J. Jones and J. Dubey, Foodborne Toxoplasmosis, Clinical Infectious Diseases, vol.55, issue.6, pp.845-51, 2012.
DOI : 10.1093/cid/cis508

E. Shwab, X. Zhu, D. Majumdar, H. Pena, S. Gennari et al., Geographical patterns of Toxoplasma gondii genetic diversity revealed by multilocus PCR-RFLP genotyping, Parasitology, vol.133, issue.04, pp.453-61, 2014.
DOI : 10.1016/j.vetpar.2007.07.003

M. Maenz, D. Schluter, O. Liesenfeld, G. Schares, U. Gross et al., Ocular toxoplasmosis past, present and new aspects of an old disease, Progress in Retinal and Eye Research, vol.39, pp.77-106, 2014.
DOI : 10.1016/j.preteyeres.2013.12.005

M. Demar, D. Hommel, F. Djossou, C. Peneau, R. Boukhari et al., Acute toxoplasmoses in immunocompetent patients hospitalized in an intensive care unit in French Guiana, Clinical Microbiology and Infection, vol.18, issue.7, pp.221-252, 2012.
DOI : 10.1111/j.1469-0691.2011.03648.x

URL : https://hal.archives-ouvertes.fr/hal-00678752

A. De-la-torre, A. Sauer, A. Pfaff, T. Bourcier, J. Brunet et al., Severe South American ocular toxoplasmosis is associated with decreased Ifn-gamma/Il-17a and increased Il-6/Il-13 intraocular levels, PLoS Negl Trop Dis, vol.7, issue.11, p.24278490, 2013.

S. Abgrall, C. Rabaud, and D. Costagliola, Incidence and Risk Factors for Toxoplasmic Encephalitis in Human Immunodeficiency Virus???Infected Patients before and during the Highly Active Antiretroviral Therapy Era, Clinical Infectious Diseases, vol.33, issue.10, pp.1747-55, 2001.
DOI : 10.1086/322622

J. Jones and J. Roberts, Toxoplasmosis Hospitalizations in the United States, 2008, and Trends, 1993-2008, Clinical Infectious Diseases, vol.54, issue.7, pp.58-61, 1993.
DOI : 10.1093/cid/cir990

B. George, E. Schneider, and A. Venkatesan, Encephalitis hospitalization rates and inpatient mortality in the United States, PLoS One, vol.9, issue.9, p.25192177, 2000.

B. Luft, R. Hafner, A. Korzun, C. Leport, D. Antoniskis et al., Toxoplasmic Encephalitis in Patients with the Acquired Immunodeficiency Syndrome, New England Journal of Medicine, vol.329, issue.14, pp.995-1000, 1993.
DOI : 10.1056/NEJM199309303291403

F. Raffi, J. Aboulker, C. Michelet, V. Reliquet, H. Pelloux et al., A prospective study of criteria for the diagnosis of toxoplasmic encephalitis in 186 AIDS patients, AIDS, vol.11, issue.2, pp.177-84, 1997.
DOI : 10.1097/00002030-199702000-00007

B. Luft and J. Remington, Toxoplasmic Encephalitis in AIDS, Clinical Infectious Diseases, vol.15, issue.2, pp.211-233, 1992.
DOI : 10.1093/clinids/15.2.211

K. Ke, -. Roth, A. Roth, B. Arasteh, K. Janitschke et al., Value of PCR for evaluating occurrence of parasitemia in immunocompromised patients with cerebral and extracerebral toxoplasmosis, J Clin Microbiol, vol.32, issue.11, pp.2813-2822, 1994.

M. Dupon, J. Cazenave, J. Pellegrin, J. Ragnaud, A. Cheyrou et al., Detection of Toxoplasma gondii by PCR and tissue culture in cerebrospinal fluid and blood of human immunodeficiency virusseropositive patients, J Clin Microbiol, vol.33, issue.9, pp.2421-2427, 1995.

J. Lamoril, J. Molina, A. De-gouvello, Y. Garin, J. Deybach et al., Detection by PCR of Toxoplasma gondii in blood in the diagnosis of cerebral toxoplasmosis in patients with AIDS., Journal of Clinical Pathology, vol.49, issue.1, pp.89-92, 1996.
DOI : 10.1136/jcp.49.1.89

H. Pelloux, J. Dupouy-camet, F. Derouin, J. Aboulker, and F. Raffi, A multicentre prospective study for the polymerase chain reaction detection of Toxoplasma gondii DNA in blood samples from 186 AIDS patients with suspected toxoplasmic encephalitis, AIDS, vol.11, issue.15, pp.1888-90, 1997.
DOI : 10.1097/00002030-199715000-00018

C. Franzen, M. Altfeld, P. Hegener, P. Hartmann, G. Arendt et al., Limited value of PCR for detection of Toxoplasma gondii in blood from human immunodeficiency virus-infected patients, J Clin Microbiol, vol.35, issue.10, pp.2639-2680, 1997.

