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Nawfal Dagher T, Al-Bayssari C, Diene SM, Azar E, Rolain JM. Emergence of plasmid-encoded VIM-2-producing Pseudomonas aeruginosa isolated from clinical samples in Lebanon. New Microbes New Infect 2019; 29:100521. [PMID: 30976429 PMCID: PMC6438892 DOI: 10.1016/j.nmni.2019.100521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 10/24/2018] [Revised: 02/06/2019] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
The present study aimed to describe the emergence of carbapenem-resistant Pseudomonas aeruginosa isolated from clinical Lebanese patients. The resistance of these isolates is due to the presence of the plasmid-encoded blaVIM-2 gene. We provide its first description in Lebanon, as well as a description of disruption of the oprD gene by mutations.
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Affiliation(s)
- T Nawfal Dagher
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille, Cedex 05 France.,Saint George Hospital University Medical Center, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - C Al-Bayssari
- Faculty of Sciences III, Lebanese University, Tripoli, Lebanon
| | - S M Diene
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille, Cedex 05 France
| | - E Azar
- Saint George Hospital University Medical Center, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - J-M Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 boulevard Jean Moulin, 13385 Marseille, Cedex 05 France
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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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3
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Affiliation(s)
- C Abat
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - J-M Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
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4
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Leangapichart T, Gautret P, Nguyen TT, Armstrong N, Rolain JM. Genome sequence of " Leucobacter massiliensis" sp. nov. isolated from human pharynx after travel to the 2014 Hajj. New Microbes New Infect 2017; 21:42-48. [PMID: 29204283 PMCID: PMC5709290 DOI: 10.1016/j.nmni.2017.10.007] [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: 06/26/2017] [Revised: 10/09/2017] [Accepted: 10/17/2017] [Indexed: 01/12/2023] Open
Abstract
“Leucobacter massiliensis” strain 122RC15T sp. nov. is a new species within the genus Leucobacter. The genome of this strain is described here. It was isolated from the pharynx of a 76-year-old Algerian female after travelling from the 2014 Hajj. “Leucobacter massiliensis” is a Gram-positive, aerobic bacillus. Here we describe the features including complete genome and annotation of this strain. The 3 136 406-bp long genome contains 2797 protein-coding genes and 49 RNA genes.
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Affiliation(s)
- T Leangapichart
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - P Gautret
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - T T Nguyen
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - N Armstrong
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - J-M Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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5
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Mathlouthi N, Traore SI, Cimmino T, Khelaifia S, Nguyen TT, Cadoret F, Couderc C, Raoult D, Rolain JM. Genome sequence and description of Mobilicoccus massiliensis sp. nov. isolated from the stool of a Nigerian boy with kwashiorkor. New Microbes New Infect 2017; 20:18-24. [PMID: 29158905 PMCID: PMC5682880 DOI: 10.1016/j.nmni.2017.08.007] [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: 08/16/2016] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/08/2022] Open
Abstract
Mobilicoccus massiliensis strain SIT2 (= CSUR P1306 = DSM 29065) is a new type strain of Mobilicoccus sp. nov. isolated from the stool of a 2-year-old Nigerian boy with kwashiorkor. M. massiliensis is Gram positive, facultatively anaerobic, nonsporulating and motile. The 3 842 438 bp long genome contains 3362 protein-coding and 49 RNA genes, including one 5S rRNA gene, one 16S rRNA gene, one 23S rRNA gene and 46 tRNA genes.
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Affiliation(s)
- N Mathlouthi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - S I Traore
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - T Cimmino
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - S Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - T T Nguyen
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - F Cadoret
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - C Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - J-M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
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Mlaga KD, Lotte R, Montaudié H, Rolain JM, Ruimy R. ' Nissabacter archeti' gen. nov., sp. nov., a new member of Enterobacteriaceae family, isolated from human sample at Archet 2 Hospital, Nice, France. New Microbes New Infect 2017; 17:81-83. [PMID: 28392923 PMCID: PMC5377011 DOI: 10.1016/j.nmni.2017.02.001] [Citation(s) in RCA: 8] [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: 02/02/2017] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 11/28/2022] Open
Abstract
We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.
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Affiliation(s)
- K D Mlaga
- URMITE, Université Aix-Marseille, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU-Méditerranée Infection, Marseille, France
| | - R Lotte
- Department of Microbiology, Nice Academic Hospital, and University Nice Côte d'Azur, Nice, France; INSERM U1065 (C3M), Bacterial Toxins in Host-Pathogen Interactions, C3M, Bâtiment Universitaire Archimed, Nice, France
| | - H Montaudié
- Department of Dermatology, Nice Academic Hospital, and University Nice Côte d'Azur, Nice, France
| | - J-M Rolain
- URMITE, Université Aix-Marseille, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU-Méditerranée Infection, Marseille, France
| | - R Ruimy
- Department of Microbiology, Nice Academic Hospital, and University Nice Côte d'Azur, Nice, France; INSERM U1065 (C3M), Bacterial Toxins in Host-Pathogen Interactions, C3M, Bâtiment Universitaire Archimed, Nice, France
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7
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Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 2016; 23:2-22. [PMID: 27890457 DOI: 10.1016/j.cmi.2016.11.012] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
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Affiliation(s)
- M J Ellington
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - O Ekelund
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - F M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - R Canton
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - M Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - C Giske
- Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - H Grundman
- University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Hasman
- Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark
| | - M T G Holden
- School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK
| | - K L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - J Iredell
- Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia
| | - G Kahlmeter
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - A MacGowan
- Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - D Mevius
- Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - M Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - T Naas
- French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France
| | - T Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - J-M Rolain
- PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Ø Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.
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Chabou S, Leangapichart T, Okdah L, Le Page S, Hadjadj L, Rolain JM. Real-time quantitative PCR assay with Taqman(®) probe for rapid detection of MCR-1 plasmid-mediated colistin resistance. New Microbes New Infect 2016; 13:71-4. [PMID: 27489722 PMCID: PMC4961677 DOI: 10.1016/j.nmni.2016.06.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [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: 05/04/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 12/02/2022] Open
Abstract
Here we report the development of two rapid real-time quantitative PCR assays with TaqMan® probes to detect the MCR-1 plasmid-mediated colistin resistance gene from bacterial isolates and faecal samples from chickens. Specificity and sensitivity of the assay were 100% on bacterial isolates including 18 colistin-resistant isolates carrying the mcr-1 gene (six Klebsiella pneumoniae and 12 Escherichia coli) with a calibration curve that was linear from 101 to 108 DNA copies. Five out of 833 faecal samples from chickens from Algeria were positive, from which three E. coli strains were isolated and confirmed to harbour the mcr-1 gene by standard PCR and sequencing.
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Affiliation(s)
- S Chabou
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - T Leangapichart
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - L Okdah
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - S Le Page
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - L Hadjadj
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - J-M Rolain
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
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9
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Le Page S, Cimmino T, Togo A, Million M, Michelle C, Khelaifia S, Lagier JC, Raoult D, Rolain JM. Noncontiguous finished genome sequence and description of Enterococcus massiliensis sp. nov. New Microbes New Infect 2016; 12:90-5. [PMID: 27330820 PMCID: PMC4913184 DOI: 10.1016/j.nmni.2016.04.011] [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: 02/04/2016] [Revised: 04/19/2016] [Accepted: 04/28/2016] [Indexed: 11/23/2022] Open
Abstract
Enterococcus massiliensis strain sp. nov. (= CSUR P1927 = DSM 100308) is a new species within the genus Enterococcus. This strain was first isolated from a fresh stool sample of a man during culturomics study of intestinal microflora. Enterococcus massiliensis is a Gram-positive cocci, facultative anaerobic and motile. E. massiliensis is negative for mannitol and positive for β-galactosidase, contrary to E. gallinarum. The complete genome sequence is 2 712 841 bp in length with a GC content of 39.6% and contains 2617 protein-coding genes and 70 RNA genes, including nine rRNA genes.
