% of all EN cases in these centres. The median age of patients was 38 (range 16-51) years; 68.4% were women. Overall, 63.2% (n = 12) of cases required intensive care unit admission and 15.8% (n = 3) died at the acute phase. Histology showed the same patterns of early- to late-stage EN with no difference between DIEN and IEN cases. One toxicology analysis showed unexpected traces of carbamazepine; results for other cases were negative. Metagenomics analysis revealed no unexpected pathological microorganism. Transcriptomic analysis highlighted a different pro-apoptotic pathway in IEN compared to DIEN, with an overexpression of apoptosis effectors TWEAK/TRAIL. CONCLUSIONS IEN affects young people and is a severe form of EN. A large toxicologic investigation is warranted. Different pathways seem involved in IEN and DIEN, leading to the same apoptotic effect, but the primary trigger remains unknown.
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Affiliation(s)
- P Monnet
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - C Rodriguez
- Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,INSERM U955, Université Paris Est Créteil Val de Marne, UPEC, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France
| | - O Gaudin
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France
| | - P Cirotteau
- Dermatology Department, Saint André Hospital, Bordeaux, France
| | - B Papouin
- Pathology Department, AP-HP, Henri Mondor Hospital, Créteil, France
| | - O Dereure
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Dermatology Department, Saint Eloi Hospital, Montpellier, France
| | - F Tetart
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Dermatology Department, Charles Nicole Hospital, Rouen, France
| | - S Lalevee
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Immunology Department, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, AP-HP, Henri Mondor Hospital, Créteil, France
| | - A Colin
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France
| | - B Lebrun-Vignes
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Pharmacovigilance Department, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - E Abe
- Pharmacology and Toxicology Department, AP-HP, Raymond Poincaré Hospital, Garches, France
| | - J-C Alvarez
- Pharmacology and Toxicology Department, AP-HP, Raymond Poincaré Hospital, Garches, France
| | - V Demontant
- Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,INSERM U955, Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - G Gricourt
- Microbiology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,INSERM U955, Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - N de Prost
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Intensive Care Unit, AP-HP, Henri Mondor Hospital, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - C Barau
- Clinical Investigation Center, Henri Mondor Hospital, Créteil, France
| | - O Chosidow
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - P Wolkenstein
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - S Hue
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Immunology Department, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, AP-HP, Henri Mondor Hospital, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - N Ortonne
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Pathology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Université Paris Est Créteil Val de Marne, UPEC, Créteil, France
| | - B Milpied
- Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Dermatology Department, Saint André Hospital, Bordeaux, France
| | - S Ingen-Housz-Oro
- Dermatology Department, AP-HP, Henri Mondor Hospital, Créteil, France.,Reference Center for Toxic Bullous Diseases and Severe Drug Reactions TOXIBUL, Créteil, France.,Univ Paris Est Créteil EpidermE, Créteil, France
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18
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Royer G, Roisin L, Demontant V, Lo S, Coutte L, Lim P, Pawlotsky JM, Jacquier H, Lepeule R, Rodriguez C, Woerther PL. Microdiversity of Enterococcus faecalis isolates in cases of infective endocarditis: selection of non-synonymous mutations and large deletions is associated with phenotypic modifications. Emerg Microbes Infect 2021; 10:929-938. [PMID: 33913790 PMCID: PMC8158287 DOI: 10.1080/22221751.2021.1924865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Context: Today, infective endocarditis (IE) caused by Enterococcus faecalis represents 10% of all IE and is marked by its difficult management and the frequency of relapses. Although the precise reasons for that remain to be elucidated, the evolution of the culprit strain under selective pressure through microdiversification could be, at least in part, involved. Material and methods: To further study the in situ genetic microdiversity and its possible phenotypic manifestations in E. faecalis IE, we sequenced and compared multiple isolates from the valves, blood culture and joint fluid of five patients who underwent valvular surgery. Growth rate and early biofilm production of selected isolates were also compared. Results: By sequencing a total of 58 E. faecalis genomes, we detected a considerable genomic microdiversity, not only among strains from different anatomical origins, but also between isolates from the same studied cardiac valves. Interestingly, deletions of thousands of bases including the well-known virulence factors ebpA/B/C, and srtC, as well as other large prophage sequences containing genes coding for proteins implicated in platelet binding (PlbA and PlbB) were evidenced. The study of mutations helped unveil common patterns in genes related to the cell cycle as well as central metabolism, suggesting an evolutionary convergence in these isolates. As expected, such modifications were associated with a significant impact on the in-vitro phenotypic heterogeneity, growth, and early biofilm production. Conclusion: Genome modifications associated with phenotypic variations may allow bacterial adaptation to both antibiotic and immune selective pressures, and thus promote relapses.
