1
|
Colson P, Fournier PE, Chaudet H, Delerce J, Giraud-Gatineau A, Houhamdi L, Andrieu C, Brechard L, Bedotto M, Prudent E, Gazin C, Beye M, Burel E, Dudouet P, Tissot-Dupont H, Gautret P, Lagier JC, Million M, Brouqui P, Parola P, Fenollar F, Drancourt M, La Scola B, Levasseur A, Raoult D. Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics. Front Microbiol 2022; 12:786233. [PMID: 35197938 PMCID: PMC8859183 DOI: 10.3389/fmicb.2021.786233] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.
Collapse
Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | | | | | | | | | | | | | | | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Brouqui
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- *Correspondence: Didier Raoult,
| |
Collapse
|
2
|
Menu E, Landier J, Prudent E, Ranque S, L’Ollivier C. Evaluation of 11 DNA Automated Extraction Protocols for the Detection of the 5 Mains Candida Species from Artificially Spiked Blood. J Fungi (Basel) 2021; 7:jof7030228. [PMID: 33808911 PMCID: PMC8003619 DOI: 10.3390/jof7030228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/02/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
The molecular detection of Candida plays an important role in the diagnosis of candidaemia, a major cause of morbidity and mortality. The sensitivity of this diagnosis is partly related to the efficiency of yeast DNA extraction. In this monocentric study, we investigated the suitability of 11 recent automated procedures for the extraction of low and high amounts of Candida DNA from spiked blood. The efficacy of the DNA extraction procedures to detect Candida spp. in blood samples ranged from 31.4% to 80.6%. The NucliSENSTM easyMAGTM procedure was the most efficient, for each species and each inoculum. It significantly outperformed the other procedures at the lower Candida inocula mimicking the clinical setting. This study highlighted a heterogeneity in DNA extraction efficacy between the five main Candida species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis and Candida krusei). Up to five automated procedures were appropriate for C. krusei DNA extraction, whereas only one method yielded an appropriate detection of low amount of C. tropicalis. In the era of the syndromic approach to bloodstream infection diagnosis, this evaluation of 11 automated DNA extraction methods for the PCR diagnosis of candidaemia, puts the choice of an appropriate method in routine diagnosis within the reach of laboratories.
Collapse
Affiliation(s)
- Estelle Menu
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 13385 Marseille, France; (S.R.); (C.L.)
- IHU Méditerranée Infection, 13385 Marseille, France;
- Correspondence:
| | - Jordi Landier
- Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, Institut de Recherche pour le Développement, Institut National de Santé et de Recherche Médicale, Aix Marseille Université, 13385 Marseille, France;
| | - Elsa Prudent
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Stéphane Ranque
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 13385 Marseille, France; (S.R.); (C.L.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| | - Coralie L’Ollivier
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs—Infections Tropicales et Méditerranéennes, 13385 Marseille, France; (S.R.); (C.L.)
- IHU Méditerranée Infection, 13385 Marseille, France;
| |
Collapse
|
3
|
Million M, Gaudin M, Melenotte C, Chasson L, Edouard S, Verdonk C, Prudent E, Amphoux B, Meresse S, Dorent R, Lepidi H, La Scola B, Gorvel JP, Desnues C, Raoult D. Metagenomic Analysis of Microdissected Valvular Tissue for Etiological Diagnosis of Blood Culture-Negative Endocarditis. Clin Infect Dis 2021; 70:2405-2412. [PMID: 31309973 DOI: 10.1093/cid/ciz655] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/12/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Etiological diagnosis is a key to therapeutic adaptation and improved prognosis, particularly for infections such as endocarditis. In blood culture-negative endocarditis (BCNE), 22% of cases remain undiagnosed despite an updated comprehensive syndromic approach. This prompted us to develop a new diagnostic approach. METHODS Eleven valves from 10 BCNE patients were analyzed using a method that combines human RNA bait-depletion with phi29 DNA polymerase-based multiple displacement amplification and shotgun DNA sequencing. An additional case in which a microbe was serendipitously visualized by immunofluorescence was analyzed using the same method, but after laser capture microdissection. RESULTS Background DNA prevented any diagnosis in cases analyzed without microdissection because the majority of sequences were contaminants. Moraxella sequences were dramatically enriched in the stained microdissected region of the additional case. A consensus genome sequence of 2.4 Mbp covering more than 94% of the Moraxella osloensis KSH reference genome was reconstructed with 234X average coverage. Several antibiotic-resistance genes were observed. Etiological diagnosis was confirmed using Western blot and specific polymerase chain reaction with sequencing on a different valve sample. CONCLUSIONS Microdissection could be a key to the metagenomic diagnosis of infectious diseases when a microbe is visualized but remains unidentified despite an updated optimal approach. Moraxella osloensis should be tested in blood culture-negative endocarditis.
