1
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Ghez N, Mazenq J, Bosdure E, Dubourg G, Morand A, Dubus JC. Real-life requests for Bordetella polymerase chain reaction testing in children presenting to hospital. Arch Pediatr 2021; 29:72-74. [PMID: 34848130 DOI: 10.1016/j.arcped.2021.11.003] [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: 06/18/2020] [Revised: 09/07/2021] [Accepted: 11/06/2021] [Indexed: 12/01/2022]
Abstract
From 2015 to 2017, 3197 interpretable Bordetella polymerase chain reaction (PCR) tests were performed for 2760 children presenting to our tertiary university hospital. Requests mainly came from the emergency department (62%) and for children older than 1 year (68%). Only 32 PCR (1%) results were positive, mainly in children younger than 1 year (n = 29/32, 90.6%; p<0.001). When focusing on the PCR indications in 2017, we found the requests were mainly based on nonspecific respiratory symptoms and were clinically unjustified in 383 cases (39%). Pediatricians overused Bordetella PCR in clinical practice. They should reserve their requests for cases of young children with symptoms suggestive of respiratory illness and/or incomplete pertussis immunization.
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Affiliation(s)
- N Ghez
- Pediatric Pulmonology Department, Timone Hospital for Children, 264 rue Saint Pierre, Marseille 13385, France
| | - J Mazenq
- Pediatric Pulmonology Department, Timone Hospital for Children, 264 rue Saint Pierre, Marseille 13385, France
| | - E Bosdure
- Pediatric Pulmonology Department, Timone Hospital for Children, 264 rue Saint Pierre, Marseille 13385, France
| | - G Dubourg
- Aix Marseille University, IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - A Morand
- Pediatric Pulmonology Department, Timone Hospital for Children, 264 rue Saint Pierre, Marseille 13385, France; Aix Marseille University, IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - J C Dubus
- Pediatric Pulmonology Department, Timone Hospital for Children, 264 rue Saint Pierre, Marseille 13385, France; Aix Marseille University, IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France.
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2
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Million M, Gautret P, Colson P, Roussel Y, Dubourg G, Chabriere E, Honore S, Rolain JM, Fenollar F, Fournier PE, Lagier JC, Parola P, Brouqui P, Raoult D. Clinical efficacy of chloroquine derivatives in COVID-19 infection: comparative meta-analysis between the big data and the real world. New Microbes New Infect 2020; 38:100709. [PMID: 33088574 PMCID: PMC7558783 DOI: 10.1016/j.nmni.2020.100709] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 05/08/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 12/23/2022] Open
Abstract
In the context of the current coronavirus disease 2019 (COVID-19) pandemic, we conducted a meta-analysis on the effects of chloroquine derivatives in patients, based on unpublished and published reports available publicly on the internet as of 27 May 2020. The keywords 'hydroxychloroquine', 'chloroquine', 'coronavirus', 'COVID-19' and 'SARS-Cov-2' were used in the PubMed, Google Scholar and Google search engines without any restrictions as to date or language. Twenty studies were identified involving 105 040 patients (19 270 treated patients) from nine countries (Brazil, China, France, Iran, Saudi Arabia, South Korea, Spain and the USA). Big data observational studies were associated with conflict of interest, lack of treatment dosage and duration, and absence of favourable outcome. Clinical studies were associated with favourable outcomes and details on therapy. Among clinical studies, three of four randomized controlled trials reported a significant favourable effect. Among clinical studies, a significant favourable summary effect was observed for duration of cough (OR 0.19, p 0.00003), duration of fever (OR 0.11, p 0.039), clinical cure (OR 0.21, p 0.0495), death (OR 0.32, p 4.1 × 10-6) and viral shedding (OR 0.43, p 0.031). A trend for a favourable effect was noted for the outcome 'death and/or intensive care unit transfer' (OR 0.29, p 0.069) with a point estimate remarkably similar to that observed for death (∼0.3). In conclusion, a meta-analysis of publicly available clinical reports demonstrates that chloroquine derivatives are effective to improve clinical and virological outcomes, but, more importantly, they reduce mortality by a factor of 3 in patients with COVID-19. Big data are lacking basic treatment definitions and are linked to conflict of interest. The retraction of the only big data study associated with a significantly deleterious effect the day after (June 5, 2020) the acceptance of the present work (June 4, 2020) confirms the relevance of this work.
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Affiliation(s)
- M. Million
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - P. Gautret
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P. Colson
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - Y. Roussel
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - G. Dubourg
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - E. Chabriere
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - S. Honore
- Service de Pharmacie, Hôpital Timone, AP-HM, Marseille, France
- Laboratoire de Pharmacie Clinique, Aix Marseille Université, Marseille, France
| | - J.-M. Rolain
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - J.-C. Lagier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - P. Parola
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P. Brouqui
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
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3
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Afouda P, Dubourg G, Tomeï E, Raoult D, Fournier PE. Dialister massiliensis sp. nov., a new bacterium isolated from the human gut. New Microbes New Infect 2020; 34:100657. [PMID: 32194963 PMCID: PMC7075989 DOI: 10.1016/j.nmni.2020.100657] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/02/2020] [Accepted: 02/10/2020] [Indexed: 12/22/2022] Open
Abstract
Dialister massiliensis strain Marseille-P5638T (= CSUR P5638) is a new species from the genus Dialister and family Veillonellaceae which was isolated from the gut microbiota of a healthy individual.