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Affiliation(s)
- S Le Page
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - T Cimmino
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - A Togo
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - M Million
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - C Michelle
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - S Khelaifia
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - J-C Lagier
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - J-M Rolain
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
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10
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Cimmino T, Traore SI, Valentini C, le Page S, Sokhna C, Diallo A, Raoult D, Rolain JM. Noncontiguous finished genome sequence and description of Bacillus testis strain SIT10 sp. nov. New Microbes New Infect 2016; 12:18-23. [PMID: 27222713 PMCID: PMC4873691 DOI: 10.1016/j.nmni.2016.03.007] [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: 03/12/2016] [Accepted: 03/22/2016] [Indexed: 11/26/2022] Open
Abstract
Bacillus testis strain SIT10 (= CSUR P1492 = DSMZ 101190) is the new type strain collected from stool from a 2-year-old boy from Senegal during a culturomics study. This Gram-positive bacterium is a facultative anaerobic rod and a member of the Bacillaceae family. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 3 987 349 bp long genome (one chromosome but no plasmid) with 42.8% GC content contains 4005 protein-coding and 171 sRNA genes, including 19 5S rRNA gene, 15 16S rRNA genes and ten 23S rRNA genes.
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Affiliation(s)
- T Cimmino
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - S I Traore
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France; Département d'Epidémiologie des Affections Parasitaires, Faculté de médecine et de pharmacie de Bamako, Bamako, Mali
| | - C Valentini
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - S le Page
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, 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
- URMITE, UMR CNRS 6236, IRD 198, Aix Marseille Université, Marseille, Joint Campus UCAD-IRD of Hann, BP 1386 CP 18524, Dakar, Senegal
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - J M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
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11
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Cimmino T, Metidji S, Labas N, Le Page S, Musso D, Raoult D, Rolain JM. Genome sequence and description of Actinomyces polynesiensis str. MS2 sp. nov. isolated from the human gut. New Microbes New Infect 2016; 12:1-5. [PMID: 27200177 PMCID: PMC4864249 DOI: 10.1016/j.nmni.2016.02.014] [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: 02/04/2016] [Accepted: 02/29/2016] [Indexed: 11/07/2022] Open
Abstract
Actinomyces polynesiensis strain MS2 gen. nov., sp. nov. is a newly proposed genus within the family Actinomycetaceae, isolated from the stools of a healthy individual in Raiatea Island (French Polynesia, South Pacific). Actinomyces massiliensis is an anaerobic, Gram-positive organism. Here we describe the features of this organism, together with the complete genome sequence and annotation—2 943 271 bp with a 70.80% G+C content, assembled into 15 scaffolds and containing 2080 genes.
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Affiliation(s)
- T Cimmino
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - S Metidji
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - N Labas
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - S Le Page
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - D Musso
- Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - D Raoult
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - J-M Rolain
- Aix-Marseille Univ., URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
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12
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Rolain JM, Loucif L, Al-Maslamani M, Elmagboul E, Al-Ansari N, Taj-Aldeen S, Shaukat A, Ahmedullah H, Hamed M. Emergence of multidrug-resistant Acinetobacter baumannii producing OXA-23 Carbapenemase in Qatar. New Microbes New Infect 2016; 11:47-51. [PMID: 27054039 PMCID: PMC4802191 DOI: 10.1016/j.nmni.2016.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 12/02/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 11/03/2022] Open
Abstract
The objective of our study was to describe the molecular support of carbapenem resistance from randomly selected clinical isolates of multidrug-resistant (MDR) Acinetobacter baumannii as a pilot study from the Hamad Medical Corporation (HMC), Qatar. Results of our report will be used to study carbapenemases using molecular techniques in all isolated MDR A. baumannii. Forty-eight MDR A. baumannii were randomly selected from isolates preserved at HMC. Identification of all isolates was confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Antibiotic resistance was tested phenotypically by Phoenix and confirmed by Etest. The molecular support of carbapenemases (bla OXA-23, bla OXA-24, bla OXA-58, bla NDM) was investigated by real-time PCR. The epidemiologic relatedness of the isolates was verified by phylogenetic analysis based on partial sequences of CsuE and bla OXA-51 genes. All 48 isolates were identified as A. baumannii and were confirmed to be resistant to most antibiotics, especially meropenem, imipenems, ciprofloxacin, levofloxacin, amikacin, gentamicin and most of the β-lactams; they were sensitive to colistin. All the isolates were positive for bla OXA-23 and negative for the other tested carbapenemase genes. Clonality analysis demonstrated that different lineages were actually circulating in Qatar; and we suggest that an outbreak occurred in the medical intensive care unit of HMC between 2011 and 2012. Here we report the emergence of MDR A. baumannii producing the carbapenemase OXA-23 in Qatar.
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Affiliation(s)
- J-M Rolain
- Unité de Recherche sur les Maladies infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la méditerranée, Marseille, France
| | - L Loucif
- Unité de Recherche sur les Maladies infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la méditerranée, Marseille, France; Laboratoire de biotechnologie des molecules bioactives et de la physiopathologie cellulaire, Université El Hadj Lakhdar, Batna, Algeria
| | - M Al-Maslamani
- Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
| | - E Elmagboul
- Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
| | - N Al-Ansari
- Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
| | - S Taj-Aldeen
- Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
| | - A Shaukat
- Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
| | - H Ahmedullah
- Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
| | - M Hamed
- Unité de Recherche sur les Maladies infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD 198, INSERM 1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Université de la méditerranée, Marseille, France; Hamad Medical Corporation, Department of Microbiology and Infectious Diseases, Doha, Qatar
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13
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Traore SI, Cimmino T, Lagier JC, Khelaifia S, Brah S, Michelle C, Caputo A, Diallo BA, Fournier PE, Raoult D, Rolain JM. Noncontiguous finished genome sequence and description of Bacillus andreraoultii strain SIT1(T) sp. nov. New Microbes New Infect 2015; 10:25-35. [PMID: 27257486 PMCID: PMC4877607 DOI: 10.1016/j.nmni.2015.12.005] [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: 09/14/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/24/2023] Open
Abstract
Bacillus andreraoultii strain SIT1T (= CSUR P1162 = DSM 29078) is the type strain of B. andreraoultii sp. nov. This bacterium was isolated from the stool of a 2-year-old Nigerian boy with a severe form of kwashiorkor. Bacillus andreraoultii is an aerobic, Gram-positive rod. We describe here the features of this bacterium, together with the complete genome sequencing and annotation. The 4 092 130 bp long genome contains 3718 protein-coding and 116 RNA genes.
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Affiliation(s)
- S I Traore
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France; Département d'Epidémiologie des Affections Parasitaires, Faculté de médecine et de pharmacie de Bamako, Mali
| | - T Cimmino
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, 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 U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - S Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - S Brah
- Hôpital National de Niamey, Niamey, Niger
| | - C Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - A Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - B A Diallo
- Laboratoire de Microbiologie, Département de Biologie, Université Abdou Moumouni de Niamey, Niamey, Niger
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, 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 U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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14
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Abat C, Garcia V, Rolain JM. Facklamia hominis scapula abscess, Marseille, France. New Microbes New Infect 2015; 9:13-4. [PMID: 26862429 PMCID: PMC4706599 DOI: 10.1016/j.nmni.2015.11.003] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 11/23/2022] Open
Abstract
Facklamia hominis is a Gram-positive bacterium that was first isolated from various human samples, excluding abscesses of the scapula. We here report the first scapular abscess infection due to F. hominis, found in Marseille, France. We also reviewed all cases published in the literature.
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Affiliation(s)
- C Abat
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - V Garcia
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
| | - J-M Rolain
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
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15
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Hadjadj L, Bentorki AA, Michelle C, Amoura K, Djahoudi A, Rolain JM. Genome sequence and description of Mannheimia massilioguelmaensis sp. nov. New Microbes New Infect 2015; 8:131-6. [PMID: 26693284 PMCID: PMC4660222 DOI: 10.1016/j.nmni.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 08/07/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 11/24/2022] Open
Abstract
Strain MG13T sp. nov. is the type strain of Mannheimia massilioguelmaensis, a new species within the genus Mannheimia. This strain was isolated from the exudate of a skin lesion of an Algerian man. Mannheimia massilioguelmaensis is a Gram-negative, facultative anaerobic rod, member of the family Pasteurellaceae. Here we describe this organism, together with the complete genome sequence and annotation. The 2 186 813 bp long genome contains 2048 protein-coding and 55 RNA genes, including eight rRNA genes.