Collapse
Affiliation(s)
- Matthieu Million
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Maxime Gaudin
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Cléa Melenotte
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Lionel Chasson
- Aix Marseille Univ, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML)
| | - Sophie Edouard
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Constance Verdonk
- Department of Cardiology, Hôpital Bichat, Assistance Publique - Hôpitaux de Paris (APHP), Paris
| | - Elsa Prudent
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Bernard Amphoux
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Stéphane Meresse
- Aix Marseille Univ, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML)
| | - Richard Dorent
- Department of Cardiology, Hôpital Bichat, Assistance Publique - Hôpitaux de Paris (APHP), Paris
| | - Hubert Lepidi
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI).,Service d'anatomie et cytologie pathologique et de neuropathologie, Centre Hospitalo-Universitaire (CHU) Timone, Assistance Publique Hôpitaux de Marseille,, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| | - Jean-Pierre Gorvel
- Aix Marseille Univ, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML)
| | - Christelle Desnues
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI).,Aix Marseille Univ, Université de Toulon, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire (IHU) -Méditerranée Infection, Marseille.,Aix Marseille Univ, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille, Unité Microbes Evolution Phylogenie et Infections (MEPHI)
| |
Collapse
|
4
|
Fournier PE, Zandotti C, Ninove L, Prudent E, Colson P, Gazin C, Million M, Tissot-Dupont H, Fenollar F. Contribution of VitaPCR SARS-CoV-2 to the emergency diagnosis of COVID-19. J Clin Virol 2020; 133:104682. [PMID: 33152666 PMCID: PMC7598902 DOI: 10.1016/j.jcv.2020.104682] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/25/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND With the persistent COVID-19 pandemic, there is an urgent need to use rapid and reliable diagnostic tools for highly urgent cases. Antigen tests are disappointing with their lack of sensitivity. Among molecular tools allowing a diagnosis in less than an hour, only one, the Cepheid Xpert Xpress SARS-CoV-2 assay, has exhibited a good sensitivity. However, we are also facing a global shortage of reagents and kits. Thus, it is imperative to evaluate other point-of-care molecular tests. METHODS We evaluated the VitaPCR™ RT-PCR assay, whose sample analysis time is of approximately 20 min, in nasopharyngeal secretions from 534 patients presenting to our Institute, for the diagnosis of COVID-19, and compared it to our routine RT-PCR assay. We also compared the two assays with tenfold dilutions of a SARS-CoV-2 strain. RESULTS Compared to our routine RT-PCR and the previous diagnosis of COVID-19, the sensitivity, specificity, positive and negative predictive values of VitaPCR™ can be evaluated to be 99.3 % (155/156), 94.7 % (358/378), 88.6 % (155/175) and 99.7 % (358/359), respectively. Tenfold dilutions of a SARS-CoV-2 strain show that the VitaPCR™ was more sensitive that our routine RT-PCR assay. CONCLUSION The VitaPCR™ SARS-CoV-2 is an accurate rapid test, suitable for clinical practice that can be performed as part of a point-of-care testing, for the rapid diagnosis of COVID-19.