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Affiliation(s)
- P Afouda
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - E Tomeï
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Special Infections Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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4
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Afouda P, Dubourg G, Nguyen TT, Raoult D, Fournier PE. Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. New Microbes New Infect 2020; 34:100645. [PMID: 32071725 PMCID: PMC7011079 DOI: 10.1016/j.nmni.2019.100645] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/27/2019] [Indexed: 12/20/2022] Open
Abstract
Pseudoruminococcus massiliensis strain Marseille-P3876T (= CSUR P3876) is a new genus from the family Ruminococcaceae that was isolated from the gut microbiota of a healthy Senegalese man.
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Affiliation(s)
- P Afouda
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - G Dubourg
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - T T Nguyen
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Special Infections Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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5
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Diallo O, Baron S, Jimeno M, Abat C, Dubourg G, Chaudet H, Raoult D, Rolain J. Hospital mortality and positive blood culture with Difficult-to threat (DTR), Marseille, France. J Infect Public Health 2020. [DOI: 10.1016/j.jiph.2020.01.035] [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: 10/25/2022] Open
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6
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Baron S, Cassir N, Hamel M, Hadjadj L, Saidani N, Dubourg G, Rolain J. Colistin-resistant Klebsiella pneumoniae ST307 clone: Epidemiological, risk factors and massive molecular analysis of bacterial genomes linked to an outbreak in Marseille, France. J Infect Public Health 2020. [DOI: 10.1016/j.jiph.2020.01.036] [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: 11/28/2022] Open
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7
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Bilen M, Cadoret F, Dubourg G, Fournier PE, Daoud Z, Raoult D. Corrigendum to 'Phoenicibacter congonensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman. New Microbes New Infect 2019; 30:100553. [PMID: 31061712 DOI: 10.1016/j.nmni.2019.100553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
[This corrects the article DOI: 10.1016/j.nmni.2017.04.003.].
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Affiliation(s)
- M Bilen
- Aix-Marseille Université, MEPHI, IHU Méditerranée-Infection, Marseille, France.,Clinical Microbiology Laboratory, Saint George University Hospital, Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - F Cadoret
- Aix-Marseille Université, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Z Daoud
- Clinical Microbiology Laboratory, Saint George University Hospital, Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - D Raoult
- Aix-Marseille Université, MEPHI, IHU Méditerranée-Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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8
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Mbogning Fonkou MD, Bilen M, Gouba N, Khelaifia S, Cadoret F, Nguyen TT, Richez M, Bittar F, Fournier PE, Raoult D, Dubourg G. Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum. New Microbes New Infect 2019; 29:100532. [PMID: 31011427 PMCID: PMC6461582 DOI: 10.1016/j.nmni.2019.100532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 11/08/2018] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Enterococcus timonensis sp. nov., strain Marseille-P2817T, is a facultatively anaerobic, motile and non-spore-forming Gram-positive coccus which was isolated from the sputum of a healthy adult man in Marseilles. We present herein its phenotypic description together with MALDI-TOF (matrix-assisted laser-desorption/ionization time-of-flight) mass spectrometry analysis and genome sequencing and comparison. The genome of Enterococcus timonensis is 2 123 933 bp long with 38.46 mol% of G+C content, and it contains 1983 protein-coding genes and 65 RNA genes (including nine rRNA genes).
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Affiliation(s)
- M D Mbogning Fonkou
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - M Bilen
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - N Gouba
- Institut Supérieur des Sciences de La Santé (INSSA), Université Polytechnique de Bobo Dioulasso, Burkina Faso
| | - S Khelaifia
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - F Cadoret
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - T T Nguyen
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - M Richez
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - F Bittar
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - P-E Fournier
- Aix Marseille Univ, IRD, VITROME, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - D Raoult
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
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9
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Togo AH, Diop A, Dubourg G, Khelaifia S, Richez M, Armstrong N, Maraninchi M, Fournier PE, Raoult D, Million M. Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery. New Microbes New Infect 2019; 29:100508. [PMID: 30891246 PMCID: PMC6403417 DOI: 10.1016/j.nmni.2019.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 12/26/2018] [Accepted: 01/15/2019] [Indexed: 12/30/2022] Open
Abstract
A new bacterium, strain AT3T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565T = CCUG 45055T = CIP 107754T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3T = CSUR P2007T = DSM 100567T.
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Affiliation(s)
- A H Togo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - A Diop
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Université, IRD, VITROME, France
| | - G Dubourg
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - S Khelaifia
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - M Richez
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - N Armstrong
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - M Maraninchi
- Aix-Marseille Université, NORT 'Nutrition, Obesity and Risk of Thrombosis,' INSERM1062, INRA1260, Marseille, France
| | | | - D Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - M Million
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
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10
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Ndongo S, Beye M, Dubourg G, Nguyen TT, Couderc C, Fabrizio DP, Fournier PE, Raoult D, Angelakis E. Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces. New Microbes New Infect 2018; 26:63-72. [PMID: 30258635 PMCID: PMC6154774 DOI: 10.1016/j.nmni.2018.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/12/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022] Open
Abstract
Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%.