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Affiliation(s)
- L Hadjadj
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - A A Bentorki
- Laboratoire de Microbiologie, CHU Dorban, Algeria
| | - C Michelle
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - K Amoura
- Laboratoire de Microbiologie, Faculté de Médecine, Université Badji Mokhtar, Annaba, Algeria
| | - A Djahoudi
- Laboratoire de Microbiologie, Faculté de Médecine, Université Badji Mokhtar, Annaba, Algeria
| | - J-M Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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16
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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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17
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Bergal A, Loucif L, Benouareth DE, Bentorki AA, Abat C, Rolain JM. Molecular epidemiology and distribution of serotypes, genotypes, and antibiotic resistance genes of Streptococcus agalactiae clinical isolates from Guelma, Algeria and Marseille, France. Eur J Clin Microbiol Infect Dis 2015; 34:2339-48. [PMID: 26415872 DOI: 10.1007/s10096-015-2487-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 09/03/2015] [Indexed: 02/05/2023]
Abstract
This study describes, for the first time, the genetic and phenotypic diversity among 93 Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected from Guelma, Algeria and Marseille, France. All strains were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The molecular support of antibiotic resistance and serotyping were investigated by polymerase chain reaction (PCR). The phylogenetic lineage of each GBS isolate was determined by multilocus sequence typing (MLST) and grouped into clonal complexes (CCs) using eBURST. The isolates represented 37 sequence types (STs), 16 of which were novel, grouped into five CCs, and belonging to seven serotypes. Serotype V was the most prevalent serotype in our collection (44.1%). GBS isolates of each serotype were distributed among multiple CCs, including cps III/CC19, cps V/CC1, cps Ia/CC23, cps II/CC10, and cps III/CC17. All isolates presented susceptibility to penicillin, whereas resistance to erythromycin was detected in 40% and tetracycline in 82.2% of isolates. Of the 37 erythromycin-resistant isolates, 75.7% showed the macrolide-lincosamide-streptogramin B (MLSB)-resistant phenotype and 24.3% exhibited the macrolide (M)-resistant phenotype. Constitutive MLSB resistance (46%) mediated by the ermB gene was significantly associated with the Guelma isolates, whereas the M resistance phenotype (24.3%) mediated by the mefA/E gene dominated among the Marseille isolates and belonged to ST-23. Tetracycline resistance was predominantly due to tetM, which was detected alone (95.1%) or associated with tetO (3.7%). These results provide epidemiological data in these regions that establish a basis for monitoring increased resistance to erythromycin and also provide insight into correlations among clones, serotypes, and resistance genes.
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Affiliation(s)
- A Bergal
- Facultés de Médecine et de Pharmacie, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Marseille, France.,Département d'Écologie et Génie de l'Environnement, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre et de l'Univers, Université 8 Mai 1945, Guelma, Algeria
| | - L Loucif
- Facultés de Médecine et de Pharmacie, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Marseille, France.,Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Université El Hadj Lakhdar, Batna, Algeria
| | - D E Benouareth
- Département d'Écologie et Génie de l'Environnement, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre et de l'Univers, Université 8 Mai 1945, Guelma, Algeria
| | - A A Bentorki
- Laboratoire de Microbiologie, CHU Dorban, Annaba, Algeria
| | - C Abat
- Facultés de Médecine et de Pharmacie, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Marseille, France
| | - J-M Rolain
- Facultés de Médecine et de Pharmacie, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Marseille, France.
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18
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Yousfi M, Mairi A, Bakour S, Touati A, Hassissen L, Hadjadj L, Rolain JM. First report of NDM-5-producing Escherichia coli ST1284 isolated from dog in Bejaia, Algeria. New Microbes New Infect 2015; 8:17-8. [PMID: 26566444 PMCID: PMC4600852 DOI: 10.1016/j.nmni.2015.09.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/04/2015] [Accepted: 09/02/2015] [Indexed: 11/19/2022] Open
Affiliation(s)
- M Yousfi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Algeria
| | - A Mairi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Algeria
| | - S Bakour
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Algeria ; Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - A Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Algeria
| | - L Hassissen
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Algeria
| | - L Hadjadj
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - J-M Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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Bourafa N, Loucif L, Boutefnouchet N, Rolain JM. Enterococcus hirae, an unusual pathogen in humans causing urinary tract infection in a patient with benign prostatic hyperplasia: first case report in Algeria. New Microbes New Infect 2015; 8:7-9. [PMID: 26543562 PMCID: PMC4590716 DOI: 10.1016/j.nmni.2015.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/10/2015] [Indexed: 12/17/2022] Open
Abstract
Enterococcus hirae is a zoonotic pathogen rarely isolated from human infections. This case is the first description of E. hirae causing urinary tract infection in a diabetic man with benign prostatic hyperplasia from Algeria. The clinical isolate was identified by MALDI-TOF MS and displayed a multisensitivity antibiotic profile.
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Affiliation(s)
- N Bourafa
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditérranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France ; Laboratoire de microbiologie et biochimie appliquée, Département de biochimie, Université Badji mokhtar Annaba, Algeria ; Département de biologie, Faculté des sciences de la nature et de la vie, Université Mohamed Cherif Messaadia-Souk-ahras, Algeria
| | - L Loucif
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditérranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France ; Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Université El Hadj Lakhdar, Batna, Algeria
| | - N Boutefnouchet
- Laboratoire de microbiologie et biochimie appliquée, Département de biochimie, Université Badji mokhtar Annaba, Algeria
| | - J-M Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditérranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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20
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Bakour S, Garcia V, Loucif L, Brunel JM, Gharout-Sait A, Touati A, Rolain JM. Rapid identification of carbapenemase-producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii using a modified Carba NP test. New Microbes New Infect 2015; 7:89-93. [PMID: 26442150 PMCID: PMC4552816 DOI: 10.1016/j.nmni.2015.07.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [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: 06/24/2015] [Accepted: 07/02/2015] [Indexed: 01/16/2023] Open
Abstract
Biochemical tests have been previously developed to identify carbapenemase-producing Enterobacteriaceae, Pseudomonas spp. (Carba NP test) and Acinetobacter spp. (CarbAcineto NP test). We evaluated a modified Carba NP test to detect carbapenemase production in Enterobacteriaceae, Pseudomonas and Acinetobacter species using a single protocol with rapid results and found good reliability and speed.
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Affiliation(s)
- S Bakour
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France ; Laboratoire d'Ecologie Microbienne, FSNV, Université de Béjaia, Béjaia, Algeria
| | - V Garcia
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - L Loucif
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - J-M Brunel
- Laboratory of Integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, CNRS UMR 7258, Faculté de Pharmacie, Marseille, France
| | - A Gharout-Sait
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Béjaia, Béjaia, Algeria
| | - A Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Béjaia, Béjaia, Algeria
| | - J-M Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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21
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Al-Bayssari C, Gupta SK, Dabboussi F, Hamze M, Rolain JM. MUS-2, a novel variant of the chromosome-encoded β-lactamase MUS-1, from Myroides odoratimimus. New Microbes New Infect 2015; 7:67-71. [PMID: 26257915 PMCID: PMC4522612 DOI: 10.1016/j.nmni.2015.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 04/08/2015] [Accepted: 06/22/2015] [Indexed: 11/28/2022] Open
Abstract
The aim of the present study was to investigate the molecular mechanism of carbapenem resistance of three imipenem-resistant isolates of Myroides odoratimimus recovered from two livestock farms of cows and pigeons by rectal swab in Lebanon in January 2014. Investigation of imipenem resistance of these isolates using the modified Hodge test, the EDTA test, the modified CarbaNP test and the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Ultraflex assay showed a carbapenemase activity due to the presence of a chromosome-encoded β-lactamase MUS, verified by PCR. However amplification and sequencing of this chromosomal gene showed a novel variant of it designated MUS-2 by the curators of the Lahey database of β-lactamases (http://www.lahey.org/Studies/webt.asp). Cloning of the blaMUS-2 was performed, followed by protein expression in Escherichia coli TOP 10. Pulsed-field gel electrophoresis clearly showed that the three isolates belonged to the same clone. This study reports a novel variant of the chromosome-encoded blaMUS-1 associated with carbapenem resistance in Myroides odoratimimus and shows that animals may represent a reservoir of bacteria harbouring several variants of resistance genes.