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Affiliation(s)
- G Royer
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - L Roisin
- EA 7380, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France
| | - V Demontant
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France
| | - S Lo
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France
| | - L Coutte
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France
| | - P Lim
- Department of Cardiovascular Medicine and SOS Endocardites Unit, Henri-Mondor University Hospital, AP-HP, Créteil, France
| | - J M Pawlotsky
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France.,INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - H Jacquier
- Bacteriology Unit, Lariboisière Hospital, APHP, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, UFR de Médecine, Paris, France
| | - R Lepeule
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France
| | - C Rodriguez
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France.,INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - P L Woerther
- Department of Microbiology, Henri Mondor Hospital, AP-HP, Université Paris-Est, Créteil, France.,EA 7380, Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC Anses, Créteil, France
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19
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Bailly B, Guilpain L, Bouiller K, Chirouze C, N'Debi M, Soulier A, Demontant V, Pawlotsky JM, Rodriguez C, Fourati S. BNT162b2 mRNA vaccination did not prevent an outbreak of SARS COV-2 variant 501Y.V2 in an elderly nursing home but reduced transmission and disease severity. Clin Infect Dis 2021; 74:517-520. [PMID: 33993228 PMCID: PMC8241482 DOI: 10.1093/cid/ciab446] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 12/01/2022] Open
Abstract
We report an outbreak of SARS-CoV-2 501Y.V2 in a nursing home. All non-vaccinated
residents (5/5) versus half of those vaccinated with BNT162b2
(13/26) were infected. Two of 13 vaccinated versus 4 of 5
non-vaccinated residents presented severe disease. BNT162b2 did not prevent the
outbreak, but reduced transmission and disease severity.
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Affiliation(s)
- Benoit Bailly
- Department of infectious disease, University Hospital of Besançon, F-25000 Besançon, France.,Department of infectious disease, hospital of Lons Le Saunier, F-39000 Lons Le Saunier, France
| | - Luc Guilpain
- Department of medical laboratory, hospital of Lons Le Saunier, F-39000 Lons Le Saunier, France
| | - Kevin Bouiller
- Department of infectious disease, hospital of Lons Le Saunier, F-39000 Lons Le Saunier, France.,UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, 25000 Besançon, France
| | - Catherine Chirouze
- Department of infectious disease, hospital of Lons Le Saunier, F-39000 Lons Le Saunier, France.,UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, 25000 Besançon, France
| | - Melissa N'Debi
- Genomics Platform, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
| | - Alexandre Soulier
- Virology Unit, Department of Prevention, Diagnosis and Treatment of Infections, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
| | - Vanessa Demontant
- Genomics Platform, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Virology Unit, Department of Prevention, Diagnosis and Treatment of Infections, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France.,Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - Christophe Rodriguez
- Genomics Platform, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France.,Virology Unit, Department of Prevention, Diagnosis and Treatment of Infections, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France.,Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - Slim Fourati
- Virology Unit, Department of Prevention, Diagnosis and Treatment of Infections, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France.,Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
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20
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Rodriguez C, de Prost N, Fourati S, Lamoureux C, Gricourt G, N’debi M, Canoui-Poitrine F, Désveaux I, Picard O, Demontant V, Trawinski E, Lepeule R, Surgers L, Vindrios W, Lelièvre JD, Mongardon N, Langeron O, Cohen JL, Mekontso-Dessap A, Woerther PL, Pawlotsky JM. Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19. PLoS Pathog 2021; 17:e1009416. [PMID: 33780519 PMCID: PMC8032121 DOI: 10.1371/journal.ppat.1009416] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/08/2021] [Accepted: 02/22/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 is characterized by respiratory symptoms of various severities, ranging from mild upper respiratory signs to acute respiratory failure/acute respiratory distress syndrome associated with a high mortality rate. However, the pathophysiology of the disease is largely unknown. Shotgun metagenomics from nasopharyngeal swabs were used to characterize the genomic, metagenomic and transcriptomic features of patients from the first pandemic wave with various forms of COVID-19, including outpatients, patients hospitalized not requiring intensive care, and patients in the intensive care unit, to identify viral and/or host factors associated with the most severe forms of the disease. Neither the genetic characteristics of SARS-CoV-2, nor the detection of bacteria, viruses, fungi or parasites were associated with the severity of pulmonary disease. Severe pneumonia was associated with overexpression of cytokine transcripts activating the CXCR2 pathway, whereas patients with benign disease presented with a T helper "Th1-Th17" profile. The latter profile was associated with female gender and a lower mortality rate. Our findings indicate that the most severe cases of COVID-19 are characterized by the presence of overactive immune cells resulting in neutrophil pulmonary infiltration which, in turn, could enhance the inflammatory response and prolong tissue damage. These findings make CXCR2 antagonists, in particular IL-8 antagonists, promising candidates for the treatment of patients with severe COVID-19.