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Affiliation(s)
- S Ndongo
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - M Beye
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - T T Nguyen
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - C Couderc
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - D P Fabrizio
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E Angelakis
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
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11
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Al-Bayssari C, Dubourg G, Cimmino T, Okdah L, Mathlouthi N, Nguyen TT, Andrieu C, Rathored J, Fournier PE, Raoult D, Rolain JM. Genome sequence and description of Paenibacillus ihuae strain GD6 sp. nov., isolated from the stool of a 62-year-old Frenchman. New Microbes New Infect 2018; 23:77-82. [PMID: 29692909 PMCID: PMC5913357 DOI: 10.1016/j.nmni.2018.02.010] [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] [Received: 08/31/2017] [Revised: 02/14/2018] [Accepted: 02/20/2018] [Indexed: 11/30/2022] Open
Abstract
Paenibacillus ihuae strain GD6 (=CSUR P892 = DSMZ 45751T) is the new type strain collected from the stool of a 69-year-old Frenchman admitted to an intensive care unit and receiving a 10-day course of imipenem at the time of stool collection. This is a Gram-positive, facultative anaerobic, rod-shaped bacterium. We describe here the features of this organism, together with its complete genome sequence and annotation. The genome size is 6 719 043 bp with 49.6% G+C content and contains 6211 protein-coding and 65 sRNA genes, including four 5S rRNA genes, one 16S rRNA gene and one 23S rRNA gene.
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Affiliation(s)
- C Al-Bayssari
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - G Dubourg
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - T Cimmino
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - L Okdah
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - N Mathlouthi
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - T T Nguyen
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - C Andrieu
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - J Rathored
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - J-M Rolain
- Aix-Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
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12
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Dubourg G, Lamy B, Ruimy R. Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result. Clin Microbiol Infect 2018; 24:935-943. [PMID: 29605563 DOI: 10.1016/j.cmi.2018.03.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [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: 12/29/2017] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection. AIMS We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing. SOURCES A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source. CONTENT Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered. IMPLICATIONS The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.
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Affiliation(s)
- G Dubourg
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France.
| | - B Lamy
- Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France; Faculté de Médecine, Université Côte d'Azur, Nice, France
| | - R Ruimy
- Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France; Faculté de Médecine, Université Côte d'Azur, Nice, France.
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13
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Bilen M, Founkou MDM, Cadoret F, Dubourg G, Daoud Z, Raoult D. Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples. New Microbes New Infect 2018; 24:21-25. [PMID: 29922471 PMCID: PMC6004731 DOI: 10.1016/j.nmni.2018.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 02/09/2018] [Revised: 03/05/2018] [Accepted: 03/09/2018] [Indexed: 02/06/2023] Open
Abstract
We present the description of Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.
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Affiliation(s)
- M Bilen
- Aix Marseille Univ, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | | | - F Cadoret
- Assistance Publique Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection, Marseille, France
| | - G Dubourg
- Aix Marseille Univ, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Z Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - D Raoult
- Aix Marseille Univ, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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14
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Afouda P, Dubourg G, Cadoret F, Fournier P, Raoult D. ‘ Massilimalia timonensis ’ sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol. New Microbes New Infect 2018; 21:86-87. [PMID: 29379603 PMCID: PMC5785910 DOI: 10.1016/j.nmni.2017.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/14/2017] [Accepted: 10/26/2017] [Indexed: 11/06/2022] Open
Abstract
We describe the main characteristics of a new bacterial species ‘Massilimalia timonensis’ sp. nov. The type strain Marseille-P3753T (=CSUR P3753) was isolated from the stool of a healthy Senegalese man.
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15
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Dubourg G, Katona J, Rodović M, Savić S, Kitic G, Niarchos G, Jancović N, Crnojević-Bengin V. Flexible and highly sensitive humidity sensors using screen-printed TiO2 nanoparticles as sensitive layer. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1742-6596/939/1/012008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Fonkou MM, Bilen M, Cadoret F, Fournier PE, Dubourg G, Raoult D. 'Enterococcus timonensis' sp. nov., 'Actinomyces marseillensis' sp. nov., 'Leptotrichia massiliensis' sp. nov., 'Actinomyces pacaensis' sp. nov., 'Actinomyces oralis' sp. nov., 'Actinomyces culturomici' sp. nov. and 'Gemella massiliensis' sp. nov., new bacterial species isolated from the human respiratory microbiome. New Microbes New Infect 2017; 22:37-43. [PMID: 29556407 PMCID: PMC5857164 DOI: 10.1016/j.nmni.2017.12.005] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
We report the main characteristics of ‘Enterococcus timonensis’ strain Marseille-P2817T (CSUR P2817), ‘Leptotrichia massiliensis’ sp. nov., strain Marseille-P3007T (CSUR P3007), ‘Actinomyces marseillensis’ sp. nov., strain Marseille-P2818T (CSUR P2818), ‘Actinomyces pacaensis’ sp. nov., strain Marseille-P2985T (CSUR P2985), ‘Actinomyces oralis’ sp. nov., strain Marseille-P3109T (CSUR P3109), ‘Actinomyces culturomici’ sp. nov., strain Marseille-P3561T (CSUR P3561) and ‘Gemella massiliensis’ sp. nov., strain Marseille-P3249T (CSUR P3249) which were isolated from human sputum samples.