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Affiliation(s)
- C Al-Bayssari
- Laboratoire Microbiologie Santé et Environnement (LMSE), Centre Azm pour la Recherche en Biotechnologie et ses Applications, Ecole Doctorale de Sciences et de Technologie, Université Libanaise, Tripoli, Libya ; Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
| | - S Kumar Gupta
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
| | - F Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Centre Azm pour la Recherche en Biotechnologie et ses Applications, Ecole Doctorale de Sciences et de Technologie, Université Libanaise, Tripoli, Libya
| | - M Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Centre Azm pour la Recherche en Biotechnologie et ses Applications, Ecole Doctorale de Sciences et de Technologie, Université Libanaise, Tripoli, Libya
| | - J-M Rolain
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Marseille, France
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22
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Le Page S, van Belkum A, Fulchiron C, Huguet R, Raoult D, Rolain JM. Evaluation of the PREVI® Isola automated seeder system compared to reference manual inoculation for antibiotic susceptibility testing by the disk diffusion method. Eur J Clin Microbiol Infect Dis 2015; 34:1859-69. [PMID: 26092031 DOI: 10.1007/s10096-015-2424-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
The disk diffusion (DD) method remains the most popular manual technique for antibiotic susceptibility testing (AST) in clinical microbiology laboratories. This is because of its simplicity, reproducibility, and limited cost compared to (automated) microdilution systems, which are usually less sensitive at detecting certain important mechanisms of resistance. Here, we evaluate the PREVI® Isola automated seeder system using a new protocol for spreading bacterial suspensions (eight deposits of calibrated inocula of bacteria, followed by two rounds of rotation) in comparison with manual DD reference testing on a large series of clinical and reference strains. The average time required for seeding one agar plate for DD with this new protocol was 51 s per plate, i.e., 70 agar plates/h. Reproducibility and repeatability was assessed on three reference and three randomly chosen clinical strains, as usually requested by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and was excellent compared to the manual method. The standard deviations of zones of growth inhibition showed no statistical discrimination. The correlation between the two methods, assessed using 294 clinical isolates and a panel of six antibiotics (n = 3,528 zones of growth inhibition measured), was excellent, with a correlation coefficient of 0.977. The new PREVI® Isola protocol adapted for DD had a sensitivity of 99 % and a specificity of 100 % compared to the manual technique for interpreting DD as recommended by the EUCAST.
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Affiliation(s)
- S Le Page
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
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23
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Abstract
Enterococcus cecorum is a bacterium of the intestinal tract of many domestic animals that is rarely reported as human pathogen. Here we report the first case of incisional hernia plate infection and the first case of urinary tract colonization due to E. cecorum from patients in Marseille, France.
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Affiliation(s)
- E Delaunay
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - C Abat
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J-M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
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24
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Al-Bayssari C, Valentini C, Gomez C, Reynaud-Gaubert M, Rolain JM. First detection of insertion sequence element ISPa1328 in the oprD porin gene of an imipenem-resistant Pseudomonas aeruginosa isolate from an idiopathic pulmonary fibrosis patient in Marseille, France. New Microbes New Infect 2015; 7:26-7. [PMID: 26137309 PMCID: PMC4484542 DOI: 10.1016/j.nmni.2015.05.004] [Citation(s) in RCA: 9] [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: 02/24/2015] [Accepted: 05/06/2015] [Indexed: 12/02/2022] Open
Abstract
We report here the first case of a carbapenem-resistant Pseudomonas aeruginosa clinical isolate harboring the insertion sequence (IS) element ISPa1328 in the oprD gene in an idiopathic pulmonary fibrosis patient in France previously treated with imipenem.
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Affiliation(s)
- C Al-Bayssari
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, France
| | - C Valentini
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, France
| | - C Gomez
- Service de Pneumologie, Centre de Soins de la Mucoviscidose (CRCM) et en Transplantation Pulmonaire Adulte, Hôpital Nord, Marseille, France
| | - M Reynaud-Gaubert
- Service de Pneumologie, Centre de Soins de la Mucoviscidose (CRCM) et en Transplantation Pulmonaire Adulte, Hôpital Nord, Marseille, France
| | - J-M Rolain
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, France
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25
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Rolain JM, Abat C, Brouqui P, Raoult D. Worldwide decrease in methicillin-resistant Staphylococcus aureus: do we understand something? Clin Microbiol Infect 2015; 21:515-7. [PMID: 25941171 DOI: 10.1016/j.cmi.2015.04.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
Affiliation(s)
- J-M Rolain
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculty of Medicine and Pharmacy, Aix-Marseille University, Marseille, France.
| | - C Abat
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculty of Medicine and Pharmacy, Aix-Marseille University, Marseille, France
| | - P Brouqui
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculty of Medicine and Pharmacy, Aix-Marseille University, Marseille, France
| | - D Raoult
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculty of Medicine and Pharmacy, Aix-Marseille University, Marseille, France.
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26
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Roca I, Akova M, Baquero F, Carlet J, Cavaleri M, Coenen S, Cohen J, Findlay D, Gyssens I, Heuer OE, Kahlmeter G, Kruse H, Laxminarayan R, Liébana E, López-Cerero L, MacGowan A, Martins M, Rodríguez-Baño J, Rolain JM, Segovia C, Sigauque B, Tacconelli E, Wellington E, Vila J. The global threat of antimicrobial resistance: science for intervention. New Microbes New Infect 2015; 6:22-9. [PMID: 26029375 PMCID: PMC4446399 DOI: 10.1016/j.nmni.2015.02.007] [Citation(s) in RCA: 620] [Impact Index Per Article: 68.9] [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: 01/06/2015] [Revised: 02/09/2015] [Accepted: 02/25/2015] [Indexed: 12/11/2022] Open
Abstract
In the last decade we have witnessed a dramatic increase in the proportion and absolute number of bacterial pathogens resistant to multiple antibacterial agents. Multidrug-resistant bacteria are currently considered as an emergent global disease and a major public health problem. The B-Debate meeting brought together renowned experts representing the main stakeholders (i.e. policy makers, public health authorities, regulatory agencies, pharmaceutical companies and the scientific community at large) to review the global threat of antibiotic resistance and come up with a coordinated set of strategies to fight antimicrobial resistance in a multifaceted approach. We summarize the views of the B-Debate participants regarding the current situation of antimicrobial resistance in animals and the food chain, within the community and the healthcare setting as well as the role of the environment and the development of novel diagnostic and therapeutic strategies, providing expert recommendations to tackle the global threat of antimicrobial resistance.
