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Bordigoni A, Lo C, Yimagou E, Diop K, Nicaise B, Raoult D, Desnues C, Fenollar F. Megasphaera vaginalis sp. nov. and Anaerococcus vaginimassiliensis sp. nov., new bacteria isolated from vagina of French woman with bacterial vaginosis. New Microbes New Infect 2020; 37:100706. [PMID: 32774867 PMCID: PMC7404545 DOI: 10.1016/j.nmni.2020.100706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. Megasphaera vaginalis sp. nov. strain Marseille-P4512 (= CSURP4512) and Anaerococcus vaginimassiliensis sp. nov. strain Marseille-P4857 (= CSURP4857) were isolated from the vagina of a French woman. The phylogenic tree, phenotypic criteria and genomic analysis described here clearly show that these two bacteria are different from previously known bacterial species with standing in nomenclature and new members of Firmicutes phylum.
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Affiliation(s)
- A. Bordigoni
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E.K. Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - K. Diop
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - B. Nicaise
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Desnues
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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2
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Kalia N, Singh J, Kaur M. Microbiota in vaginal health and pathogenesis of recurrent vulvovaginal infections: a critical review. Ann Clin Microbiol Antimicrob 2020; 19:5. [PMID: 31992328 PMCID: PMC6986042 DOI: 10.1186/s12941-020-0347-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Recurrent vulvovaginal infections (RVVI) has not only become an epidemiological and clinical problem but also include large social and psychological consequences. Understanding the mechanisms of both commensalism and pathogenesis are necessary for the development of efficient diagnosis and treatment strategies for these enigmatic vaginal infections. Through this review, an attempt has been made to analyze vaginal microbiota (VMB) from scratch and to provide an update on its current understanding in relation to health and common RVVI i.e. bacterial vaginosis, vulvovaginal candidiaisis and Trichomoniasis, making the present review first of its kind. For this, potentially relevant studies were retrieved from data sources and critical analysis of the literature was made. Though, culture-independent methods have greatly unfolded the mystery regarding vaginal bacterial microbiome, there are only a few studies regarding the composition and diversity of vaginal mycobiome and different Trichomonas vaginalis strains. This scenario suggests a need of further studies based on comparative genomics of RVVI pathogens to improve our perceptive of RVVI pathogenesis that is still not clear (Fig. 5). Besides this, the review details the rationale for Lactobacilli dominance and changes that occur in healthy VMB throughout a women’s life. Moreover, the list of possible agents continues to expand and new species recognised in both health and VVI are updated in this review. The review concludes with the controversies challenging the widely accepted dogma i.e. “VMB dominated with Lactobacilli is healthier than a diverse VMB”. These controversies, over the past decade, have complicated the definition of vaginal health and vaginal infections with no definite conclusion. Thus, further studies on newly recognised microbial agents may reveal answers to these controversies. Conversely, VMB of women could be an answer but it is not enough to just look at the microbiology. We have to look at the woman itself, as VMB which is fine for one woman may be troublesome for others. These differences in women’s response to the same VMB may be determined by a permutation of behavioural, cultural, genetic and various other anonymous factors, exploration of which may lead to proper definition of vaginal health and disease.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, 143005, India
| | - Jatinder Singh
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, 143005, India.
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, 143005, India.
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3
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Nicaise B, Maaloum M, Lo CI, Armstrong N, Bretelle F, Fournier PÉ, Diop K, Fenollar F. Taxono-genomics description of 'Lactobacillus raoultii sp. nov.', strain Marseille-P4006 T, a new Lactobacillus species isolated from the female genital tract of a patient with bacterial vaginosis. New Microbes New Infect 2019; 29:100534. [PMID: 31011428 PMCID: PMC6462780 DOI: 10.1016/j.nmni.2019.100534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/14/2019] [Indexed: 12/31/2022] Open
Abstract
Strain Marseille-P4006T, a Gram-stain-positive, rod-shaped, non-sporulating, facultatively anaerobic bacterium, was isolated from the vaginal swab of a 45-year-old woman with recurrent bacterial vaginosis. We studied its phenotypic characteristics and sequenced its whole genome. The major fatty acids were C16:0 (48%), C19:1n9 (14%) and C18:0 (11%). The 3 070 142-bp-long genome contains 2855 protein-coding genes and 68 RNAs. Strain Marseille-P4006T exhibited 98.1% 16S rRNA similarity with Lactobacillus farraginis, the closest species phylogenetically. Thus, strain Marseille-P4006 is distinct enough to represent a new species for which we propose the name Lactobacillus raoultii sp. nov. The type strain is Marseille-P4006T.
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Affiliation(s)
- B Nicaise
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Maaloum
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Faculty of Sciences Ben M'Sik, Laboratory of Biology and Health, Hassan II University, Casablanca, Morocco
| | - C I Lo
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France
| | - F Bretelle
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,Department of Gynaecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France
| | - P-É Fournier
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - K Diop
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F Fenollar
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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Diop K, Dufour JC, Levasseur A, Fenollar F. Exhaustive repertoire of human vaginal microbiota. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.humic.2018.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Lagier JC, Bilen M, Cadoret F, Drancourt M, Fournier PE, La Scola B, Raoult D. Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France. New Microbes New Infect 2018; 26:S89-S95. [PMID: 30402249 PMCID: PMC6205575 DOI: 10.1016/j.nmni.2018.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.