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Affiliation(s)
- M.D. Mbogning Fonkou
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - M. Bilen
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - G. Dubourg
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding author: D. Raoult, Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS 7278, IRD 198, INSERM 1095, UM63, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille cedex 5, FranceAix-Marseille UniversitéUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE)CNRS 7278IRD 198INSERM 1095UM63Institut Hospitalo-Universitaire Méditerranée-InfectionFaculté de médecine27 Boulevard Jean MoulinMarseille cedex 513385France
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17
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Bichon A, Aubry C, Dubourg G, Drouet H, Lagier JC, Raoult D, Parola P. Escherichia coli spontaneous community-acquired meningitis in adults: A case report and literature review. Int J Infect Dis 2017; 67:70-74. [PMID: 29225070 DOI: 10.1016/j.ijid.2017.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 10/02/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/25/2022] Open
Abstract
Gram-negative bacillary meningitis occurring post-trauma and following neurosurgical procedures has been described widely. However, reports of spontaneous cases are sparse, particularly community-acquired cases. Spontaneous community-acquired Escherichia coli meningitis is a rare (although increasingly seen) and specific entity that is poorly reported in the literature. A review of the literature identified only 43 cases of community-acquired E. coli meningitis reported between 1946 and 2016. This article describes two new cases of spontaneous community-acquired E. coli meningitis encountered in Marseille, France, and presents the results of a literature review on spontaneous community-acquired E. coli meningitis.
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Affiliation(s)
- A Bichon
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - C Aubry
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - G Dubourg
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - H Drouet
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - J-C Lagier
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - D Raoult
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France
| | - P Parola
- Aix Marseille Université, CNRS 7278, IRD 198, INSERM 1095, AP-HM, URMITE, IHU Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385 Marseille, Cedex 5, France.
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18
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Bilen M, Cadoret F, Dubourg G, Fournier PE, Daoud Z, Raoult D. ' Phoenicibacter massiliensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman. New Microbes New Infect 2017; 19:43-44. [PMID: 28706722 PMCID: PMC5496386 DOI: 10.1016/j.nmni.2017.04.003] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 11/18/2022] Open
Abstract
This study supports the main characteristics of the new genus and new species 'Phoenicibacter massiliensis' strain Marseille-P3241T (CSUR P3241), a new bacterium isolated from a stool sample of a healthy 47-year-old pygmy woman.
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Affiliation(s)
- M. Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Clinical Microbiology Laboratory, Saint George University Hospital, Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - G. Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Z. Daoud
- Clinical Microbiology Laboratory, Saint George University Hospital, Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding author: D. Raoult, Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS 7278, IRD 198, INSERM 1095, UM63, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille cedex 5, France.Aix-Marseille UniversitéUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE)CNRS 7278IRD 198INSERM 1095UM63Institut Hospitalo-Universitaire Méditerranée-InfectionFaculté de médecine27 Boulevard Jean MoulinMarseille cedex 513385France
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19
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Ndongo S, Cadoret F, Dubourg G, Delerce J, Fournier PE, Raoult D, Lagier JC. ' Collinsella phocaeensis' sp. nov., ' Clostridium merdae' sp. nov., ' Sutterella massiliensis' sp. nov., ' Sutturella timonensis' sp. nov., ' Enorma phocaeensis' sp. nov., ' Mailhella massiliensis' gen. nov., sp. nov., ' Mordavella massiliensis' gen. nov., sp. nov. and ' Massiliprevotella massiliensis' gen. nov., sp. nov., 9 new species isolated from fresh stool samples of healthy French patients. New Microbes New Infect 2017; 17:89-95. [PMID: 28409003 PMCID: PMC5382032 DOI: 10.1016/j.nmni.2017.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 01/16/2017] [Revised: 02/20/2017] [Accepted: 02/27/2017] [Indexed: 12/22/2022] Open
Abstract
Here we report of summary of the characteristics of 'Collinsella phocaeensis' strain Marseille-P3245T sp. nov., 'Clostridium merdae' strain Marseille-P2953T, 'Sutterella massiliensis' strain Marseille-P2435T sp. nov., 'Sutturella timonensis' strain Marseille-P3282T sp. nov., 'Enorma phocaeensis' Marseille-P3242T sp. nov., 'Mailhella massiliensis' strain Marseille-P3199T gen. nov., sp. nov., 'Mordavella massiliensis' strain Marseille-P3246T sp. nov. and 'Massiliprevotella massiliensis' strain Marseille-P2439T sp. nov. isolated from fresh stool samples of healthy French patients.
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Affiliation(s)
- S Ndongo
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - J Delerce
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - J-C Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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20
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Bilen M, Cadoret F, Dubourg G, Daoud Z, Fournier PE, Raoult D. ' Raoultibacter timonensis' gen. nov., sp. nov. , a new bacterium isolated from the human gut of a Pygmy woman. New Microbes New Infect 2017; 16:45-46. [PMID: 28203374 PMCID: PMC5292757 DOI: 10.1016/j.nmni.2016.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 12/01/2016] [Revised: 12/16/2016] [Accepted: 12/23/2016] [Indexed: 10/25/2022] Open
Abstract
We report the main characteristics of a new species 'Raoultibacter timonensis' strain Marseille-P3277 (CSUR P3277), a new member of the genus Raoultibacter, that was isolated from a stool sample of a healthy 11-year-old Pygmy woman.
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Affiliation(s)
- M Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - F Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Z Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - P E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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21
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Bilen M, Cadoret F, Dubourg G, Daoud Z, Fournier PE, Raoult D. ‘Gabonibacter timonensis’ sp. nov., a new bacterium isolated from the human gut of a Pygmy woman. New Microbes New Infect 2017; 16:39-40. [PMID: 28179984 PMCID: PMC5279693 DOI: 10.1016/j.nmni.2016.12.017] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 12/16/2016] [Accepted: 12/23/2016] [Indexed: 11/17/2022] Open
Affiliation(s)
- M. Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
- Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G. Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Z. Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
- Corresponding author: D. Raoult, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.Aix-Marseille UniversitéURMITE, UM63, CNRS7278, IRD198, Inserm 1095Institut Hospitalo-Universitaire Méditerranée-InfectionFaculté de médecine27 Boulevard Jean MoulinMarseille Cedex 0513385France
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Fonkou MDM, Morand A, Fournier PE, Raoult D, Dubourg G. 'Bacteroides ihuae' sp. nov., a new bacterial species isolated from the human respiratory microbiome. New Microbes New Infect 2017; 17:52-53. [PMID: 28289545 PMCID: PMC5338718 DOI: 10.1016/j.nmni.2017.01.011] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 11/26/2022] Open
Abstract
We present the main features of ‘Bacteroides ihuae’ sp. nov., strain Marseille-P2824T (CSUR P2824), isolated from the sputum of healthy Frenchwoman living in Marseille.