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Affiliation(s)
- I Roca
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - M Akova
- Department of Medicine, Section of Infectious Diseases, Hacettepe University School of Medicine, Ankara, Turkey ; ESCMID Executive Committee, Basel, Switzerland
| | - F Baquero
- Department of Microbiology at the Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Division for Research in Microbial Biology and Evolution, CIBERESP, Madrid, Spain
| | - J Carlet
- Fondation Hôpital St, Joseph, Paris, France and World Alliance Against Antibiotic Resistance (WAAAR), Creteil, France
| | - M Cavaleri
- European Medicines Agency (EMA), London, UK
| | - S Coenen
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - J Cohen
- Brighton and Sussex Medical School, Brighton, UK
| | - D Findlay
- Global Commercial Lead, GlaxoSmithKline (GSK), London, UK
| | - I Gyssens
- Department of Medicine, Radboud University Medical Center and Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - O E Heuer
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - G Kahlmeter
- Clinical Microbiology, Central Hospital, Växjö, Sweden ; ESCMID Executive Committee, Basel, Switzerland ; EUCAST Steering Committee, Växjö, Sweden
| | - H Kruse
- WHO Regional Office for Europe, UN City, Marmorvej, Copenhagen, Denmark
| | - R Laxminarayan
- Center for Disease Dynamics, Economics and Policy, Washington, DC, USA ; Princeton University, Princeton, NJ, USA
| | - E Liébana
- Scientific Unit on Biological Hazards, European Food Safety Authority (EFSA), Parma, Italy
| | - L López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
| | - A MacGowan
- Department of Medical Microbiology, Southmead Hospital, Bristol, UK ; EUCAST Steering Committee, Växjö, Sweden
| | - M Martins
- School of Public Health, Physiotherapy and Population Science, UCD Centre for Food and Safety, Molecular Innovation and Drug Discovery, University College Dublin, Dublin, Ireland
| | - J Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, and Departamento de Medicina, Universidad de Sevilla, Seville, Spain ; ESCMID Executive Committee, Basel, Switzerland
| | - J-M Rolain
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Inserm, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, and APHM, CHU Timone, Pôle Infectieux, Marseille, France
| | - C Segovia
- Instituto de Salud Carlos III, ISCIII, Madrid, Spain
| | - B Sigauque
- Centro de Investigação em Saúde da Manhiça and Instituto Nacional de Saúde/Ministério de Saúde, Maputo, Mozambique
| | - E Tacconelli
- Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University Hospital, Tübingen, Germany ; ESCMID Executive Committee, Basel, Switzerland
| | - E Wellington
- School of Life Sciences, University of Warwick, Coventry, UK
| | - J Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain ; ESCMID Executive Committee, Basel, Switzerland
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Bakour S, Sahli F, Touati A, Rolain JM. Emergence of KPC-producing Klebsiella pneumoniae ST512 isolated from cerebrospinal fluid of a child in Algeria. New Microbes New Infect 2014; 3:34-6. [PMID: 25755890 PMCID: PMC4337933 DOI: 10.1016/j.nmni.2014.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/15/2014] [Accepted: 09/26/2014] [Indexed: 11/27/2022] Open
Abstract
We report class A carbapenemase (KPC)-3-producing Klebsiella pneumoniae meningitis in a 6-month-old child in Algeria. Multilocus sequence typing showed that the sequence type obtained corresponded to ST512, an allelic single-locus variant of the pandemic ST258 widely distributed in KPC producers from Europe. To our knowledge, this is the first report of KPC-3-producing K. pneumoniae ST512 in a North African country.
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Affiliation(s)
- S Bakour
- Laboratoire d'Ecologie Microbienne, Université de Bejaia, Bejaia, Algeria ; Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - F Sahli
- Laboratoire de Microbiologie, CHU de Sétif, Algeria
| | - A Touati
- Laboratoire d'Ecologie Microbienne, Université de Bejaia, Bejaia, Algeria
| | - J-M Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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28
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Diene SM, Rolain JM. Carbapenemase genes and genetic platforms in Gram-negative bacilli: Enterobacteriaceae, Pseudomonas and Acinetobacter species. Clin Microbiol Infect 2014; 20:831-8. [PMID: 24766097 DOI: 10.1111/1469-0691.12655] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The emergence and rapid spread of carbapenemases in Enterobacteriaceae, Pseudomonas and Acinetobacter (EPA) species is becoming a major public health crisis worldwide, and is responsible for large number of hospital-acquired and nosocomial infections. In this article, we review the current knowledge on the classification, phylogeny and genetic platforms of the main carbapenemases already described in Gram-negative bacteria.
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Affiliation(s)
- S M Diene
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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29
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Berrazeg M, Diene SM, Medjahed L, Parola P, Drissi M, Raoult D, Rolain JM. New Delhi Metallo-beta-lactamase around the world: An eReview using Google Maps. Euro Surveill 2014; 19. [DOI: 10.2807/1560-7917.es2014.19.20.20809] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative carbapenem-resistant bacteria, in particular those producing New Delhi Metallo-beta-lactamase-1 (NDM-1), are a major global health problem. To inform the scientific and medical community in real time about worldwide dissemination of isolates of NDM-1-producing bacteria, we used the PubMed database to review all available publications from the first description in 2009 up to 31 December 2012, and created a regularly updated worldwide dissemination map using a web-based mapping application. We retrieved 33 reviews, and 136 case reports describing 950 isolates of NDM-1-producing bacteria. Klebsiella pneumoniae (n= 359) and Escherichia coli (n=268) were the most commonly reported bacteria producing NDM-1 enzyme. Several case reports of infections due to imported NDM-1 producing bacteria have been reported in a number of countries, including the United Kingdom, Italy, and Oman. In most cases (132/153, 86.3%), patients had connections with the Indian subcontinent or Balkan countries. Those infected were originally from these areas, had either spent time and/or been hospitalised there, or were potentially linked to other patients who had been hospitalised in these regions. By using Google Maps, we were able to trace spread of NDM-1-producing bacteria. We strongly encourage epidemiologists to use these types of interactive tools for surveillance purposes and use the information to prevent the spread and outbreaks of such bacteria.
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Affiliation(s)
- M Berrazeg
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Marseille, France
- Laboratoire Antibiotiques, Antifongiques: physico- chimie, Synthèse et Activité Biologiques, Faculté des Sciences de la Nature, de la Vie, de la Terre et de l’Univers, Université Abou Bekr Belkaid, Tlemcen, Algeria
| | - S M Diene
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Marseille, France
| | - L Medjahed
- Département d'Informatique, Faculté de technologie, Université Abou Bekr Belkaid, Tlemcen, Algeria
| | - P Parola
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Marseille, France
| | - M Drissi
- Laboratoire Antibiotiques, Antifongiques: physico- chimie, Synthèse et Activité Biologiques, Faculté des Sciences de la Nature, de la Vie, de la Terre et de l’Univers, Université Abou Bekr Belkaid, Tlemcen, Algeria
| | - D Raoult
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Marseille, France
| | - J M Rolain
- Aix-Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Marseille, France
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Diene SM, Fenollar F, Fall B, Sow K, Niang B, Samba Ba P, Wade B, Raoult D, Rolain JM. CTX-M-15-producing Morganella morganii from Hôpital Principal de Dakar, Senegal. New Microbes New Infect 2014; 2:46-9. [PMID: 25356341 PMCID: PMC4184590 DOI: 10.1002/nmi2.41] [Citation(s) in RCA: 3] [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: 12/13/2013] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 01/29/2023] Open
Abstract
We report the detection and molecular characterization of extended spectrum β-lactamases in a series of 112 clinical isolates of Enterobacteriaceae from the Hôpital Principal de Dakar, Senegal, including five CTX-M-15-producing Morganella morganii isolates, which are reported for the first time in this country.
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Affiliation(s)
- S M Diene
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Aix-Marseille II 13385 Marseille, Cedex, 05, France ; Campus and campus commun UCAD-IRD of Hann BP 1386 CP 18524, Dakar, Sénégal
| | - F Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Aix-Marseille II 13385 Marseille, Cedex, 05, France ; Campus and campus commun UCAD-IRD of Hann BP 1386 CP 18524, Dakar, Sénégal
| | - B Fall
- Hôpital Principal de Dakar, Hôpital d'instruction des Armées B.P 3006, Dakar, Sénégal
| | - K Sow
- Hôpital Principal de Dakar, Hôpital d'instruction des Armées B.P 3006, Dakar, Sénégal
| | - B Niang
- Hôpital Principal de Dakar, Hôpital d'instruction des Armées B.P 3006, Dakar, Sénégal
| | - P Samba Ba
- Hôpital Principal de Dakar, Hôpital d'instruction des Armées B.P 3006, Dakar, Sénégal
| | - B Wade
- Hôpital Principal de Dakar, Hôpital d'instruction des Armées B.P 3006, Dakar, Sénégal
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Aix-Marseille II 13385 Marseille, Cedex, 05, France ; Campus and campus commun UCAD-IRD of Hann BP 1386 CP 18524, Dakar, Sénégal
| | - J-M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Aix-Marseille II 13385 Marseille, Cedex, 05, France ; Campus and campus commun UCAD-IRD of Hann BP 1386 CP 18524, Dakar, Sénégal
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Kokcha S, Bittar F, Reynaud-Gaubert M, Mely L, Gomez C, Gaubert JY, Thomas P, Rolain JM. Pandoraea pulmonicola chronic colonization in a cystic fibrosis patient, France. New Microbes New Infect 2013; 1:27-9. [PMID: 25356323 PMCID: PMC4184697 DOI: 10.1002/2052-2975.16] [Citation(s) in RCA: 12] [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: 06/07/2013] [Accepted: 08/02/2013] [Indexed: 11/13/2022] Open
Abstract
Pandoraea are considered emerging multidrug resistant pathogens in the context of cystic fibrosis. We report herein for the first time the case of a 30-year-old woman with cystic fibrosis, living in France, who was chronically infected with Pandoraea pulmonicola and who died of Pseudomonas aeruginosa sepsis 3 weeks after bilateral lung transplantation.