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Affiliation(s)
- Christophe Rodriguez
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Nicolas de Prost
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- CARMAS Clinical Research Group, Université Paris-Est, Créteil, France
| | - Slim Fourati
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Claudie Lamoureux
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Guillaume Gricourt
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Melissa N’debi
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
| | - Florence Canoui-Poitrine
- Université Paris-Est-Créteil, INSERM, IMRB, Créteil, France
- Public Health and Clinical Research Unit, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Isaac Désveaux
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Oriane Picard
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Vanessa Demontant
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Elisabeth Trawinski
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Laure Surgers
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - William Vindrios
- Department of Clinical Immunology and Infectious Diseases, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Jean-Daniel Lelièvre
- Department of Clinical Immunology and Infectious Diseases, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Nicolas Mongardon
- Department of Anesthesiology and Surgical Intensive Care, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - Olivier Langeron
- Department of Anesthesiology and Surgical Intensive Care, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
| | - José L. Cohen
- Center for Clinical Investigation and Biotherapies, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Immunoregulation and biotherapies”, Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris-Est, Créteil, France
| | - Armand Mekontso-Dessap
- Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- CARMAS Clinical Research Group, Université Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team DYNAMIC, Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Microbiology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France
- Team “Viruses, Hepatology, Cancer”, Institut Mondor de Recherche Biomédicale (IMRB), INSERM U955, Université Paris-Est, Créteil, France
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21
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Solaguren-Beascoa M, Bujakowska KM, Méjécase C, Emmenegger L, Orhan E, Neuillé M, Mohand-Saïd S, Condroyer C, Lancelot ME, Michiels C, Demontant V, Antonio A, Letexier M, Saraiva JP, Lonjou C, Carpentier W, Léveillard T, Pierce EA, Dollfus H, Sahel JA, Bhattacharya SS, Audo I, Zeitz C. WDR34, a candidate gene for non-syndromic rod-cone dystrophy. Clin Genet 2020; 99:298-302. [PMID: 33124039 DOI: 10.1111/cge.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/01/2020] [Accepted: 10/26/2020] [Indexed: 01/30/2023]
Abstract
Rod-cone dystrophy (RCD), also called retinitis pigmentosa, is characterized by rod followed by cone photoreceptor degeneration, leading to gradual visual loss. Mutations in over 65 genes have been associated with non-syndromic RCD explaining 60% to 70% of cases, with novel gene defects possibly accounting for the unsolved cases. Homozygosity mapping and whole-exome sequencing applied to a case of autosomal recessive non-syndromic RCD from a consanguineous union identified a homozygous variant in WDR34. Mutations in WDR34 have been previously associated with severe ciliopathy syndromes possibly associated with a retinal dystrophy. This is the first report of a homozygous mutation in WDR34 associated with non-syndromic RCD.