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Affiliation(s)
- M D M Fonkou
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - A Morand
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM 63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
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Ndongo S, Dubourg G, Bittar F, Sokhna C, Fournier PE, Raoult D. Marseillibacter massiliensis gen. nov., sp. nov., a new bacterial genus isolated from the human gut. New Microbes New Infect 2017; 16:30-31. [PMID: 28127439 PMCID: PMC5247566 DOI: 10.1016/j.nmni.2016.12.006] [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] [Received: 08/05/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 11/04/2022] Open
Abstract
In this manuscript, we report the main characteristics of Marseillibacter massiliensis gen. nov., sp. nov., strain Marseille-P2840T (CSUR P2840), a new member of the family Oscillospiraceae that was isolated from the stool of a healthy 29-year-old Senegalese woman.
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Affiliation(s)
- S Ndongo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
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24
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Afouda P, Dubourg G, Cadoret F, Fournier PE, Raoult D. 'Bacillus massiliglaciei', a new bacterial species isolated from Siberian permafrost. New Microbes New Infect 2017; 15:92-93. [PMID: 28053706 PMCID: PMC5196234 DOI: 10.1016/j.nmni.2016.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/26/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 10/27/2022] Open
Abstract
We describe here the main characteristics of a new species isolated from Siberian permafrost dated around 10 million years. This species was named 'Bacillus massiliglaciei' strain Marseille-P2600T (= CSUR P2600 = DSM 102861).
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Affiliation(s)
- P Afouda
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F Cadoret
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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25
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Bilen M, Ndongo S, Cadoret F, Dubourg G, Daoud Z, Fournier PE, Raoult D. ‘Mobilibacterium massiliense’ gen. nov. and ‘Mobilibacterium timonense’ sp. nov., identified in a human stool specimen. New Microbes New Infect 2017; 15:61-62. [PMID: 28053704 PMCID: PMC5199148 DOI: 10.1016/j.nmni.2016.11.008] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- M. Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G. Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Z. Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
- Corresponding author: D. Raoult, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille cedex 05, FranceAix-Marseille UniversitéURMITEUM63CNRS7278IRD198Inserm 1095Institut Hospitalo-Universitaire Méditerranée-InfectionFaculté de médecine27 Boulevard Jean MoulinMarseille cedex 0513385France
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26
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Bilen M, Mbogning MD, Cadoret F, Dubourg G, Daoud Z, Fournier PE, Raoult D. ' Pygmaiobacter massiliensis' sp. nov., a new bacterium isolated from the human gut of a Pygmy woman. New Microbes New Infect 2016; 16:37-38. [PMID: 28179983 PMCID: PMC5284491 DOI: 10.1016/j.nmni.2016.12.015] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 12/14/2016] [Accepted: 12/14/2016] [Indexed: 10/31/2022] Open
Abstract
This study supports the main characteristics of a new genus 'Pygmaiobacter' and a new species 'Pygmaiobacter massiliensis' strain Marseille-P3336 (CSUR P3336); that was isolated from a stool sample of a healthy 47-year-old Pygmy woman. The Institut Fédératif de Recherche ethics committee, gave approval for this study under the number 09-022. Samples were collected for microbial content description as part of the human microbiome description by culturomics.
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Affiliation(s)
- M Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille Cedex 05, France; Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - M D Mbogning
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille Cedex 05, France
| | - F Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille Cedex 05, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille Cedex 05, France
| | - Z Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - P E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille Cedex 05, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille Cedex 05, France
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27
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Tidjani Alou M, Rathored J, Nguyen TT, Andrieu C, Couderc C, Brah S, Diallo BA, Fournier PE, Raoult D, Dubourg G. Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant. New Microbes New Infect 2016; 16:13-24. [PMID: 28116105 PMCID: PMC5233791 DOI: 10.1016/j.nmni.2016.12.001] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 12/20/2022] Open
Abstract
Paenibacillus phocaensis sp. nov. strain mt24T (= CSUR P2238 = DSM 101777) is a Gram-negative, facultative anaerobic, spore-forming and motile bacilli. This strain was isolated from the stool sample of a healthy infant from Niger. Its genome was estimated to a size of 5 521 415 bp with a 53.54% GC content. It contains 4835 protein-coding genes and 89 RNAs, among which two were 16S rRNA genes. There were also 101 genes (2.09%) identified as ORFans.
