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Kaboré OD, Millogo A, Sanogo B, Birba E, Poda A, Nacro B, Marcy O, Godreuil S, Ouédraogo AS. Analytical performances of the Xpert MTB/RIF assay using stool specimens to improve the diagnosis of pulmonary tuberculosis in Burkina Faso, a tuberculosis endemic country. PLoS One 2023; 18:e0288671. [PMID: 37523357 PMCID: PMC10389731 DOI: 10.1371/journal.pone.0288671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023] Open
Abstract
Timely diagnosis of Pulmonary Tuberculosis (PTB) is associated with good prognosis, but remains difficult in primary healthcare facilities and particularly in children and patients living with HIV. The aim of this study was to compare the GeneXpert ® MTB/RIF assay (Xpert) performed using a stool sample (3-5 g) and using the first Respiratory Tract Sample (RTS; i.e., sputum, bronchoalveolar or gastric aspirate; as normally done) concomitantly collected from 119 patients with suspected PTB to improve PTB diagnosis in Burkina Faso, a high tuberculosis burden country with limited resources. Overall, microbiological, microscopic and molecular analysis of the 119 first RTS and 119 stool specimens led to Mycobacterium tuberculosis complex detection in 28 patients (23 positive RTS cultures and 5 negative RTS cultures-RTS Xpert positive). When using the 28 clinical confirmed cases as reference standard, the sensitivities of the stool-based and RTS-based Xpert assays were not different (24/28, 85.7%, versus 26/28, 92.86%; p > 0.30), and 22 results were fully concordant. Considering the first RTS culture as the gold standard, the sensitivities of the stool-based and RTS-based Xpert assays to detect PTB in patients with positive RTS culture were 100% (23/23) and 91.3% (21/23), respectively (p >0.05). The stool-based Xpert assay specificity for excluding PTB was 99% (95/96) (compared with 95%, 91/96, when using RTS) and its negative and positive predictive values were 100% (95/95) and 96% (23/24), respectively. Compared with the 23 positive RTS cultures, the incremental yield rates of the RTS-based and stool-based Xpert assays were 4.2% (5/119) and 0.84% (1/119), respectively. Overall, our findings support using the stool-based Xpert assay as an alternative method for earlier PTB diagnosis, when RTS are difficult to obtain.
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Affiliation(s)
- Odilon D Kaboré
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso, Burkina Faso
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso, Burkina Faso
| | - Anselme Millogo
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso, Burkina Faso
| | - Bintou Sanogo
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Département de Pédiatrie du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Emile Birba
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Service de Pneumologie-Phtisiologie du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Armel Poda
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Service des Maladies Infectieuses du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Boubacar Nacro
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Département de Pédiatrie du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Olivier Marcy
- Bordeaux Population Health Research Center Inserm U1219, University of Bordeaux, Bordeaux, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, CHU de Montpellier, MIVEGEC (IRD, CNRS, Université de Montpellier), Montpellier, France
| | - Abdoul-Salam Ouédraogo
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso, Burkina Faso
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Muraz Center, Bobo Dioulasso, Burkina Faso
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TB-QUICK: CRISPR-Cas12b-assisted rapid and sensitive detection of Mycobacterium tuberculosis. J Infect 2021; 83:54-60. [PMID: 33951419 DOI: 10.1016/j.jinf.2021.04.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/27/2021] [Accepted: 04/18/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Tuberculosis (TB) remains one of the public health problems worldwide. Rapid, sensitive and cost-effective diagnosis of Mycobacterium tuberculosis (M.tb) is critical for TB control. METHODS We developed a novel M.tb DNA detection platform (nominated as TB-QUICK) which combined loop-mediated isothermal amplification (LAMP) and CRISPR-Cas12b detection. TB-QUICK was performed on pulmonary or plasma samples collected from 138 pulmonary TB (PTB) patients, 21 non-TB patients and 61 close contacts to TB patients. Acid-fast bacillus (AFB) smear, M.tb culture and GeneXpert MTB/RIF (Xpert) assays were routinely conducted in parallel. RESULTS By targeting M.tb IS6110, TB-QUICK platform could detect as low as 1.3 copy/μL M.tb DNA within 2 h. In pulmonary TB samples, TB-QUICK exhibited improved overall sensitivity of 86.8% over M.tb culture (66.7%) and Xpert (70.4%), with the specificity of 95.2%. More significantly, TB-QUICK exhibited a superior sensitivity in AFB-negative samples (80.5%) compared to Xpert (57.1%) and M.tb culture (46.2%). In the detection of plasma M.tb DNA by TB-QUICK, 41.2% sensitivity for AFB-positive and 31.7% for AFB-negative patients were achieved. CONCLUSION In conclusion, TB-QUICK exhibits rapidity and sensitivity for M.tb DNA detection with the superiority in smear-negative paucibacillary TB patients. The clinical application of TB-QUICK in TB diagnosis needs to be further validated in larger cohort.