Collapse
Affiliation(s)
- Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Christine Zandotti
- IHU-Méditerranée Infection, Marseille, France; Aix-Marseille Univ, IRD, Inserm, AP-HM, UVE, Marseille, France
| | - Laetitia Ninove
- IHU-Méditerranée Infection, Marseille, France; Aix-Marseille Univ, IRD, Inserm, AP-HM, UVE, Marseille, France
| | | | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | | | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Hervé Tissot-Dupont
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
| |
Collapse
|
5
|
Prudent E, Raoult D. Fluorescence in situ hybridization, a complementary molecular tool for the clinical diagnosis of infectious diseases by intracellular and fastidious bacteria. FEMS Microbiol Rev 2018; 43:88-107. [DOI: 10.1093/femsre/fuy040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Elsa Prudent
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
| |
Collapse
|
6
|
Prudent E, Le Guenno G, Jonckheere S, Vankeerberghen A, Lepidi H, Angelakis E, Raoult D. Fluorescent in situ hybridization can be used as a complementary assay for the diagnosis of Tropheryma whipplei infection. Infection 2018; 47:317-321. [PMID: 30368732 DOI: 10.1007/s15010-018-1243-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/22/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Immunohistochemistry and Periodic acid-Schiff (PAS) staining have been routinely used for the diagnosis of Whipple's disease (WD). However, these methods present limitations. As a result, the last years, Fluorescence in situ hybridization (FISH) has been increasingly used as a complementary tool for the diagnosis of WD from various tissue samples. CASE REPORT In this study, we visualized, by FISH, Tropheryma whipplei within macrophages of a lymph node from a patient with WD. Moreover, we report in this study a patient with a pulmonary biopsy compatible with WD by PAS, immunostaining and FISH, although the specific molecular assays for T. whipplei were negative. Sequencing analysis of the 16S rDNA revealed a T. whipplei-related species with unknown classification. CONCLUSION FISH can be a valuable method for the detection of Tropheryma species in formalin-fixed paraffin-embedded tissues. FISH cannot replace the other already approved diagnostic techniques for WD, it can be used as a complementary tool and can provide supplementary information in a relatively short time.
Collapse
Affiliation(s)
- Elsa Prudent
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Guillaume Le Guenno
- Department of Internal Medicine, Hôpital Estaing, Centre, Hospitaliser Universitaire, Clermont-Ferrand, France
| | - Stijn Jonckheere
- Laboratory of Clinical Microbiology, OLV Hospital Aalst, Aalst, Belgium
| | | | - Hubert Lepidi
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Emmanouil Angelakis
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece.
| | - Didier Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| |
Collapse
|
7
|
Prudent E, Lepidi H, Angelakis E, Raoult D. Fluorescence In Situ Hybridization (FISH) and Peptide Nucleic Acid Probe-Based FISH for Diagnosis of Q Fever Endocarditis and Vascular Infections. J Clin Microbiol 2018; 56:e00542-18. [PMID: 29899006 PMCID: PMC6113452 DOI: 10.1128/jcm.00542-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/11/2018] [Indexed: 01/07/2023] Open
Abstract
Endocarditis and vascular infections are common manifestations of persistent localized infection due to Coxiella burnetii, and recently, fluorescence in situ hybridization (FISH) was proposed as an alternative tool for their diagnosis. In this study, we evaluated the efficiency of FISH in a series of valve and vascular samples infected by C. burnetii We tested 23 C. burnetii-positive valves and thrombus samples obtained from patients with Q fever endocarditis. Seven aneurysms and thrombus specimens were retrieved from patients with Q fever vascular infections. Samples were analyzed by culture, immunochemistry, and FISH with oligonucleotide and PNA probes targeting C. burnetii-specific 16S rRNA sequences. The immunohistochemical analysis was positive for five (17%) samples with significantly more copies of C. burnetii DNA than the negative ones (P = 0.02). FISH was positive for 13 (43%) samples and presented 43% and 40% sensitivity compared to that for quantitative PCR (qPCR) and culture, respectively. PNA FISH detected C. burnetii in 18 (60%) samples and presented 60% and 55% sensitivity compared to that for qPCR and culture, respectively. Immunohistochemistry had 38% and 28% sensitivity compared to that for FISH and PNA FISH, respectively. Samples found positive by both immunohistochemistry and PNA FISH contained significantly more copies of C. burnetii DNA than the negative ones (P = 0.03). Finally, PNA FISH was more sensitive than FISH (60% versus 43%, respectively) for the detection of C. burnetii We provide evidence that PNA FISH and FISH are important assays for the diagnosis of C. burnetii endocarditis and vascular infections.