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Affiliation(s)
- S Kokcha
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Marseille, France
| | - F Bittar
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Marseille, France
| | - M Reynaud-Gaubert
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Marseille, France ; Service de Pneumologie et de Transplantation Pulmonaire, Hôpital Nord Marseille, France
| | - L Mely
- Centre de Ressources et de Compétences pour la Mucoviscidose (CRCM), Hôpital Renée Sabran Hyères, France
| | - C Gomez
- Service de Pneumologie et de Transplantation Pulmonaire, Hôpital Nord Marseille, France
| | - J-Y Gaubert
- Service de Radiologie adulte, Hôpital de la Timone Marseille, France
| | - P Thomas
- Service de Chirurgie Thoracique et Transplantation Pulmonaire, Hôpital Nord Marseille, France
| | - J-M Rolain
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée Marseille, France
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Angelakis E, Million M, D'Amato F, Rouli L, Richet H, Stein A, Rolain JM, Raoult D. Q fever and pregnancy: disease, prevention, and strain specificity. Eur J Clin Microbiol Infect Dis 2012; 32:361-8. [PMID: 23052984 DOI: 10.1007/s10096-012-1750-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
The link between fetal morbidity and Q fever and the necessity of long-term antibiotics for Coxiella burnetii infection during pregnancy have been recently questioned in the Netherlands, where the clone responsible for the Q fever outbreak harbors the QpH1 plasmid. In this context, we assessed pregnancy outcomes according to antibiotic administration in a new series and compared the plasmid type between isolates associated with abortion and other clinical isolates to determine if there is a link between genotype and abortion in humans. All French patients who received a diagnosis of Q fever during pregnancy at the French National Referral Centre for Q Fever from 2006 through July 2011 were included. On the other hand, the plasmid types of 160 clinical isolates, including seven isolates from patients who experienced an abortion, were compared. The differences between the QpDV and QpH1 plasmid sequences were analyzed. Acute Q fever was a cause of fetal morbidity, and the absence of long-term cotrimoxazole therapy was associated with fetal death (p < 0.0001). Genotypic analysis showed that the QpDV plasmid was more frequent in isolates associated with abortion (p = 0.03). A comparison of the plasmid sequences revealed that four QpDV proteins had no direct counterparts in QpH1, with two whose functions were not present in QpH1. The different obstetrical morbidity of C. burnetii relative to different geographical areas could be related to strain specificity, possibly based on differences in plasmid sequences, or to a failure of public health authorities to detect early miscarriages.
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Affiliation(s)
- E Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, CNRS UMR 7278, IRD 198, Aix-Marseille Université, 27 Bd. Jean Moulin, 13005 Marseille, France
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Li W, Raoult D, Rolain JM, La Scola B. Evidence of circulation of an epidemic strain of Francisella tularensis in France by multispacer typing. Eur J Clin Microbiol Infect Dis 2011; 30:1135-8. [PMID: 21611870 DOI: 10.1007/s10096-011-1186-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 01/18/2011] [Indexed: 11/25/2022]
Abstract
Multispacer typing (MST) was used to type ten Francisella tularensis strains detected in French patients. Incorporating 79 Swedish F. tularensis strains, phylogenetic analysis demonstrated that although tularemia appears as a sporadic disease in France, it is caused by an epidemic cluster of strains.
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Affiliation(s)
- W Li
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD UMR 6236, Faculté de Médecine, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
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Abstract
Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.
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Affiliation(s)
- F Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille Cedex 05, France
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Adams NG, Adekambi T, Afeltra J, Aguado J, Aires de Sousa M, Akiyoshi K, Al Hasan M, Ala-Kokko T, Albert M, Alfandari S, Allen D, Allerberger F, Almyroudis N, Alp E, Amin R, Anderson-Berry A, Andes DR, Andremont A, Andreu A, Angelakis M, Antachopoulos C, Antoniadou A, Arabatzis M, Arlet G, Arnez M, Arnold C, Asensio A, Asseray N, Ausiello C, Avni T, Ayling R, Baddour L, Baguelin M, Bányai K, Barbour A, Basco LK, Bauer D, Bayston R, Beall B, Becker K, Behr M, Bejon P, Belliot G, Benito-Fernandez J, Benjamin D, Benschop K, Berencsi G, Bergeron MG, Bernard K, Berner R, Beyersmann J, Bille J, Bizzini A, Bjarnsholt T, Blanc D, Blanco J, Blot S, Bohnert J, Boillat N, Bonomo R, Bonten M, Bordon JM, Borel N, Boschiroli ML, Bosilkovski M, Bosso JA, Botelho-Nevers E, Bou G, Bretagne S, Brouqui P, Brun-Buisson C, Brunetto M, Bucher H, Buchheidt D, Buckling A, Bulpa P, Cambau E, Canducci F, Cantón R, Capobianchi M, Carattoli A, Carcopino X, Cardona-Castro N, Carling PC, Carrat F, Castilla J, Castilletti C, Cavaco L, Cavallo R, Ceccherini-Silberstein F, Centrón D, Chappuis F, Charrel R, Chen M, Chevaliez S, Chezzi C, Chomel B, Chowers M, Chryssanthou E, Ciammaruconi A, Ciccozzi M, Cid J, Ciofu O, Cisneros D, Ciufolini MG, Clark C, Clarke SC, Clayton R, Clementi M, Clemons K, Cloeckaert A, Cloud J, Coenye T, Cohen Bacri S, Cohen R, Coia J, Colombo A, Colson P, Concerse P, Cordonnier C, Cormican M, Cornaglia G, Cornely O, Costa S, Cots F, Craxi A, Creti R, Crnich C, Cuenca Estrella M, Cusi MG, d'Ettorre G, da Cruz Lamas C, Daikos G, Dannaoui E, De Barbeyrac B, De Grazia S, de Jager C, de Lamballerie X, de Marco F, del Palacio A, Delpeyroux F, Denamur E, Denis O, Depaquit J, Deplano A, Desenclos JC, Desjeux P, Deutch S, Di Luca D, Dianzani F, Diep B, Diestra K, Dignani C, Dimopoulos G, Divizia M, Doi Y, Dornbusch HJ, Dotis J, Drancourt M, Drevinek P, Dromer F, Dryden M, Dubreuil L, Dubus JC, Dumitrescu O, Dumke R, DuPont H, Edelstein M, Eggimann P, Eis-Huebinger AM, El Atrouni WI, Entenza J, Ergonul O, Espinel-Ingroff A, Esteban J, Etienne J, Fan XG, Fenollar F, Ferrante P, Ferrieri P, Ferry T, Feuchtinger T, Finegold S, Fingerle V, Fitch M, Fitzgerald R, Flori P, Fluit A, Fontana R, Fournier PE, François M, Francois P, Freedman DO, Friedrich A, Gallego L, Gallinella G, Gangneux JP, Gannon V, Garbarg-Chenon A, Garbino J, Garnacho-Montero J, Gatermann S, Gautret P, Gentile G, Gerlich W, Ghannoum M, Ghebremedhin B, Ghigo E, Giamarellos-Bourboulis E, Girgis R, Giske C, Glupczynski Y, Gnarpe J, Gomez-Barrena E, Gorwitz RJ, Gosselin R, Goubau P, Gould E, Gradel K, Gray J, Gregson D, Greub G, Grijalva CG, Groll A, Groschup M, Gutiérrez J, Hackam DG, Hall WA, Hallett R, Hansen S, Harbarth S, Harf-Monteil C, Hasanjani RMR, Hasler P, Hatchette T, Hauser P, He Q, Hedges A, Helbig J, Hennequin C, Herrmann B, Hezode C, Higgins P, Hoesli I, Hoiby N, Hope W, Houvinen P, Hsu LY, Huard R, Humphreys