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Bonnet M, Lagier JC, Raoult D, Khelaifia S. Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. New Microbes New Infect 2019; 34:100622. [PMID: 31956419 PMCID: PMC6961714 DOI: 10.1016/j.nmni.2019.100622] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Microbiology has been largely developed thanks to the discovery and optimization of culture media. The first liquid artificial culture medium was created by Louis Pasteur in 1860. Previously, bacterial growth on daily materials such as some foods had been observed. These observations highlighted the importance of the bacteria's natural environment and their nutritional needs in the development of culture media for their isolation. A culture medium is essentially composed of basic elements (water, nutrients), to which must be added different growth factors that will be specific to each bacterium and necessary for their growth. The evolution of bacterial culture through the media used for their culture began with the development of the first solid culture medium by Koch, allowing not only the production of bacterial colonies, but also the possibility of purifying a bacterial clone. The main gelling agent used in solid culture media is agar. However, some limits have been observed in the use of agar because of some extremely oxygen-sensitive bacteria that do not grow on agar media, and other alternatives were proposed and tested. Then, the discovery of antimicrobial agents and their specific targets prompted the emergence of selective media. These inhibiting agents make it possible to eliminate undesirable bacteria from the microbiota and select the bacteria desired. Thanks to a better knowledge of the bacterial environment, it will be possible to develop new culture media and new culture conditions, better adapted to certain fastidious bacteria that are difficult to isolate.
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Affiliation(s)
- M Bonnet
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - J C Lagier
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseillle, France
| | - D Raoult
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseillle, France
| | - S Khelaifia
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseillle, France
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Malaria, tuberculosis and HIV: what's new? Contribution of the Institut Hospitalo-Universitaire Méditerranée Infection in updated data. New Microbes New Infect 2018; 26:S23-S30. [PMID: 30402240 PMCID: PMC6205578 DOI: 10.1016/j.nmni.2018.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 11/22/2022] Open
Abstract
The Institut Hospitalo-Universitaire Méditerranée Infection is positioned for the diagnosis, prevention and treatment of the ‘big three’ killer diseases: malaria, tuberculosis and HIV. We implemented the use of new diagnostic samples such as stools and new diagnostic tests such as mass spectrometry for the dual identification of vectors and pathogens. Furthermore, advances in the prevention and treatment of malaria and tuberculosis are reviewed, along with advances in the understanding of the role of microbiota in the resistance to HIV infection. These achievements represent a major step towards a better management of the ‘big three’ diseases worldwide.