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Affiliation(s)
- Maria Solaguren-Beascoa
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Kinga M Bujakowska
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA
| | - Cécile Méjécase
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Lisa Emmenegger
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elise Orhan
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marion Neuillé
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Saddek Mohand-Saïd
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France
| | - Christel Condroyer
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marie-Elise Lancelot
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Christelle Michiels
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Vanessa Demontant
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | | | - Christine Lonjou
- Plateforme Post-Génomique P3S, Hôpital Pitié Salpêtrière, Paris, France
| | - Wassila Carpentier
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Plateforme Post-Génomique P3S, Hôpital Pitié Salpêtrière, Paris, France
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eric A Pierce
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA
| | - Hélène Dollfus
- Centre de Référence Pour les Affections Rares en Génétique Ophtalmologique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Laboratoire UMRS_1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - José-Alain Sahel
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine University, Pittsburgh, USA.,Académie des Sciences-Institut de France, Paris, France
| | - Shomi S Bhattacharya
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,UCL-Institute of Ophthalmology, London, UK.,Department of Cellular Therapy and Regenerative Medicine, Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Isabelle Audo
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS, CIC 1423, Paris, France.,UCL-Institute of Ophthalmology, London, UK
| | - Christina Zeitz
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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22
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Fourati S, Rodriguez C, Soulier A, Donati F, Hamadat S, Poiteau L, Demontant V, Brillet R, Ahnou N, Gricourt G, Chevaliez S, Ahmed-Belkacem A, Pawlotsky JM. Fitness-associated substitutions following failure of direct-acting antivirals assessed by deep sequencing of full-length hepatitis C virus genomes. Aliment Pharmacol Ther 2020; 52:1583-1591. [PMID: 32886807 DOI: 10.1111/apt.16054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/20/2020] [Accepted: 08/02/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND In hepatitis C virus (HCV) infection, treatment failure is generally associated with the selection of resistance-associated substitutions (RAS) conferring reduced susceptibility to direct-acting antiviral (DAA) drugs. Resistant variants continue to replicate after the end of treatment with potential for transmission. This may result from the selection of "fitness-associated substitutions". AIM To characterise potential "fitness-associated substitutions" in patients infected with genotype 3a failing DAA drugs METHODS: By means of shotgun metagenomics, we sequenced full-length HCV genomes at treatment initiation and at virological relapse in eight patients infected with genotype 3a with cirrhosis failing sofosbuvir and an NS5A inhibitor. The impact of amino acid changes occurring outside of DAA target regions selected in at least two patients were assessed on the in vitro susceptibility to an NS5A inhibitor and replication capacity. RESULTS At treatment failure, besides selection of known NS5A RASs, especially Y93H, a large number of amino acid changes was observed outside of DAA target regions. We identified four amino acid positions at which observed changes substantially improved in vitro replication capacity without affecting NS5A inhibitor susceptibility. CONCLUSIONS This is the first in vivo observation combined with in vitro confirmation of selection of phenotypically characterised "fitness-associated substitutions" together with RASs at the time of sofosbuvir-NS5A inhibitor treatment failure in patients infected with genotype 3a with cirrhosis. Our findings may explain the persistence of resistant HCV variants after treatment in patients who did not achieve sustained virological remission.
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Affiliation(s)
- Slim Fourati
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Christophe Rodriguez
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Alexandre Soulier
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Flora Donati
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Sabah Hamadat
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Lila Poiteau
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | | | | | - Nazim Ahnou
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | | | - Stéphane Chevaliez
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Abdelhakim Ahmed-Belkacem
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Jean-Michel Pawlotsky
- Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Henri Mondor Hospital, University of Paris-Est, Créteil, France.,INSERM U955, Créteil, France
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23
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Mounier R, Kapandji N, Gricourt G, Lobo D, Rodriguez C, Pons S, Djediat C, Woerther PL, Mellano V, Aït-Mamar B, Demontant V, Nebbad B, Senova S, Arnaud M, Cook F, Dhonneur G, Lebeaux D. Correction to: Assessment of Bacterial Colonization of Intracranial Pressure Transducers: A Prospective Study. Neurocrit Care 2020; 33:868. [PMID: 33063265 DOI: 10.1007/s12028-020-01130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roman Mounier
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France. .,INSERM U955, team 15, Mondor Institute for Biomedical Research, University Paris-Est-Créteil (UPEC), Créteil, France.