Collapse
Affiliation(s)
- Elsa Prudent
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Hubert Lepidi
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Emmanouil Angelakis
- Aix Marseille Université, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France
- French Reference Center for the Diagnosis and Study of Rickettsioses, Q fever and Bartonelloses, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
8
|
Melenotte C, Izaaryene JJ, Gomez C, Delord M, Prudent E, Lepidi H, Mediannikov O, Lacoste M, Djossou F, Mania A, Bernard N, Huchot E, Mège JL, Brégeon F, Raoult D. Coxiella burnetii: A Hidden Pathogen in Interstitial Lung Disease? Clin Infect Dis 2018; 67:1120-1124. [DOI: 10.1093/cid/ciy278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/05/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Cléa Melenotte
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| | | | - Carine Gomez
- Service de Pneumologie et Transplantation Pulmonaire, Centre de Compétences des Maladies Rares Pulmonaires et de l’Hypertension Pulmonaire, Centre Hospitalo Universitaire (CHU) Nord de Marseille, Aix-Marseille Université
| | - Marion Delord
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| | - Elsa Prudent
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| | - Hubert Lepidi
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| | - Oleg Mediannikov
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| | - Marion Lacoste
- Centre Hospitalier de Troyes, Service de Médecine Interne et Maladies Infectieuses
| | - Felix Djossou
- Centre Hospitalier André Rosemon de Cayenne, Unité de Maladies Infectieuses et Tropicales
| | - Alexandre Mania
- Service de Médecine Interne, Centre Hospitalier Universitaire de Clermont-Ferrand Gabriel-Montpied, France
| | - Noelle Bernard
- Service de Médecine Interne et Maladies Infectieuse, Hôpital Saint André, Assistance Publique des Hôpitaux de Paris, France
| | - Eric Huchot
- Centre Hospitalier de la Réunion, Service de Pneumologie, Saint Pierre, France
| | - Jean-Louis Mège
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| | - Fabienne Brégeon
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
- Service d’Explorations Fonctionnelles Respiratoires, Pôle CVT 16, CHU Nord, APHM, Marseille, France
| | - Didier Raoult
- IRD, Assistance Publique des Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-Universitaire-Méditerranée Infection, Aix-Marseille Université
| |
Collapse
|
9
|
Prudent E, La Scola B, Drancourt M, Angelakis E, Raoult D. Molecular strategy for the diagnosis of infectious lymphadenitis. Eur J Clin Microbiol Infect Dis 2018; 37:1179-1186. [DOI: 10.1007/s10096-018-3238-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/19/2018] [Indexed: 02/08/2023]
|
10
|
de Worm S, Giot JB, Courtoy C, Gillet E, Amrane S, Huynen P, Van Esbroeck M, Prudent E, Lepidi H, Million M, Moutschen M, Raoult D. A case of giant cell arteritis associated with culture-proven Coxiella burnetii aortitis. Int J Infect Dis 2018; 69:50-54. [PMID: 29408476 DOI: 10.1016/j.ijid.2018.01.028] [Citation(s) in RCA: 11] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/24/2018] [Accepted: 01/27/2018] [Indexed: 01/15/2023] Open
Abstract
A case of proven Coxiella burnetii aortitis, possibly associated with giant cell arteritis (GCA), is reported. A 72-year-old man, who is a hunter, presented with weight loss, fever, jaw claudication, and hardened temporal arteries associated with a persistent inflammatory syndrome and arteritis of the whole aorta, including the brachiocephalic arteries, as seen on 18F-fluorodeoxyglucose positron emission tomography/computed tomography. The diagnosis of GCA was retained, and treatment with prednisolone was started. Given the aneurysm of the abdominal aorta, the patient underwent replacement of the abdominal aorta with an allograft. Histology showed intense chronic arteritis attributed to atherosclerosis with dissection. However, Coxiella burnetii infection was confirmed by serology and then by culture and molecular biology on the surgical specimen. A combination of hydroxychloroquine and doxycycline was added to tapered prednisolone and the outcome was favourable.
Collapse
Affiliation(s)
- S de Worm
- Internal General Medicine and Infectious Diseases, CHU de Liège, 4000 Liège, Belgium
| | - J B Giot
- Internal General Medicine and Infectious Diseases, CHU de Liège, 4000 Liège, Belgium.
