المؤلفون: Diallo, Amadou Daye, Desfeux, Victor, Stolowy, Natacha, L'Ollivier, Coralie, Javelle, Emilie, David, Thierry, Cassir, Nadim

المساهمون: Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix-Marseille Université - École de médecine (AMU SMPM MED), Aix-Marseille Université - Faculté des sciences médicales et paramédicales (AMU SMPM), Aix Marseille Université (AMU)-Aix Marseille Université (AMU), Ophtalmologie Hôpital de la Timone - APMH, Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Hôpital de la Timone CHU - APHM (TIMONE), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées Brétigny-sur-Orge (IRBA), Service de Santé des Armées, Département de recherche sur les Procédés et Matériaux pour les Environnements complexes (DPME), Institut des Sciences et technologies pour une Economie Circulaire des énergies bas carbone (ISEC), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

المصدر: ISSN: 1477-8939 ; Travel Medicine and Infectious Disease ; https://amu.hal.science/hal-04279285Test ; Travel Medicine and Infectious Disease, 2023, 55, pp.102643. ⟨10.1016/j.tmaid.2023.102643⟩.

مصطلحات موضوعية: Malaria, Retinal ischemia, Cerebral malaria, Malarial retinopathy, Plasmodium falciparum, Travel medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology

الوصف: International audience

العلاقة: hal-04279285; https://amu.hal.science/hal-04279285Test; https://amu.hal.science/hal-04279285/documentTest; https://amu.hal.science/hal-04279285/file/1-s2.0-S1477893923001035-main.pdfTest

الإتاحة: https://doi.org/10.1016/j.tmaid.2023.102643Test
https://amu.hal.science/hal-04279285Test
https://amu.hal.science/hal-04279285/documentTest
https://amu.hal.science/hal-04279285/file/1-s2.0-S1477893923001035-main.pdfTest

المؤلفون: Achache, Wafaa, Boualam, Mahmoud, A, Cassir, Nadim, Mimari, Clémence, Poitrenaud, Delphine, Mezouar, Soraya, Mège, Jean, Louis, Drancourt, Michel, Lepidi, Hubert

المساهمون: Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix-Marseille Université - École de médecine (AMU SMPM MED), Aix-Marseille Université - Faculté des sciences médicales et paramédicales (AMU SMPM), Aix Marseille Université (AMU)-Aix Marseille Université (AMU), Centre hospitalier d'Ajaccio, Institut universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)

المصدر: ISSN: 2076-0817 ; Pathogens ; https://amu.hal.science/hal-04509468Test ; Pathogens, 2023, 12 (12), pp.1413. ⟨10.3390/pathogens12121413⟩.

مصطلحات موضوعية: larynx, tuberculosis, granuloma, Mycobacterium tuberculosis, laryngitis, extrapulmonary tuberculosis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology

الوصف: International audience ; Laryngeal tuberculosis is a rare form of extrapulmonary tuberculosis that questions the natural history of this infection. We report one such case in which a pathological examination of a laryngeal biopsy revealed granulomatous inflammation with caseous necrosis. Further investigations combining immunofluorescence detection of macrophages and in situ hybridization of Mycobacterium tuberculosis indicated the presence of Mycobacterium tuberculosis (M. tuberculosis) in laryngeal granulomatous inflammatory lesions. This observation suggests that the natural history of laryngeal tuberculosis does not differ from that of other forms, guiding early diagnosis in patients with laryngeal lesions to ensure appropriate check-ups and treatment.

العلاقة: hal-04509468; https://amu.hal.science/hal-04509468Test; https://amu.hal.science/hal-04509468/documentTest; https://amu.hal.science/hal-04509468/file/pathogens-12-01413.pdfTest

الإتاحة: https://doi.org/10.3390/pathogens12121413Test
https://amu.hal.science/hal-04509468Test
https://amu.hal.science/hal-04509468/documentTest
https://amu.hal.science/hal-04509468/file/pathogens-12-01413.pdfTest

المؤلفون: Boxberger, Manon, Magnien, Sibylle, Antezack, Angeline, Rolland, Clara, Makoa Meng, Marine, Lo, Cheikh, Ibrahima, La Scola, Bernard, Cassir, Nadim

المساهمون: Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix-Marseille Université - Faculté d'odontologie (AMU ODONTO), Aix Marseille Université (AMU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées Brétigny-sur-Orge (IRBA), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010)

المصدر: ISSN: 2076-2607 ; Microorganisms ; https://amu.hal.science/hal-04462954Test ; Microorganisms, 2023, 11 (10), pp.2535. ⟨10.3390/microorganisms11102535⟩.