| | - Natacha Kapandji
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Guillaume Gricourt
- Department of Microbiology, Platform NGS Henri Mondor University Hospital of Paris, Institut Mondor de la Recherche Biomédicale, Paris-Est Créteil University, 94000, Créteil, France
| | - David Lobo
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Christophe Rodriguez
- Department of Microbiology, Platform NGS Henri Mondor University Hospital of Paris, Institut Mondor de la Recherche Biomédicale, Paris-Est Créteil University, 94000, Créteil, France
| | - Stéphanie Pons
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Chakib Djediat
- Plateau Technique de Microscopie Électronique, MET, UMR7245, Département AVIV, Museum National d'Histoire Naturelle, Paris, France
| | - Paul-Louis Woerther
- Department of Microbiology, Henri Mondor University Hospital Assitance Publique-Hôpitaux de Paris (APHP), University Paris-Est-Créteil (UPEC), Paris, France
| | - Vincent Mellano
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Bouziane Aït-Mamar
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Vanessa Demontant
- Department of Microbiology, Platform NGS Henri Mondor University Hospital of Paris, Institut Mondor de la Recherche Biomédicale, Paris-Est Créteil University, 94000, Créteil, France
| | - Biba Nebbad
- Plateau Technique de Microscopie Électronique, MET, UMR7245, Département AVIV, Museum National d'Histoire Naturelle, Paris, France
| | - Suhan Senova
- INSERM U955, team 15, Mondor Institute for Biomedical Research, University Paris-Est-Créteil (UPEC), Créteil, France.,Department of Neurosurgery, Henri Mondor University Hospital of Paris, Paris XII School of Medicine, 94000, Créteil, France
| | - Melissa Arnaud
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Fabrice Cook
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - Gilles Dhonneur
- Department of Anesthesia and Surgical Intensive Care, Henri Mondor University Hospital of Paris, Paris-Est Créteil University, 51, Avenue du Maréchal de Lattre de Tassigny, 94000, Créteil, France
| | - David Lebeaux
- Université de Paris, 75006, Paris, France.,Service de Microbiologie, Unité Mobile D'Infectiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015, Paris, France
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24
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Woerther P, Surgers L, Lamoureux C, Lepeule R, Demontant V, Gricourt G, Pawlotsky J, Rodriguez C. Diagnostic microbiologique pan-pathogène par métagénomique clinique, retour d’expérience en routine. Med Mal Infect 2020. [DOI: 10.1016/j.medmal.2020.06.437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Rodriguez C, Nere ML, Demontant V, Charreau I, Mercier-Darty M, Delagreverie H, Salmona M, de Castro N, Chaix ML, Molina JM, Delaugerre C. Ultra-deep sequencing improves the detection of drug resistance in cellular DNA from HIV-infected patients on ART with suppressed viraemia. J Antimicrob Chemother 2019; 73:3122-3128. [PMID: 30137335 DOI: 10.1093/jac/dky315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
Background Standard genotypic tests performed on HIV DNA from patients on suppressive ART, with previous resistance-associated mutations (RAMs) detected in their plasma, underestimate resistance. We thus compared ultra-deep sequencing (UDS) with bulk sequencing of DNA to detect RAMs previously identified in plasma. Methods We sequenced the DNA of 169 highly treatment experienced patients with suppressed viraemia (ANRS 138-EASIER trial). Protease (PR) and reverse transcriptase (RT) genes from HIV DNA were sequenced by bulk sequencing and UDS, comparing 1% and 20% as thresholds of detection for UDS. Results Patients were highly treatment experienced (13.6 years). UDS of DNA was successful for the RT and PR genes in 133 (79%) and 137 (81%) patients, respectively. The detection of RAMs was similar by bulk sequencing and UDS with a 20% cut-off. However, the detection of RAMs by UDS with a 1% cut-off was significantly higher than that of bulk sequencing for RT codons D67N (65.4% versus 52.3%), M184V (66.2% versus 52.3%), L210W (48.9% versus 36.4%) and T215Y (57.9% versus 42.1%) and PR codons M46I (46% versus 26%), I54L (12.4% versus 3.9%), V82A (44.5% versus 29.9%) and L90M (57.7% versus 42.5%). Conclusions Genotypic resistance testing of cellular HIV DNA of well-controlled patients should use UDS technology with a sensitivity threshold of 1% to improve the detection of the resistant reservoir.