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Affiliation(s)
- M Tidjani Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J Rathored
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - T T Nguyen
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C Couderc
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - S Brah
- Hôpital National de Niamey, BP 238, Niamey, Niger
| | - B A Diallo
- Laboratoire de microbiologie, département de biologie, Université Abdou Moumouni de Niamey, BP 237, Niamey, Niger
| | - P-E Fournier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - D Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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28
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Mailhe M, Ricaboni D, Vitton V, Benezech A, Dubourg G, Michelle C, Andrieu C, Armstrong N, Bittar F, Fournier PE, Raoult D, Million M. Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum. New Microbes New Infect 2016; 16:3-12. [PMID: 28116104 PMCID: PMC5225283 DOI: 10.1016/j.nmni.2016.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/28/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
The strain Marseille-P2749T (= CSUR P2749 = DSM 103085) was isolated as part of culturomics study from a liquid duodenum sample from a French man. Bacterial cells were Gram-negative bacilli, fusiform shaped and non–spore forming, and they grew in microaerophilic and anaerobic atmosphere. Its genome is 1 809 169 bp long and contains 1646 protein-coding genes. The DNA G+C content was 27.33 mol%. This strain exhibited a 95.9% sequence similarity with Fusobacterium periodonticum, the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2749T is suggested to be a novel species belonging to the genus Fusobacterium, for which the name Fusobacterium massiliense sp. nov. is proposed.
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Affiliation(s)
- M Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - V Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Bittar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M Million
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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29
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Durand G, Afouda P, Raoult D, Dubourg G. " Intestinimonas massiliensis" sp. nov, a new bacterium isolated from human gut. New Microbes New Infect 2016; 15:1-2. [PMID: 27830078 PMCID: PMC5094204 DOI: 10.1016/j.nmni.2016.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022] Open
Abstract
Here we report the main features of the proposed new bacterial species “Intestinimonas massiliensis” sp. nov. The type strain GD2T (CSUR = P1930) was isolated from the gut microbiota of a healthy patient using a culturomics approach combined with taxonogenomics.
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Affiliation(s)
- G Durand
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University Hospital Centre Timone, Marseille, France
| | - P Afouda
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France; Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University Hospital Centre Timone, Marseille, France
| | - G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University Hospital Centre Timone, Marseille, France
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Abstract
Preexposure prophylaxis (PrEP) against HIV is currently the subject of great interest, as clinical trials have shown high efficacy in terms of decreasing transmission among men who have sex with men. Because the prevalence of bacterial sexual transmitted infections (STIs) is increasing within this community, a recent pilot study demonstrated the efficacy of reducing transmission of bacterial STIs by administering PrEP with daily doxycycline to men who have sex with men. This creative initiative raises several questions which are discussed in this review. Relevant information should be drawn from the huge amount of available epidemiologic data to identify those who could benefit from such prophylactic treatment. The choice of antimicrobial agents is crucial, as antimicrobial susceptibility of STI agents is heterogeneous. Finally, we discuss challenges to improve the control of STIs through the use of PrEP.
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Affiliation(s)
- G Dubourg
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Timone University Hospital Centre, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France.
| | - D Raoult
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Timone University Hospital Centre, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France
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31
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Traore SI, Khelaifia S, Dubourg G, Sokhna C, Raoult D, Fournier PE. " Lagierella massiliensis," a new bacterium detected in human feces. New Microbes New Infect 2016; 14:53-55. [PMID: 27699050 PMCID: PMC5035340 DOI: 10.1016/j.nmni.2016.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 06/12/2016] [Revised: 07/05/2016] [Accepted: 07/25/2016] [Indexed: 11/08/2022] Open
Abstract
We report here the main characteristics of “Lagierella massiliensis” strain SIT14 (CSUR P2012), which was isolated from a stool specimen from a healthy 28-month-old Senegalese boy.
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Affiliation(s)
- S I Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - S Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Sokhna
- Campus international UCAD-IRD, Dakar, Senegal
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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32
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Seck E, Traore SI, Khelaifia S, Beye M, Michelle C, Couderc C, Brah S, Fournier PE, Raoult D, Dubourg G. Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut. New Microbes New Infect 2016; 13:3-12. [PMID: 27358740 PMCID: PMC4916054 DOI: 10.1016/j.nmni.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 02/23/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 11/22/2022] Open
Abstract
A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7T (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.
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Affiliation(s)
- E Seck
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - S I Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - S Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - M Beye
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - C Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - C Couderc
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - S Brah
- Hôpital National de Niamey, Niamey, Niger
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
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Bessis S, Amadou T, Dubourg G, Raoult D, Fournier PE. "Bariatricus massiliensis" as a new bacterial species from human gut microbiota. New Microbes New Infect 2016; 12:54-5. [PMID: 27222720 PMCID: PMC4872373 DOI: 10.1016/j.nmni.2016.04.003] [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] [Received: 04/01/2016] [Revised: 04/05/2016] [Accepted: 04/05/2016] [Indexed: 12/01/2022] Open
Abstract
We report here the main phenotypic characteristics of “Bariatricus massiliensis” strain AT12 (CSUR P2179), isolated from the stool of a 58-year-old woman who underwent bariatric surgery.
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Affiliation(s)
- S Bessis
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - T Amadou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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Ndongo S, Dubourg G, Khelaifia S, Fournier PE, Raoult D. Christensenella timonensis, a new bacterial species isolated from the human gut. New Microbes New Infect 2016; 13:32-3. [PMID: 27408737 PMCID: PMC4925455 DOI: 10.1016/j.nmni.2016.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 05/10/2016] [Revised: 05/17/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
We propose a new species, Christensenella timonensis, strain Marseille-P2437(T) (CSUR P2437(T)), which was isolated from gut microbiota of a 66-year-old patient as a part of culturomics study. C. timonensis represents the second species isolated within the Christensenella genus.