مصطلحات موضوعية: culturomics, human skin microbiota, new species, Leucobacter, bacteria, taxonogenomics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology

الوصف: International audience ; Extending our knowledge on human skin microbiota is a challenge to better decipher its role in health and disease. Using the culturomics method, we isolated strain Marseille-Q4368 from the healthy forehead of a 59-year-old woman. We describe here the main characteristics of this bacterium using a taxonogenomic approach. This new bacterial species is Gram-positive, non-motile, and non-spore-forming. Its 16S rRNA sequence exhibited a similarity of 99.59% with Leucobacter chromiiresistens, the most closely related species in terms of nomenclature. However, a digital DNA–DNA hybridization analysis between these two species revealed a maximum identity similarity of only 27.5%. We found phenotypical and genomic differences between strain Marseille-Q4368 and its closely related species. These findings underscore the classification of this bacterium as a distinct species. Hence, we propose the name Leucobacter manosquensis sp. nov. strain Marseille-Q4368 (=CSUR Q4368 = DSM 112403) for this newly identified bacterial species.

العلاقة: hal-04462954; https://amu.hal.science/hal-04462954Test; https://amu.hal.science/hal-04462954/documentTest; https://amu.hal.science/hal-04462954/file/microorganisms-11-02535.pdfTest

الإتاحة: https://doi.org/10.3390/microorganisms11102535Test
https://amu.hal.science/hal-04462954Test
https://amu.hal.science/hal-04462954/documentTest
https://amu.hal.science/hal-04462954/file/microorganisms-11-02535.pdfTest

المؤلفون: Levêque, Manon, Cassir, Nadim, Mathias, Fanny, Fevre, Cindy, Daviet, Florence, Bermudez, Julien, Brioude, Geoffrey, Peyron, Florence, Reynaud-Gaubert, Martine, Coiffard, Benjamin

المصدر: Infection and Drug Resistance ; volume Volume 16, page 4265-4271 ; ISSN 1178-6973

الإتاحة: https://doi.org/10.2147/idr.s413900Test
https://www.dovepress.com/getfile.php?fileID=90840Test

المؤلفون: Beudet, Hugues, L’Ollivier, Coralie, Bouabdallah, Reda, Campana, Fabrice, Bagonchy, Anaïs, Lepidi, Hubert, Parola, Philippe, Cassir, Nadim

المصدر: Travel Medicine and Infectious Disease ; volume 52, page 102519 ; ISSN 1477-8939

مصطلحات موضوعية: Infectious Diseases, Public Health, Environmental and Occupational Health

الإتاحة: https://doi.org/10.1016/j.tmaid.2022.102519Test
https://api.elsevier.com/content/article/PII:S1477893922002654?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S1477893922002654?httpAccept=text/plainTest

المؤلفون: Cassir, Nadim

مرشدي الرسالة: Aix-Marseille, La Scola, Bernard

مصطلحات موضوعية: Microbiote digestif, Entérocolite nécrosante, Clostridium butyricum, Microbiote cutané, Infections nosocomiales, Réanimation, Gut microbiota, Necrotizing enterocolitis, Skin microbiota, Healthcare associated infections, Intensive care unit, Gramnegative bacteria