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Affiliation(s)
| | - M. Bilen
- Aix-Marseille Univ, IRD, MEPHI, France
| | | | | | - P.-E. Fournier
- Aix-Marseille Univ, IRD, VITROME, APHM, IHU Méditerranée Infection, Marseille, France
| | | | - D. Raoult
- Aix-Marseille Univ, IRD, MEPHI, France
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6
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Danylec N, Göbl A, Stoll DA, Hetzer B, Kulling SE, Huch M. Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces. Int J Syst Evol Microbiol 2018. [PMID: 29537365 DOI: 10.1099/ijsem.0.002705] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel, anaerobic, Gram-positive, rod-shaped bacterial strains, ResAG-85T and ResAG-96T, were isolated from a faecal sample of a male human. 16S rRNA gene sequences analyses indicated that these strains represent a distinct lineage within the family Eggerthellaceae. Strain ResAG-85T showed 92.3 % similarity to the type strains of the genera Eggerthella and Gordonibacter. Strain ResAG-96T clustered together with Paraeggerthella hongkongensis and the newly (but not validly) published genus 'Arabia massiliensis' (94.8 % similarity). Analysis of quinones revealed that MK-5 (21 % in ResAG-85T and 95 % in ResAG-96T) and MK-7 (53 % in strain ResAG-85T) were present, which were described for the first time for members of the Eggerthellaceae. Furthermore, MK-6 was present in both strains (25 % ResAG-85T and 5 % in ResAG-96T). The polar lipids detected in ResAG-85T and ResAG-96T consisted of eight and six glycolipids, respectively. Both strains possessed three phospholipids, one phosphatidylglycerol and one diphosphatidylglycerol. Analysis of fatty acids revealed that the percentage of total branched fatty acids was relatively high in comparison to related strains with 42 and 50 % of strains ResAG-85T and ResAG-96T but comparable to the value obtained for Gordonibacter pamelaeae DSM 19378T. On the basis of this polyphasic approach including molecular (16S rRNA gene sequencing) and biochemical methods (analysis of fatty acids, quinones, polar lipids, Rapid ID 32A and API 20A), the new genera and species Rubneribacter badeniensis with ResAG-85T (=DSM 105129T=JCM 32272T) and Enteroscipio rubneri with ResAG-96T (=DSM 105130T=JCM 32273T) as the type and only strains are described.
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Affiliation(s)
- Nicolas Danylec
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Andrea Göbl
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
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Diop K, Diop A, Levasseur A, Mediannikov O, Robert C, Armstrong N, Couderc C, Bretelle F, Raoult D, Fournier PE, Fenollar F. Microbial Culturomics Broadens Human Vaginal Flora Diversity: Genome Sequence and Description ofPrevotella lascolaiisp. nov. Isolated from a Patient with Bacterial Vaginosis. ACTA ACUST UNITED AC 2018; 22:210-222. [DOI: 10.1089/omi.2017.0151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Khoudia Diop
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Awa Diop
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Anthony Levasseur
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Oleg Mediannikov
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Carine Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Florence Bretelle
- Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille University, Marseille, France
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8
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Diop K, Andrieu C, Michelle C, Armstrong N, Bittar F, Bretelle F, Fournier PE, Raoult D, Fenollar F. Characterization of a New Ezakiella Isolated from the Human Vagina: Genome Sequence and Description of Ezakiella massiliensis sp. nov. Curr Microbiol 2017; 75:456-463. [PMID: 29188320 DOI: 10.1007/s00284-017-1402-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022]
Abstract
The study of the vaginal microbiota using the "culturomics concept" allowed us to isolate, from the vaginal swab of an asymptomatic 20-year-old woman who had sexual relations with another woman with bacterial vaginosis, an unknown Gram-positive anaerobic coccus-shaped bacterium that was designated strain Marseille-P2951T and characterized using taxono-genomics. Strain Marseille-P2951T is non-motile and non-spore forming and exhibits catalase and oxidase activities. Its 16S rRNA gene-based identification showed 98.5% identity with Ezakiella peruensis, the phylogenetically closest species. The major fatty acids are C18:1n9 (58%) and C16:0 (22%). With a 1,741,785 bp length, the G+C content of the genome is 36.69%. Of a total of 1657 genes, 1606 are protein-coding genes and 51 RNAs. Also, 1123 genes are assigned a putative function and 127 are ORFans. Phenotypic, phylogenetic, and genomics analyses revealed that strain Marseille-P2951T (=CSUR P2951 =DSM 103122) is distinct and represents a new species of the genus Ezakiella, for which the name Ezakiella massiliensis sp. nov. is proposed.
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Affiliation(s)
- Khoudia Diop
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Claudia Andrieu
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Caroline Michelle
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Nicholas Armstrong
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Fadi Bittar
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Florence Bretelle
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France.,Department of Gynecology and Obstetrics, Gynépole, Marseille, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, Marseille Cedex 05, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Didier Raoult
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France.
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