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Affiliation(s)
- S Ndongo
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - G Dubourg
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - S Khelaifia
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Tidjani Alou M, Rathored J, Lagier JC, Khelaifia S, Labas N, Sokhna C, Diallo A, Raoult D, Dubourg G. Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut. New Microbes New Infect 2016; 10:101-11. [PMID: 26933503 PMCID: PMC4765772 DOI: 10.1016/j.nmni.2016.01.010] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 01/15/2023] Open
Abstract
Massilibacterium senegalense gen. nov., sp. nov., strain mt8T, is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes.
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Affiliation(s)
- M Tidjani Alou
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - J Rathored
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - S Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - N Labas
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - C Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France; Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - A Diallo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France; Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
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Dubourg G, Sankar SA, Rathored J, Lagier JC, Robert C, Couderc C, Papazian L, Raoult D, Fournier PE. Noncontiguous finished genome sequence and description of Nocardioides massiliensis sp. nov. GD13(T). New Microbes New Infect 2016; 10:47-57. [PMID: 27257488 PMCID: PMC4877605 DOI: 10.1016/j.nmni.2016.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 11/20/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 11/24/2022] Open
Abstract
Nocardioides massiliensis sp. nov strain GD13T is the type strain of N. massiliensis sp. nov., a new species within the genus Nocardioides. This strain was isolated from the faeces of a 62-year-old man admitted to intensive care for Guillain-Barré syndrome. Nocardioides massiliensis is a strictly aerobic Gram-positive rod. Herein we describe the features of this bacterium, together with the complete genome sequence and annotation. The 4 006 620 bp long genome contains 4132 protein-coding and 47 RNA genes.
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Affiliation(s)
- G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - S A Sankar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J Rathored
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - C Couderc
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - L Papazian
- Service de Réanimation Médicale-Détresse Respiratoires et Infections Sévères, Hôpital Nord, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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Dubourg G, Cimmino T, Senkar SA, Lagier JC, Robert C, Flaudrops C, Brouqui P, Raoult D, Fournier PE, Rolain JM. Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11(T), the type strain of Paenibacillus antibioticophila. New Microbes New Infect 2015; 8:137-47. [PMID: 27257493 PMCID: PMC4877408 DOI: 10.1016/j.nmni.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 07/23/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 11/22/2022] Open
Abstract
Paenibacillus antibioticophila strain GD11T sp. nov. is the type strain of a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from human faeces of a 63-year-old woman with multidrug-resistant tuberculosis who was receiving numerous antibiotics at the time of stool collection. P. antibioticophila is a Gram-positive aerobic bacterium. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 5 562 631 bp long genome contains 5084 protein-coding and 71 RNA genes.
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Affiliation(s)
- G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - T Cimmino
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - S A Senkar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - C Flaudrops
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - P Brouqui
- Service des Maladies Infectieuses et Tropicales. Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - J-M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
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Affiliation(s)
- G Dubourg
- Pôle des Maladies Infectieuses et Tropicales Clinique, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France
| | - F Fenollar
- Pôle des Maladies Infectieuses et Tropicales Clinique, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Marseille, France.
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Morel AS, Dubourg G, Prudent E, Edouard S, Gouriet F, Casalta JP, Fenollar F, Fournier PE, Drancourt M, Raoult D. Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases. Eur J Clin Microbiol Infect Dis 2014; 34:561-70. [PMID: 25348607 DOI: 10.1007/s10096-014-2263-z] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/07/2014] [Indexed: 12/24/2022]
Abstract
Molecular tools have shown an added value in the diagnosis of infectious diseases, in particular for those caused by fastidious intracellular microorganisms, or in patients receiving antibiotics before sampling. If 16S rDNA amplification had been gradually implemented in microbiology laboratories, specific real-time polymerase chain reaction (PCR) would have permitted an increase in the sensitivity of molecular methods and a reduction of contamination. Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad. Among these samples, 81,476 PCRs were performed, of which 1,192 were positive. Molecular techniques detected intracellular microorganisms in 31.3 % of respiratory samples, 27.8 % of endocarditis samples and 51.9 % of adenitis samples. Excluding intracellular bacteria, 25 % of the positive samples in this series were sterile in culture. Conventional broad-range PCR permitted the identification of fastidious and anaerobic microorganisms, but specific real-time PCR showed a significant superiority in the diagnosis of osteoarticular infections, in particular for those caused by Kingella kingae and Staphylococcus aureus, and for endocarditis diagnosis, specifically when Streptococcus gallolyticus and Staphylococcus aureus were involved. The sensitivity of conventional broad-range PCR was 62.9 % concerning overall diagnoses for which both techniques had been performed. These findings should lead microbiologists to focus on targeted specific real-time PCR regarding the clinical syndrome. Finally, syndrome-driven diagnosis, which consists of testing a panel of microorganisms commonly involved for each syndrome, permitted the establishment of 31 incidental diagnoses.
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Affiliation(s)
- A-S Morel
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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Dubourg G, Socolovschi C, Del Giudice P, Fournier PE, Raoult D. Scalp eschar and neck lymphadenopathy after tick bite: an emerging syndrome with multiple causes. Eur J Clin Microbiol Infect Dis 2014; 33:1449-56. [PMID: 24682865 DOI: 10.1007/s10096-014-2090-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/02/2014] [Indexed: 11/28/2022]
Abstract
The clinical and epidemiological features of 56 patients with scalp eschar associated with neck lymphadenopathy after a tick bite (SENLAT) syndrome were evaluated at the National French Rickettsial Center. Eschar swabs, crusts, and biopsies as well as ticks and blood samples were acquired for molecular and serological assays. SENLAT predominantly affects children (p < 0.05), followed by 40- to 70-year-olds, and it is found mostly in women (p < 0.05). The seasonal distribution has two peaks: one in the spring (55%) and one in the autumn (30%). The etiological agent was identified in 18 cases, which include Rickettsia slovaca in 13 cases with incidences of two co-infections with Rickettsia raoultii and one case caused by Rickettsia sibirica mongolitimonae. Other possible agents that were found in attached ticks were Candidatus R. rioja, Coxiella burnetii, and Borrelia burgdorferi. The tick vector was Dermacentor marginatus in almost all cases, with the exception of one case, in which Ixodes ricinus was identified as the vector. Our findings show that SENLAT is a clinical entity characterized as a local infection controlled by the immune system and is neither pathogen- nor vector-specific.