الوصف: Le microbiote digestif humain joue un rôle essentiel et bénéfique pour son hôte mais il est également impliqué dans un nombre croissant de pathologies. Les connaissances sur la composition de cet écosystème ont récemment été révolutionnées grâce à l’utilisation de techniques moléculaires. Cependant, ces techniques comportent des limites importantes. C’est ainsi que le concept de « culturomique » a été introduit ; il consiste en la multiplication de milieux et conditions de culture et l’identification rapide de colonies bactériennes par spectrométrie de masse (MALDITOF) ou par amplification et séquençage du gène de l’ARN ribosomal 16S. Dans la première partie de ce travail, nous avons mis en évidence une association entre la présence de Clostridium butyricum dans les selles et la survenue d’entérocolite ulcéro-nécrosante que ce soit par méthodes de pyroséquençage et culture ou par PCR quantitative en temps réel spécifique de C. butyricum; identifié après séquençage du génome complet de toutes nos souches de C. butyricum, la présence du gène de la β-hémolysine (toxine). Dans la deuxième partie de ce travail, nous avons montré par cuturomique que les bactéries à Gram-négatif (BGN) étaient fréquemment disséminées au sein du microbiote cutané transitoire des patients hospitalisés en réanimation ; le réservoir serait essentiellement digestif. En conclusion, le microbiote digestif constitue un réservoir sousestimé de bactéries pathogènes. La microbiologie moderne incluant les nouvelles méthodes de culture permet d’étendre de manière considérable les connaissances sur la composition de cet écosystème et son implication en pathologie humaine.
He human gut microbiota plays an important and beneficial role in its host but it is also involved in a growing number of diseases. Knowledge of the composition of this ecosystem have recently been revolutionized by the use of molecular techniques. However, these techniques have significant limitations. Thus, the concept of "culturomics" has been introduced; it consists of the multiplication of culture conditions and the rapid identification of bacterial colonies by mass spectrometry (MALDI-TOF) or by PCR 16S RNA gene sequencing. In the first part of this work, we have demonstrated an association between the presence of Clostridium butyricum in the stool and the occurrence of necrotizing enterocolitis whether by pyrosequencing methods and Culture or by quantitative PCR specific real time C. butyricum; identified after sequencing the complete genome of all our strains of C. butyricum, the presence of the gene of β-hemolysin (toxin). In the second part of this work, we showed by cuturomics that Gram-negative bacteria (BGN) were frequently spread out over the transitional skin microbiota of patients hospitalized in intensive care; the reservoir would essentially digestive. In conclusion, the gut microbiota is an underestimated reservoir of pathogenic bacteria. Modern microbiology including new culture-based methods is currently extending exponentially our knowledge on gut microbiota giving rise to new insights into the pathogenesis or the transmission of infectious diseases.

الإتاحة: http://www.theses.fr/2015AIXM5038/documentTest

المؤلفون: Bes-Berlandier, Hugo, Coiffard, Benjamin, Bermudez, Julien, Demazes-dufeu, Nadine, Coltey, Bérengère, Boschi, Céline, Colson, Philippe, Hraiech, Sami, Reynaud-Gaubert, Martine, Cassir, Nadim

المصدر: BMC Infectious Diseases; 5/28/2024, Vol. 24 Issue 1, p1-9, 9p

مصطلحات موضوعية: LUNG transplantation, COVID-19, CHRONIC kidney failure, IMMUNOSUPPRESSION, HIERARCHICAL clustering (Cluster analysis)

مستخلص: Background: The aim of this study was to assess the impact of immunosuppression management on coronavirus disease 2019 (COVID-19) outcomes. Methods: We performed a single-center retrospective study in a cohort of 358 lung transplant recipients (LTx) over the period from March 2020 to April 2022. All included symptomatic patients had at least one positive SARS-CoV-2 rt-PCR. We used a composite primary outcome for COVID-19 including increased need for oxygen since the hospital admission, ICU transfer, and in-hospital mortality. We assessed by univariate and multivariate analyses the risk factors for poor outcomes. Results: Overall, we included 91 LTx who contracted COVID-19. The COVID-19 in-hospital mortality rate reached 4.4%. By hierarchical clustering, we found a strong and independent association between the composite poor outcome and the discontinuation of at least one immunosuppressive molecule among tacrolimus, cyclosporine, mycophenolate mofetil, and everolimus. Obesity (OR = 16, 95%CI (1.96; 167), p = 0.01) and chronic renal failure (OR = 4.6, 95%CI (1.4; 18), p = 0.01) were also independently associated with the composite poor outcome. Conversely, full vaccination was protective (OR = 0.23, 95%CI (0.046; 0.89), p = 0.047). Conclusion: The administration of immunosuppressive drugs such as tacrolimus, cyclocporine or everolimus can have a protective effect in LTx with COVID-19, probably related to their intrinsic antiviral capacity. [ABSTRACT FROM AUTHOR]

: Copyright of BMC Infectious Diseases is the property of BioMed Central and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

المؤلفون: Levêque,Manon, Cassir,Nadim, Mathias,Fanny, Fevre,Cindy, Daviet,Florence, Bermudez,Julien, Brioude,Geoffrey, Peyron,Florence, Reynaud-Gaubert,Martine, Coiffard,Benjamin