| | - C Courtoy
- Rheumatology, CHR de Verviers, 4800 Verviers, Belgium
| | - E Gillet
- General Practitioner, 4651 Battice, Belgium
| | - Sophie Amrane
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - P Huynen
- Medical Microbiology, CHU de Liège, 4000 Liège, Belgium
| | - M Van Esbroeck
- Belgian National Reference Centre for Coxiella burnetii, Institute of Tropical Medicine, 2000 Anvers, Belgium
| | - E Prudent
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H Lepidi
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Moutschen
- Internal General Medicine and Infectious Diseases, CHU de Liège, 4000 Liège, Belgium
| | - Didier Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
11
|
El Houmami N, Bzdrenga J, Durand GA, Minodier P, Seligmann H, Prudent E, Bakour S, Bonacorsi S, Raoult D, Yagupsky P, Fournier PE. Molecular Tests That Target the RTX Locus Do Not Distinguish between Kingella kingae and the Recently Described Kingella negevensis Species. J Clin Microbiol 2017; 55:3113-3122. [PMID: 28794176 PMCID: PMC5625396 DOI: 10.1128/jcm.00736-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 11/20/2022] Open
Abstract
Kingella kingae is an important invasive pathogen in early childhood. The organism elaborates an RTX toxin presumably restricted to this species. Consequently, real-time quantitative PCR (qPCR) assays targeting the RTX locus have been developed in recent years and are gaining increasing use for the molecular diagnosis of K. kingae infections. However, the present study shows that Kingella negevensis, a Kingella species newly identified in young children, harbors an identical Kingella RTX locus, raising the question of whether K. negevensis can be misidentified as K. kingae by clinical microbiology laboratories. In silico comparison of Kingella sp. RTX and groEL genes and in vitro studies provided evidence that targeting the rtxA and rtxB genes could not differentiate between strains of K. kingae and K. negevensis, whereas targeting the groEL gene could. This prompted the design of a highly specific and sensitive qPCR assay targeting K. negevensis groEL (kngroEL). Ninety-nine culture-negative osteoarticular specimens from 99 children younger than 4 years of age were tested with a conventional 16S rRNA gene-based broad-range PCR assay and Kingella-specific rtxB, K. kingae-specific groEL (kkgroEL), and kngroEL qPCR assays. Forty-two specimens were rtxB positive, including 41 that were also kkgroEL positive and 1 (the remaining one) that was kngroEL positive. Thus, this study discloses an invasive infection caused by K. negevensis in humans and demonstrates that targeting the RTX locus cannot be used for the formal diagnosis of K. kingae infections. These findings stress the need for further studies on the epidemiology of asymptomatic carriage and invasive infections caused by K. negevensis in humans.
Collapse
Affiliation(s)
- Nawal El Houmami
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Janek Bzdrenga
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Guillaume André Durand
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Minodier
- Department of Pediatric Emergency, North Hospital, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Elsa Prudent
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Sofiane Bakour
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Stéphane Bonacorsi
- Inserm, IAME, UMR 1137, Université Paris-Diderot, Sorbonne Paris Cité, Laboratoire de Microbiologie, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Didier Raoult
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Research Unit on Infectious and Emerging Tropical Diseases (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| |
Collapse
|
12
|
Cayron J, Prudent E, Escoffier C, Gueguen E, Mandrand-Berthelot MA, Pignol D, Garcia D, Rodrigue A. Pushing the limits of nickel detection to nanomolar range using a set of engineered bioluminescent Escherichia coli. Environ Sci Pollut Res Int 2017; 24:4-14. [PMID: 26498802 DOI: 10.1007/s11356-015-5580-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
The detection of nickel in water is of great importance due to its harmfulness for living organism. A way to detect Ni is the use of whole-cell biosensors. The aim of the present work was to build a light-emitting bacterial biosensor for the detection of Ni with high specificity and low detection limit properties. For that purpose, the regulatory circuit implemented relied on the RcnR Ni/Co metallo-regulator and its rcnA natural target promoter fused to the lux reporter genes. To convert RcnR to specifically detect Ni, several mutations were tested and the C35A retained. Deleting the Ni efflux pump rcnA and introducing genes encoding several Ni-uptake systems lowered the detection thresholds. When these constructs were assayed in several Escherichia coli strains, it appeared that the detection thresholds were highly variable. The TD2158 wild-type E. coli gave rise to a biosensor ten times more active and sensitive than its W3110 E. coli K12 equivalent. This biosensor was able to confidently detect Ni concentrations as little as 80 nM (4.7 μg l-1), which makes its use compatible with the norms governing the drinking water quality.
Collapse
Affiliation(s)
- Julien Cayron
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Elsa Prudent
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Camille Escoffier
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Erwan Gueguen
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Marie-Andrée Mandrand-Berthelot
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - David Pignol
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Daniel Garcia
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Agnès Rodrigue
- Université de Lyon, Lyon, 69003, France.
- INSA de Lyon, Villeurbanne, 69621, France.