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Affiliation(s)
- G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculty of Medicine, Aix-Marseille University, Marseille, France
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Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P, Raoult D. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis 2013; 32:637-45. [PMID: 23291779 DOI: 10.1007/s10096-012-1787-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 11/18/2012] [Indexed: 01/19/2023]
Abstract
Gut microbiota consists of 10(10) bacteria per gram of stool. Many antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. We analyzed one stool sample collected from a patient treated for drug-resistant Mycobacterium tuberculosis and who ultimately died from pneumonia due to a Streptococcus pneumoniae 10 months later. We performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA amplification and sequencing, pyrosequencing, and 18S rRNA amplification and clone sequencing. Electron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. By culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. The pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. Only two phylotypes overlapped with culturomics. In contrast, an amount of chloroplasts was found. Additionally, specific molecular eukaryote detection found three fungal species. We recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. We propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of S. pneumoniae. This finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.
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Affiliation(s)
- G Dubourg
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13005 Marseille, France
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Parola P, Colson P, Dubourg G, Million M, Charrel R, Minodier P, Raoult D. Letter to the editor. Group A streptococcal infections during the seasonal influenza outbreak 2010/11 in South East England. ACTA ACUST UNITED AC 2011; 16. [PMID: 21435326 DOI: 10.2807/ese.16.11.19816-en] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Rozenberg S, Dubourg G, Khalifa P, Paolozzi L, Maheu E, Ravaud P. Efficacy of epidural steroids in low back pain and sciatica. A critical appraisal by a French Task Force of randomized trials. Critical Analysis Group of the French Society for Rheumatology. Rev Rhum Engl Ed 1999; 66:79-85. [PMID: 10084166] [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] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
OBJECTIVE Several randomized trials have suggested recently that epidural steroid injections may not be a valid treatment in common low back pain and sciatica. To clarify this issue, we conducted a critical appraisal of relevant randomized trials published up to 1997. Attention was directed to methodological quality, results, and clinical implications. METHOD A Medline search identified 13 trials published between 1966 and 1997. Trial methodology was evaluated using a 100-point grid based on four groups of items, namely study population, therapeutic intervention, evaluation method, and data presentation and analysis. RESULTS Methodology quality scores ranged from 12 to 84 and were unrelated to the results of epidural steroid therapy. Five trials demonstrated greater pain relief within the first month in the steroid group as compared to the control group. Eight trials found no measurable benefits. Obstacles to meaningful comparisons across studies included differences in the patient populations, steroid used, volume injected, and number of injections. None of the published studies used the injection modalities that are standard practice in France. CONCLUSION Whether epidural steroids are effective in common low back pain and sciatica cannot be determined based on our review.
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Affiliation(s)
- S Rozenberg
- Department of Rheumatology, Pitié Teaching Hospital, Paris, France
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Abad S, Kahn MF, Deray G, Dubourg G. [Hemophagocytic syndrome complicating seronegative rheumatoid polyarthritis: a differential diagnosis of Still's disease?]. Rev Med Interne 1998; 19:361-2. [PMID: 9775175 DOI: 10.1016/s0248-8663(98)80111-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Roche B, Rozenberg S, Cambau E, Desplaces N, Dion E, Dubourg G, Koeger AC, Robin H, Vergeron H, Bourgeois P. Efficacy of combined clarithromycin and sparfloxacin therapy in a patient with discitis: due to Mycobacterium xenopi. Rev Rhum Engl Ed 1997; 64:64-5. [PMID: 9051864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Dubourg G, Koeger AC, Huchet B, Rozenberg S, Bourgeois P. Acute monoarthritis in a patient under isotretinoin. Rev Rhum Engl Ed 1996; 63:228-9. [PMID: 8731245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Dubarry JJ, Dubourg G, Bernard JP, Quinton A, Beylot J, Le Bras M. [Gelatinous peritonits. 2 cases]. Arch Fr Mal App Dig 1969; 58:569-79. [PMID: 5398648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Broustet P, Bricaud H, Broustet JP, Lacut J, Dubourg G, Fontan F, Mounicot FB. [The place of surgery in the treatment of bacterial endocarditis]. Ann Cardiol Angeiol (Paris) 1969; 18:33-44. [PMID: 5363951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Fontan F, Galy JC, Mounicot F, Raulin Y, Dubourg G. [Ruptured aneurysm of Valsalva's sinus with aortic insufficiency. Correction by aortic valve homograft]. Ann Chir Thorac Cardiovasc 1968; 7:501-3. [PMID: 5710193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Coustou F, Crockett R, Fontan F, Dubourg G, Dulong de Rosnay H. [Aortic valve homografts. Organization of a bank]. Ann Chir Thorac Cardiovasc 1968; 7:539-41. [PMID: 5758336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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