H, Icardi M, Imoehl M, Ivanova K, Iwamoto T, Izopet J, Jackson Y, Jacobsen K, Jang TN, Jasir A, Jaulhac B, Jaureguy F, Jefferies JM, Jehl F, Johnstone J, Joly-Guillou ML, Jonas M, Jones M, Joukhadar C, Kahl B, Kaier K, Kaiser L, Kato H, Katragkou A, Kearns A, Kern W, Kerr K, Kessin R, Kibbler C, Kimberlin D, Kittang B, Klaassen C, Kluytmans J, Ko WC, Koh WJ, Kostrzewa M, Kourbeti I, Krause R, Krcmery V, Krizova P, Kuijper E, Kullberg BJ, Kumar G, Kunin CM, La Scola B, Lagging M, Lagrou K, Lamagni T, Landini P, Landman D, Larsen A, Lass-Floerl C, Laupland K, Lavigne JP, Leblebicioglu H, Lee B, Lee CH, Leggat P, Lehours P, Leibovici L, Leon L, Leonard N, Leone M, Lescure X, Lesprit P, Levy PY, Lew D, Lexau CA, Li SY, Li W, Lieberman D, Lina B, Lina G, Lindsay JA, Livermore D, Lorente L, Lortholary O, Lucet JC, Lund B, Lütticken R, MacLeod C, Madhi S, Maertens J, Maggi F, Maiden M, Maillard JY, Maira-Litran T, Maltezou H, Manian FA, Mantadakis E, Maragakis L, Marcelin AG, Marchaim D, Marchetti O, Marcos M, Markotic A, Martina B, Martínez J, Martinez JL, Marty F, Maurin M, McGee L, Mediannikov O, Meersseman W, Megraud F, Meletiadis J, Mellmann A, Meyer E, Meyer W, Meylan P, Michalopoulos A, Micol R, Midulla F, Mikami Y, Miller RF, Miragaia M, Miriagou V, Mitchell TJ, Miyakis S, Mokrousov I, Monecke S, Mönkemüller K, Monno L, Monod M, Morales G, Moriarty F, Morosini I, Mortensen E, Mubarak K, Mueller B, Mühlemann K, Muñoz Bellido JL, Murray P, Muscillo M, Mylotte J, Naessens A, Nagy E, Nahm MH, Nassif X, Navarro D, Navarro F, Neofytos D, Nes I, Ní Eidhin D, Nicolle L, Niederman MS, Nigro G, Nimmo G, Nordmann P, Nougairède A, Novais A, Nygard K, Oliveira D, Orth D, Ortiz JR, Osherov N, Österblad M, Ostrosky-Zeichner L, Pagano L, Palamara AT, Pallares R, Panagopoulou P, Pandey P, Panepinto J, Pappas G, Parkins M, Parola P, Pasqualotto A, Pasteran F, Paul M, Pawlotsky JM, Peeters M, Peixe L, Pepin J, Peralta G, Pereyre S, Perfect JR, Petinaki E, Petric M, Pettigrew M, Pfaller M, Philipp M, Phillips G, Pichichero M, Pierangeli A, Pierard D, Pigrau C, Pilishvili T, Pinto F, Pistello M, Pitout J, Poirel L, Poli G, Poppert S, Posfay-Barbe K, Pothier P, Poxton I, Poyart C, Pozzetto B, Pujol M, Pulcini C, Punyadeera C, Ramirez M, Ranque S, Raoult D, Rasigade JP, Re MC, Reilly JS, Reinert R, Renaud B, Rice L, Rich S, Richet H, Rigouts L, Riva E, Rizzo C, Robotham J, Rodicio MR, Rodriguez J, Rodriguez-Bano J, Rogier C, Roilides E, Rolain JM, Rooijakkers S, Rooney P, Rossi F, Rotimi V, Rottman M, Roux V, Ruhe J, Russo G, Sadowy E, Sagel U, Said SI, Saijo M, Sak B, Sa-Leao R, Sanders EAM, Sanguinetti M, Sarrazin C, Savelkoul P, Scheifele D, Schmidt WP, Schønheyder H, Schönrich G, Schrenzel J, Schubert S, Schwarz K, Schwarz S, Sefton A, Segondy M, Seifert H, Seng P, Senneville E, Sexton D, Shafer RW, Shalit I, Shankar N, Shata TM, Shields J, Sibley C, Sicinschi L, Siljander T, Simitsopoulou M, Simoons-Smit AM, Sissoko D, Sjögren J, Skiada A, Skoczynska A, Skov R, Slack M, Sogaard M, Sola C, Soriano A, Sotto A, Sougakoff W, Sougakoff W, Souli M, Spelberg B, Spelman D, Spiliopoulou I, Springer B, Stefani S, Stein A, Steinbach WJ, Steinbakk M, Strakova L, Strenger V, Sturm P, Sullivan P, Sutton D, Symmons D, Tacconelli E, Tamalet C, Tang JW, Tang YW, Tattevin P, Thibault V, Thomsen RW, Thuny F, Tong S, Torres C, Townsend R, Tristan A, Trouillet JL, Tsai HC, Tsitsopoulos P, Tuerlinckx D, Tulkens P, Tumbarello M, Tureen J, Turnidge JD, Turriziani O, Tutuian R, Uçkay I, Upton M, Vabret A, Vamvakas EC, van den Boom D, Van Eldere J, van Leeuwen W, van Strijp J, Van Veen S, Vandamme P, Vandenesch F, Vayssier M, Velin D, Venditti M, Venter M, Venuti A, Vergnaud G, Verheij T, Verhofstede C, Viscoli C, Vizza CD, Vogel U, Waller A, Wang YF, Warn P, Warris A, Wauters G, Weidmann M, Weill FX, Weinberger M, Welch D, Wellinghausen N, Wheat J, Widmer A, Wild F, Willems R, Willinger B, Winstanley C, Witte W, Wolff M, Wong F, Wootton M, Wyllie D, Xu W, Yamamoto S, Yaron S, Yildirim I, Zaoutis T, Zazzi M, Zbinden R, Zehender GG, Zemlickova H, Zerbini ML, Zhang L, Zhang Y, Zhao YD, Zhu Z, Zimmerli W. ACKNOWLEDGEMENT OF REVIEWERS. Clin Microbiol Infect 2011. [DOI: 10.1111/j.1469-0691.2010.03428.x] [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]
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Busa T, Stremler-Le Bel N, Bosdure E, Bittar F, Rolain JM, Dubus JC. Hygiene of nasal masks used at home for non-invasive ventilation in children. J Hosp Infect 2010; 76:187-8. [PMID: 20619930 DOI: 10.1016/j.jhin.2010.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 05/17/2010] [Indexed: 10/19/2022]
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Bitam I, Rolain JM, Kernif T, Baziz B, Parola P, Raoult D. Bartonella species detected in rodents and hedgehogs from Algeria. Clin Microbiol Infect 2009; 15 Suppl 2:102-3. [PMID: 19929978 DOI: 10.1111/j.1469-0691.2008.02180.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- I Bitam
- Unité d'Entomologie médicale,Faculté de Médecine et de Pharmacie, URMITE, CNRS-IRD UMR 6236, Institut Pasteur d'Alger, Université de la Méditerranée, Marseille Cedex, France
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Nagalingam K, Rolain JM, Thevanesam V, Lakkumar F, Gunawardana G, Raoult D. Spotted fever rickettsioses in children in Sri Lanka. Clin Microbiol Infect 2009; 15 Suppl 2:330-1. [PMID: 19793115 DOI: 10.1111/j.1469-0691.2008.02262.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K Nagalingam
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
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Angelakis E, Roux V, Raoult D, Rolain JM. Real-time PCR strategy and detection of bacterial agents of lymphadenitis. Eur J Clin Microbiol Infect Dis 2009; 28:1363-8. [PMID: 19685089 DOI: 10.1007/s10096-009-0793-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 07/24/2009] [Indexed: 12/19/2022]
Affiliation(s)
- E Angelakis
- URMITE CNRS-IRD UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 Bd Jean Moulin, 13385, Marseille Cedex 05, France
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Berrelha J, Briolant S, Muller F, Rolain JM, Marie JL, Pagés F, Raoult D, Parola P. Rickettsia felis and Rickettsia massiliae in Ivory Coast, Africa. Clin Microbiol Infect 2009; 15 Suppl 2:251-2. [PMID: 19548990 DOI: 10.1111/j.1469-0691.2008.02273.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J Berrelha
- URMITE, UMR CNRS-IRD 6236, WHO Collaborative Centre for Rickettsial Diseases and Other Arthropod-borne Bacterial Diseases, Marseille, France
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Saisongkorh W, Barrassi L, Davoust B, de Broucker CA, Raoult D, Rolain JM. First isolation of Bartonella bovis from animals in French Guyana, South America. Clin Microbiol Infect 2009; 15 Suppl 2:124-6. [PMID: 19456818 DOI: 10.1111/j.1469-0691.2008.02198.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- W Saisongkorh
- Unité des Rickettsies, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, URMITE CNRS-IRD, UMR, Marseille, France