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Affiliation(s)
- Christophe Rodriguez
- Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France
- Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France
| | - Marie Laure Nere
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | - Vanessa Demontant
- Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France
- Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France
| | | | - Mélanie Mercier-Darty
- Laboratoire de Virologie, Hôpital Henri Mondor, APHP, Créteil, France
- Université Paris Est Créteil, UPEC, U955 Inserm, Créteil, France
| | - Héloïse Delagreverie
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | - Maud Salmona
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | | | - Marie Laure Chaix
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
| | - Jean Michel Molina
- Université Paris Diderot, Inserm U941, Paris, France
- Maladies infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Constance Delaugerre
- Laboratoire de Virologie, Hôpital Saint-Louis, APHP, Paris, France
- Université Paris Diderot, Inserm U941, Paris, France
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26
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Rodriguez C, Soulier A, Demontant V, Poiteau L, Mercier-Darty M, Bouvier-Alias M, Pawlotsky JM, Chevaliez S. A novel standardized deep sequencing-based assay for hepatitis C virus genotype determination. Sci Rep 2018; 8:4180. [PMID: 29520035 PMCID: PMC5843601 DOI: 10.1038/s41598-018-22614-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) genotype and subtype (1a/1b) identification is needed to tailor anti-HCV therapy. Currently available methods accurately identify the genotype and differentiate subtypes 1a from 1b. However, these assays have not been designed to identify other HCV subtypes, nor to recognize mixed genotype/subtype infections, emphasizing the need for a high-resolution system based on phylogenetic analysis of reads obtained by deep sequencing of a relevant genome region. The aim of this study was to evaluate the performance of the Sentosa SQ HCV Genotyping Assay, a novel deep sequencing-based assay targeting the HCV nonstructural 5B (NS5B) region, in clinical samples from patients with an indication for anti-HCV therapy. A high concordance rate with Sanger sequencing of the NS5B region, the reference method, was found for genotype 1 to 6 determination, 1a/1b subtype identification, and genotype 4, 5 and 6 subtyping. Discrepancies were seen essentially for HCV genotype 2 subtyping. Overall, the performance of the deep sequencing-based assay in generating the genotypes/subtype information needed to tailor anti-HCV treatment was adequate in this study. Further improvements, such as a longer NS5B fragment analyzed and enriching the database of reference prototype strains used for subtype assignment would make it a method of choice for HCV genotyping and subtyping for future clinical practice and research.
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Affiliation(s)
- Christophe Rodriguez
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Alexandre Soulier
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Vanessa Demontant
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Lila Poiteau
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Mélanie Mercier-Darty
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Magali Bouvier-Alias
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Stéphane Chevaliez
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.
- INSERM, U955, Créteil, France.
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27
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Audo I, El Shamieh S, Méjécase C, Michiels C, Demontant V, Antonio A, Condroyer C, Boyard F, Letexier M, Saraiva JP, Blanchard S, Mohand-Saïd S, Sahel JA, Zeitz C. ARL2BP mutations account for 0.1% of autosomal recessive rod-cone dystrophies with the report of a novel splice variant. Clin Genet 2017; 92:109-111. [PMID: 27790702 DOI: 10.1111/cge.12909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 11/28/2022]
Abstract
We report a novel ARL2BP splice site mutation after whole-exome sequencing (WES) applied to a Moroccan family including two sisters affected with autosomal recessive rod-cone dystrophy (arRCD). Subsequent analysis of 844 index cases did not reveal further pathogenic chances in ARL2BP indicating that mutations in ARL2B are a rare cause of arRCD (about 0.1%) in a large cohort of French patients.
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Affiliation(s)
- I Audo
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,University College London Institute of Ophthalmology, London, UK
| | - S El Shamieh
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - C Méjécase
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - C Michiels
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - V Demontant
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - A Antonio
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - C Condroyer
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | - F Boyard
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | | | | | - S Mohand-Saïd
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - J-A Sahel
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,University College London Institute of Ophthalmology, London, UK.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences-Institut de France, Paris, France
| | - C Zeitz
- Department of Genetics, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Institut de la Vision, Paris, France
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