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Bouam A, Armstrong N, Levasseur A, Drancourt M. Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots. Sci Rep 2018; 8:9309. [PMID: 29915369 PMCID: PMC6006331 DOI: 10.1038/s41598-018-27629-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/05/2018] [Indexed: 12/04/2022] Open
Abstract
Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015-6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively. The three genomes encode for secondary metabolites, with 38, 33 and 46 genes found to be associated with polyketide synthases/non-ribosomal peptide synthases and nine, seven and ten genes encoding for bacteriocins, respectively. The genome of strain AB308 encodes for one questionable prophage and three incomplete prophages, while only incomplete prophages were predicted in AB215 and AB57 genomes. Genetic and genomic data indicate that strains AB308, AB215 and AB57 are each representative of a new Mycobacterium species that we respectively named Mycobacterium terramassiliense, Mycobacterium numidiamassiliense and Mycobacterium rhizamassiliense.
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Affiliation(s)
- A Bouam
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - N Armstrong
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - A Levasseur
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France.
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Reply to Drancourt, “Culturing Stools To Detect Mycobacterium tuberculosis”. J Clin Microbiol 2018; 56:56/5/e00056-18. [DOI: 10.1128/jcm.00056-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria. Clin Microbiol Rev 2018; 31:31/2/e00038-17. [PMID: 29386234 DOI: 10.1128/cmr.00038-17] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.
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Stool Culture for Diagnosis of Pulmonary Tuberculosis in Children. J Clin Microbiol 2017; 55:3355-3365. [PMID: 28904186 PMCID: PMC5703802 DOI: 10.1128/jcm.00801-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022] Open
Abstract
Bacteriological confirmation of Mycobacterium tuberculosis is achieved in the minority of young children with tuberculosis (TB), since specimen collection is resource intensive and respiratory secretions are mostly paucibacillary, leading to limited sensitivity of available diagnostic tests. Although molecular tests are increasingly available globally, mycobacterial culture remains the gold standard for diagnosis and determination of drug susceptibility and is more sensitive than molecular methods for paucibacillary TB. We evaluated stool culture as an alternative to respiratory specimens for the diagnosis of suspected intrathoracic TB in a subgroup of 188 children (median age, 14.4 months; 15.4% HIV infected) enrolled in a TB diagnostic study at two local hospitals in Cape Town, South Africa. One stool culture was compared to overall bacteriological confirmation by stool Xpert and by Xpert and culture of multiple respiratory specimens. After decontamination/digestion with NALC (N-acetyl-l-cysteine)-NaOH (1.25%), concentrated fluorescent smear microscopy, Xpert MTB/RIF, and liquid culture were completed for all specimens. Culture contamination of stool specimens was high at 41.5%. Seven of 90 (7.8%) children initiating TB treatment were stool culture positive for M. tuberculosis. Excluding contaminated cultures, the sensitivity of stool culture versus confirmed TB was 6/25 (24.0%; 95% confidence interval [CI] = 9.4 to 45.1%). In addition, stool culture detected TB in 1/93 (1.1%) children with “unconfirmed TB.” Testing the same stool by Xpert increased sensitivity to 33.3% (95% CI = 18.0 to 51.8%). In conclusion, stool culture had low sensitivity for M. tuberculosis detection in children with intrathoracic TB. Reducing culture contamination through improved laboratory protocols may enable more reliable estimates of its diagnostic utility.