مصطلحات موضوعية: Infection and Drug Resistance

الوصف: Manon Levêque,1 Nadim Cassir,2 Fanny Mathias,3 Cindy Fevre,4 Florence Daviet,5 Julien Bermudez,1 Geoffrey Brioude,6 Florence Peyron,3 Martine Reynaud-Gaubert,1 Benjamin Coiffard1 1Department of Respiratory Medicine and Lung Transplantation, APHM, Aix Marseille University, Hôpital Nord, Marseille, France; 2Department of Infectious Disease, APHM, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France; 3Department of Pharmacy, APHM, Aix Marseille University, Hôpital Nord, Marseille, France; 4Research and Development, Pherecydes Pharma, Romainville, France; 5Intensive Care Medicine, APHM, Aix Marseille University, Hôpital Nord, Marseille, France; 6Department of Thoracic Surgery and Lung Transplantation, APHM, Aix Marseille University, Hôpital Nord, Marseille, FranceCorrespondence: Benjamin Coiffard, Department of Respiratory Medicine and Lung Transplantation, APHM, CHU Nord, Chemin des Bourrely, Marseille, 13915, France, Tel +33491966133, Email benjamin.coiffard@ap-hm.frAbstract: Recipients transplanted for bronchiectasis in the context of a primary immune deficiency, such as common variable immunodeficiency, are at a high risk of severe infection in post-transplantation leading to poorer long-term outcomes than other transplant indications. In this report, we present a fatal case due to chronic Pseudomonas aeruginosa bronchopulmonary infection in a lung transplant recipient with common variable immunodeficiency despite successful eradication of an extensively drug-resistant (XDR) strain with IgM/IgA-enriched immunoglobulins and bacteriophage therapy. The fatal evolution despite a drastic adaptation of the immunosuppressive regimen and the maximal antibiotic therapy strategy raises the question of the contraindication of lung transplantation in such a context of primary immunodeficiency.Keywords: primary immunodeficiency diseases, lung transplantation, Pseudomonas aeruginosa, phage therapy, immunoglobulin therapy

وصف الملف: text/html

العلاقة: https://www.dovepress.com/refractory-pseudomonas-aeruginosa-bronchopulmonary-infection-after-lun-peer-reviewed-fulltext-article-IDRTest

الإتاحة: https://doi.org/10.2147/IDR.S413900Test
https://www.dovepress.com/refractory-pseudomonas-aeruginosa-bronchopulmonary-infection-after-lun-peer-reviewed-fulltext-article-IDRTest

المؤلفون: Delandre, Océane, Cassir, Nadim Shams, Taudon, Nicolas, Mosnier, Joel, Fonta, Isabelle, Benoit, Nicolas, Amalvict, Remy, Linard, Cyril, Jumpertz, Marie, L’Ollivier, Coralie, Bogreau, Hervé, Pradines, Bruno, Javelle, Emilie

المساهمون: French Institute for Public Health Surveillance, CNR Paludisme

المصدر: Journal of Travel Medicine ; volume 31, issue 3 ; ISSN 1195-1982 1708-8305

مصطلحات موضوعية: General Medicine

الوصف: We report a late dihydroartemisinin–piperaquine treatment failure of uncomplicated Plasmodium falciparum malaria infection in a traveller without evidence of drug resistance. The correct treatment intake was confirmed, isolates drugs susceptibility was confirmed by RSA-PSA and chemosusceptibility. No molecular markers associated with resistance to artemisinin derivatives or piperaquine were identified.

الإتاحة: https://doi.org/10.1093/jtm/taae043Test
https://academic.oup.com/jtm/article-pdf/31/3/taae043/57174580/taae043.pdfTest

المؤلفون: Scola, Bernard La, Hikmat, Houmadi, Targa, Lorlane Le, Boschi, Celine, PY, Justine, BEDOTTO, Marielle, Morand, Aurélie, Cassir, Nadim, Aherfi, Sarah, Colson, Philippe

الوصف: The diversity and evolution of the genomes of Human Bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients’s nasopharyngeal samples collected between 2017-2022 period (five years). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypes determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotype α tended to be significantly correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

الإتاحة: https://doi.org/10.22541/au.171260859.95768333/v1Test