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France.
| |
Collapse
|
13
|
Brutesco C, Prévéral S, Escoffier C, Descamps ECT, Prudent E, Cayron J, Dumas L, Ricquebourg M, Adryanczyk-Perrier G, de Groot A, Garcia D, Rodrigue A, Pignol D, Ginet N. Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors. Environ Sci Pollut Res Int 2017; 24:52-65. [PMID: 27234828 DOI: 10.1007/s11356-016-6952-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible Pars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.
Collapse
Affiliation(s)
- Catherine Brutesco
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Sandra Prévéral
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Camille Escoffier
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Elodie C T Descamps
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Elsa Prudent
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - Julien Cayron
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - Louis Dumas
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Manon Ricquebourg
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Géraldine Adryanczyk-Perrier
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Arjan de Groot
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Daniel Garcia
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Agnès Rodrigue
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - David Pignol
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Nicolas Ginet
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France.
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France.
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France.
| |
Collapse
|
14
|
Phelippeau M, Dubus JC, Reynaud-Gaubert M, Gomez C, Stremler le Bel N, Bedotto M, Prudent E, Drancourt M. Prevalence of Mycobacterium lentiflavum in cystic fibrosis patients, France. BMC Pulm Med 2015; 15:131. [PMID: 26503635 PMCID: PMC4621861 DOI: 10.1186/s12890-015-0123-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022] Open
Abstract
Background Mycobacterium lentiflavum is rarely isolated in respiratory tract samples from cystic fibrosis patients. We herein describe an unusually high prevalence of M. lentiflavum in such patients. Methods M. lentiflavum, isolated from the respiratory tract of cystic fibrosis patients, was identified using both rpoB partial sequencing and detected directly in the sputum by using real-time PCR targeting the smpB gene. Results M. lentiflavum emerged as the third most prevalent nontuberculous mycobacterial species isolated in cystic fibrosis patients in Marseille, France. Six such patients were all male, and two of them may have fulfilled the American Thoracic Society clinical and microbiological criteria for M. lentiflavum potential lung infection. Conclusions M. lentiflavum was the third most common mycobacteria isolated in cystic fibrosis patients, particularly in six male patients. M. lentiflavum outbreaks are emerging particularly in cystic fibrosis patients. Electronic supplementary material The online version of this article (doi:10.1186/s12890-015-0123-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael Phelippeau
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille, 13005, France.
| | - Jean-Christophe Dubus
- Centre de Ressource et de Compétences de la Mucoviscidose (CRCM) pédiatrique CHU Hôpital la Timone, Marseille, France.
| | - Martine Reynaud-Gaubert
- Centre de Ressource et de Compétences de la Mucoviscidose (CRCM) adulte; équipe de Transplantation pulmonaire, CHU Hôpital Nord, URMITE - CNRS-UMR 6236 Aix-Marseille Université, Marseille, France.
| | - Carine Gomez
- Centre de Ressource et de Compétences de la Mucoviscidose (CRCM) adulte; équipe de Transplantation pulmonaire, CHU Hôpital Nord, URMITE - CNRS-UMR 6236 Aix-Marseille Université, Marseille, France.
| | - Nathalie Stremler le Bel
- Centre de Ressource et de Compétences de la Mucoviscidose (CRCM) pédiatrique CHU Hôpital la Timone, Marseille, France.
| | - Marielle Bedotto
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille, 13005, France.
| | - Elsa Prudent
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille, 13005, France.
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille, 13005, France. .,Unité de recherche sur les maladies infectieuses et tropicales émergentes, Faculté de Médecine, 27 Bd jean Moulin, 13385, Marseille, cedex 5, France.
| |
Collapse
|
15
|
Lo CI, Padhamanabhan R, Fall B, Sambe-Ba B, Mediannikov O, Nguyen TT, Prudent E, Faye N, Wade B, Raoult D, Fournier PE, Fenollar F. Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov. New Microbes New Infect 2015; 8:41-50. [PMID: 26587237 PMCID: PMC4625094 DOI: 10.1016/j.nmni.2015.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 06/15/2015] [Revised: 09/04/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022] Open
Abstract
Strain FF6(T) was isolated from the cervical abscess of a 4-year-old Senegalese boy, in Dakar, Senegal. MALDI-TOF MS did not provide any identification. This strain exhibited a 95.17% 16S rRNA sequence identity with Necropsobacter rosorum. Using a polyphasic study including phenotypic and genomic analyses, strain FF6(T) was an aero-anaerobic Gram-negative cocobacillus, oxidase positive, and exhibited a genome of 2,493,927 bp (1 chromosome but no plasmid) with a G+C content of 46.2% that coded 2,309 protein-coding and 53 RNA genes. On the basis of these data, we propose the creation of Necropsobacter massiliensis sp. nov.