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Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, Dubus JC, Sarles J, Raoult D, La Scola B. Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing. Eur J Clin Microbiol Infect Dis 2009; 28:1151-4. [PMID: 19449045 DOI: 10.1007/s10096-009-0749-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 04/15/2009] [Indexed: 01/28/2023]
Abstract
Recent studies using 16S rRNA gene amplification followed by clonal Sanger sequencing in cystic fibrosis demonstrated that cultured microorganisms are only part of the infecting flora. The purpose of this paper was to compare pyrosequencing and clonal Sanger sequencing on sputum. The sputum of a patient with cystic fibrosis was analysed by culture, Sanger clone sequencing and pyrosequencing after 16S rRNA gene amplification. A total of 4,499 sequencing reads were obtained, which could be attributed to six consensus sequences, but the length of reads leads to fastidious data analysis. Compared to clonal Sanger sequencing and to cultivation results, pyrosequencing recovers greater species richness and gives a more reliable estimate of the relative abundance of bacterial species. The 16S pyrosequencing approach expands our knowledge of the microbial diversity of cystic fibrosis sputum. The current lack of phylogenetic resolution at the species level for the GS 20 sequencing reads will be overcome with the next generation of pyrosequencing apparatus.
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Affiliation(s)
- F Armougom
- URMITE-UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille, France
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44
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Rolain JM, Bitam I, Buffet S, Marié JL, Bourry O, Portelli-Clerc C, Beaucournu JC, Parola P, Fournier PE, Davoust B, Raoult D. Presence or absence of plasmid in Rickettsia felis depending on the source of fleas. Clin Microbiol Infect 2009; 15 Suppl 2:296-7. [PMID: 19438653 DOI: 10.1111/j.1469-0691.2008.02245.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J M Rolain
- URMITE UMR 6236, CNRS-IRD, Marseille, France
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45
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Rolain JM, Boureau-Voultoury A, Raoult D. Serological evidence of Bartonella vinsonii lymphadenopathies in a child bitten by a dog. Clin Microbiol Infect 2009; 15 Suppl 2:122-3. [PMID: 19374641 DOI: 10.1111/j.1469-0691.2008.02197.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J M Rolain
- Faculté de Médecine et de Pharmacie, URMITE UMR 6236, CNRS-IRD, Université de la Méditerranée, Marseille, France.
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Angelakis E, Khamphoukeo K, Grice D, Newton PN, Roux V, Aplin K, Raoult D, Rolain JM. Molecular detection of Bartonella species in rodents from the Lao PDR. Clin Microbiol Infect 2009; 15 Suppl 2:95-7. [PMID: 19374642 PMCID: PMC3531620 DOI: 10.1111/j.1469-0691.2008.02177.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E Angelakis
- Faculté de Médecine et de Pharmacie, Université de la Méditerranée, URMITE UMR 6236, CNRS-IRD, 27 Bd Jean Moulin, 13385 Marseille cedex 05, France
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47
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Botelho-Nevers E, Rolain JM, Espinosa L, Raoult D. Statins limit Rickettsia conorii infection in cells. Int J Antimicrob Agents 2008; 32:344-8. [PMID: 18703317 DOI: 10.1016/j.ijantimicag.2008.04.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 04/28/2008] [Indexed: 11/28/2022]
Abstract
Recent data suggest that statins may have a beneficial effect during sepsis. In this study, we tested the effect of lovastatin and pravastatin on the cellular culture of Rickettsia conorii using a quantitative plaque assay model associated with an original image analysis algorithm. Statins added at the time of infection did not modify plaque formation, whereas pre-incubation with statins for 48h resulted in a significant 30-68% plaque reduction, depending on the tested compounds and doses. These preliminary findings raise the hypothesis that statins may prevent or moderate rickettsial disease in exposed people.
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Affiliation(s)
- E Botelho-Nevers
- Unité des Rickettsies, URMITE CNRS UMR 6236, IRD 198, Marseille, France
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48
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Botelho-Nevers E, Espinosa L, Raoult D, Rolain JM. Lovastatin, but not pravastatin, limits in vitro infection due to Coxiella burnetii. J Antimicrob Chemother 2008; 62:845-7. [PMID: 18593722 DOI: 10.1093/jac/dkn282] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Fournier PE, Siritantikorn S, Rolain JM, Suputtamongkol Y, Hoontrakul S, Charoenwat S, Losuwanaluk K, Parola P, Raoult D. Detection of new genotypes of Orientia tsutsugamushi infecting humans in Thailand. Clin Microbiol Infect 2007; 14:168-73. [PMID: 18076670 DOI: 10.1111/j.1469-0691.2007.01889.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PCR screening of blood specimens taken from 195 patients with serologically confirmed scrub typhus in three Thai provinces detected the 56-kDa protein-encoding gene from Orientia tsutsugamushi in ten (5%) patients. Significant genetic diversity was found among the ten amplicons, with nine new genotypes identified that were different from those found previously in Thailand. Phylogenetically, the ten sequences obtained in the present study and sequences from 71 strains characterised previously were distributed into several clusters that included the Karp, Gilliam, Kuroki, Saitama, Kawasaki and Kato clusters. Two of the new genotypes found in the present study clearly belonged to the Karp cluster. However, the other new genotypes formed three different clusters, including one cluster that appeared to be distant from all previously known clusters, and which may therefore be representative of a previously undescribed serotype. Other genotypes formed two other clusters that may also be associated with undescribed serotypes.
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Affiliation(s)
- P-E Fournier
- Unité des Rickettsies, IFR 48, CNRS UMR6020, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Mahajan SK, Kashyap R, Sankhyan N, Sharma V, Rolain JM, Prasher BS, Raoult D. Spotted fever group rickettsioses in Himachal Pradesh. J Assoc Physicians India 2007; 55:868-870. [PMID: 18405137] [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: 05/26/2023]
Abstract
Rickettsiae are in many places of the world emerging or reemerging pathogens. The spotted fevers group (SFG) composes a large group of tick- and mite-borne zoonotic infections that are caused by closely related rickettsiae. The SFG rickettsiae of Southeast Asia are yet to be identified. Earlier reports have documented the endemicity of rickettsioses among adults in the Himalayan belt but no confirmed case of spotted fever have been reported from this region of India. We present two cases of SFG rickettsioses; from the northern hilly region of India that were confirmed using specific microimmunofluorescence assay.
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Affiliation(s)
- S K Mahajan
- Department of Medicine, IG Medical College, Shimla, India
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