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Nambiar R, Chatellier S, Bereksi N, van Belkum A, Singh N, Barua B, Shetty A, Rodrigues C. Evaluation of Mycotube, a modified version of Lowenstein-Jensen (LJ) medium, for efficient recovery of Mycobacterium tuberculosis (MTB). Eur J Clin Microbiol Infect Dis 2017; 36:1981-1988. [PMID: 28685188 DOI: 10.1007/s10096-017-3052-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 06/20/2017] [Indexed: 12/01/2022]
Abstract
Timely diagnosis of tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is only achieved for ~58% cases. An improved, accurate, time- and cost-effective method for bacteriological confirmation of MTB is necessary. We evaluated Mycotube, a new variant of Lowenstein-Jensen (LJ) culture medium, by comparing it with Mycobacterium Growth Indicator Tube (MGIT) 960 (gold standard), local LJ, and bioMérieux LJ-T in terms of isolation rate and time-to-growth. Pulmonary and extra-pulmonary samples from treatment-naïve suspects (n = 207) were decontaminated by the N-acetyl-L-cysteine-sodium hydroxide method and used to inoculate the four media. Subjective and objective parameters were used for evaluation. Mycotube yielded 140 positive results, compared to 162, 69, and 141 from MGIT, local LJ, and LJ-T, respectively. Of these, 139 (67%) were true-positive results and 1 (0.5%) was false-positive. The mean time-to-growth detection was 17.4 days for Mycotube, compared to 14.5, 28.1, and 16.5 days for MGIT, local LJ, and LJ-T, respectively. The mean time-to-growth for local LJ significantly differed from that for MGIT, but not those for LJ-T and Mycotube. No contamination was observed. Mycotube had a sensitivity of 85.8% and a specificity of 97.8% as compared to MGIT. Mycotube offers good results, comparable with those observed for conventional LJ. It requires only basic laboratory infrastructure. The overall cost of the test should be nearly three times lower than that of MGIT. Mycotube helps with TB diagnosis and generates pure isolates for drug susceptibility testing.
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Affiliation(s)
- R Nambiar
- Section of Microbiology, Department of Laboratory Medicine, PD Hinduja Hospital and Medical Research Centre, Mumbai, India.
| | - S Chatellier
- bioMérieux, 3 route de Port Michaud, 38390, La Balme Les Grottes, France
| | - N Bereksi
- bioMérieux, ZA des Lilas, 5 rue des Aqueducs, BP 10, 69290, Craponne, France
| | - A van Belkum
- bioMérieux, 3 route de Port Michaud, 38390, La Balme Les Grottes, France
| | - N Singh
- bioMérieux India Private Limited, New Delhi, India
| | - B Barua
- bioMérieux India Private Limited, New Delhi, India
| | - A Shetty
- Section of Microbiology, Department of Laboratory Medicine, PD Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - C Rodrigues
- Section of Microbiology, Department of Laboratory Medicine, PD Hinduja Hospital and Medical Research Centre, Mumbai, India
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Zingue D, Flaudrops C, Drancourt M. Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies. Eur J Clin Microbiol Infect Dis 2016; 35:1983-1987. [PMID: 27549109 DOI: 10.1007/s10096-016-2750-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/03/2016] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) identification of mycobacteria requires a standard acetonitrile/formic acid pre-MALDI-TOF-MS. We prospectively compared this standard protocol with direct deposit with matrix for the identification of mycobacteria cultured on solid media. We first verified that Mycobacterium tuberculosis was killed after it was mixed with matrix. Then, 111 Mycobacterium isolates previously identified by partial rpoB gene sequencing were tested in parallel by the two protocols. An identification score >1.7 was obtained in 86/111 (77.5 %) isolates after protein extraction versus 97/111 (87.4 %) isolates after direct deposit (p = 0.039, Chi-squared test). In a third step, we determined that direct deposit achieved identification for as few as 2.104 M. tuberculosis organisms. In a fourth step, we evaluated direct deposit of one colony for 116 solid medium-cultured clinical isolates finally identified as representative of 12 species (63.8 % M. tuberculosis). For 114/116 (98.3 %) isolates with an identification score >1.2, the MALDI-TOF-MS identification was in complete agreement with the reference rpoB gene sequencing identification. One isolate with a MALDI-TOF-MS identification score of 1.22 for M. fortuitum was identified as M. avium by partial rpoB gene sequencing. One other isolate with a MALDI-TOF-MS identification score of 1.22 for M. tuberculosis was identified as M. tuberculosis by genotyping. All the original MALDI-TOF-MS spectra reported here have been deposited in a public database. Direct deposit of one colony on a MALDI-TOF-MS plate allows for an accurate identification of mycobacteria for an identification score >1.3.
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Affiliation(s)
- D Zingue
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - C Flaudrops
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - M Drancourt
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France.
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