Collapse
Affiliation(s)
- C I Lo
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal
| | - R Padhamanabhan
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - B Fall
- Hôpital Principal, Senegal
| | | | - O Mediannikov
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal
| | - T-T Nguyen
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - E Prudent
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - N Faye
- Université Cheikh Anta Diop de Dakar, Laboratoire de Parasitologie générale, Dakar, Senegal
| | - B Wade
- Hôpital Principal, Senegal
| | - D Raoult
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - F Fenollar
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal
| |
Collapse
|
16
|
Barbi F, Bragalini C, Vallon L, Prudent E, Dubost A, Fraissinet-Tachet L, Marmeisse R, Luis P. PCR primers to study the diversity of expressed fungal genes encoding lignocellulolytic enzymes in soils using high-throughput sequencing. PLoS One 2014; 9:e116264. [PMID: 25545363 PMCID: PMC4278862 DOI: 10.1371/journal.pone.0116264] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/26/2014] [Indexed: 12/27/2022] Open
Abstract
Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities.
Collapse
Affiliation(s)
- Florian Barbi
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Claudia Bragalini
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Laurent Vallon
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Elsa Prudent
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Audrey Dubost
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Roland Marmeisse
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Patricia Luis
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne, France
| |
Collapse
|
17
|
Morel AS, Dubourg G, Prudent E, Edouard S, Gouriet F, Casalta JP, Fenollar F, Fournier PE, Drancourt M, Raoult D. Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases. Eur J Clin Microbiol Infect Dis 2014; 34:561-70. [PMID: 25348607 DOI: 10.1007/s10096-014-2263-z] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/07/2014] [Indexed: 12/24/2022]
Abstract
Molecular tools have shown an added value in the diagnosis of infectious diseases, in particular for those caused by fastidious intracellular microorganisms, or in patients receiving antibiotics before sampling. If 16S rDNA amplification had been gradually implemented in microbiology laboratories, specific real-time polymerase chain reaction (PCR) would have permitted an increase in the sensitivity of molecular methods and a reduction of contamination. Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad. Among these samples, 81,476 PCRs were performed, of which 1,192 were positive. Molecular techniques detected intracellular microorganisms in 31.3 % of respiratory samples, 27.8 % of endocarditis samples and 51.9 % of adenitis samples. Excluding intracellular bacteria, 25 % of the positive samples in this series were sterile in culture. Conventional broad-range PCR permitted the identification of fastidious and anaerobic microorganisms, but specific real-time PCR showed a significant superiority in the diagnosis of osteoarticular infections, in particular for those caused by Kingella kingae and Staphylococcus aureus, and for endocarditis diagnosis, specifically when Streptococcus gallolyticus and Staphylococcus aureus were involved. The sensitivity of conventional broad-range PCR was 62.9 % concerning overall diagnoses for which both techniques had been performed. These findings should lead microbiologists to focus on targeted specific real-time PCR regarding the clinical syndrome. Finally, syndrome-driven diagnosis, which consists of testing a panel of microorganisms commonly involved for each syndrome, permitted the establishment of 31 incidental diagnoses.
Collapse
Affiliation(s)
- A-S Morel
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Bragalini C, Ribière C, Parisot N, Vallon L, Prudent E, Peyretaillade E, Girlanda M, Peyret P, Marmeisse R, Luis P. Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples. DNA Res 2014; 21:685-94. [PMID: 25281543 PMCID: PMC4263301 DOI: 10.1093/dnares/dsu030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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] [Indexed: 12/30/2022] Open
Abstract
Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment.
Collapse
Affiliation(s)
- Claudia Bragalini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Céline Ribière
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Nicolas Parisot
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Laurent Vallon
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Elsa Prudent
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Eric Peyretaillade
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Mariangela Girlanda
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, Viale Mattioli 25, Turin 10125, Italy
| | - Pierre Peyret
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Roland Marmeisse
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Patricia Luis
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| |
Collapse
|