F. Colombo, J. Vidal, P. De-oliveira, A. Hernandez, A. Bonasser-filho et al., Diagnosis of Cerebral Toxoplasmosis in AIDS Patients in Brazil: Importance of Molecular and Immunological Methods Using Peripheral Blood Samples, Journal of Clinical Microbiology, vol.43, issue.10, pp.5044-5051, 2005.
DOI : 10.1128/JCM.43.10.5044-5047.2005

C. Correia, H. Melo, and V. Costa, Influence of neurotoxoplasmosis characteristics on real-time PCR sensitivity among AIDS patients in Brazil, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.104, issue.1, 2010.
DOI : 10.1016/j.trstmh.2009.06.012

D. Ajzenberg, Is PCR testing on blood samples useful or not in the diagnosis of Toxoplasma encephalitis?, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.104, issue.8, pp.569-70, 2010.
DOI : 10.1016/j.trstmh.2010.04.003

URL : https://hal.archives-ouvertes.fr/hal-00676916

N. Cardona, N. Basto, B. Parra, A. Zea, C. Pardo et al., DNA in the Peripheral Blood of HIV-Positive Patients with Neuro-opportunistic Infections by a Real-Time PCR Assay, Journal of Neuroparasitology, vol.2, pp.1-6, 2011.
DOI : 10.4303/jnp/N110402

W. Homan, M. Vercammen, D. Braekeleer, J. Verschueren, and H. , Identification of a 200- to 300-fold repetitive 529 bp DNA fragment in Toxoplasma gondii, and its use for diagnostic and quantitative PCR1Note: Nucleotide sequence data reported in this paper have been submitted to GenBankTM database with the accession number AF146527 (Toxoplasma gondii genomic repetitive 529 bp fragment).1, International Journal for Parasitology, vol.30, issue.1, pp.69-75, 2000.
DOI : 10.1016/S0020-7519(99)00170-8

S. Cassaing, M. Bessieres, A. Berry, A. Berrebi, R. Fabre et al., Comparison between Two Amplification Sets for Molecular Diagnosis of Toxoplasmosis by Real-Time PCR, Journal of Clinical Microbiology, vol.44, issue.3, pp.720-724, 2006.
DOI : 10.1128/JCM.44.3.720-724.2006

D. Ajzenberg, F. Collinet, A. Mercier, P. Vignoles, and M. Dardé, Isolates with 15 Microsatellite Markers in a Single Multiplex PCR Assay, Journal of Clinical Microbiology, vol.48, issue.12, pp.4641-4646, 2010.
DOI : 10.1128/JCM.01152-10

URL : https://hal.archives-ouvertes.fr/hal-00677196

A. Khan, D. Ajzenberg, A. Mercier, M. Demar, S. Simon et al., Geographic Separation of Domestic and Wild Strains of Toxoplasma gondii in French Guiana Correlates with a Monomorphic Version of Chromosome1a, PLoS Neglected Tropical Diseases, vol.108, issue.9, p.25233228, 2014.
DOI : 10.1371/journal.pntd.0003182.s001

URL : https://hal.archives-ouvertes.fr/hal-01205272

A. Mercier, D. Ajzenberg, S. Devillard, M. Demar, B. De-thoisy et al., Human impact on genetic diversity of Toxoplasma gondii: Example of the anthropized environment from French Guiana, Infection, Genetics and Evolution, vol.11, issue.6, pp.1378-87, 2011.
DOI : 10.1016/j.meegid.2011.05.003

URL : https://hal.archives-ouvertes.fr/hal-00698419

L. Cavalli-sforza and A. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.233-57, 1967.
DOI : 10.2307/2406616

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1706274

J. Landis and G. Koch, An Application of Hierarchical Kappa-type Statistics in the Assessment of Majority Agreement among Multiple Observers, Biometrics, vol.33, issue.2, pp.363-74, 1977.
DOI : 10.2307/2529786

J. Kaplan, C. Benson, K. Holmes, J. Brooks, A. Pau et al., Guidelines for prevention and treatment of opportunistic infections in HIV-infected adults and adolescents: recommendations from CDC, the National Institutes of Health, and the HIV Medicine Association of the Infectious Diseases Society of America, MMWR Recomm Rep, vol.58, issue.4, pp.1-207, 2009.
DOI : 10.1037/e537722009-001

M. Dedicoat and N. Livesley, Management of toxoplasmic encephalitis in HIV-infected adults (with an emphasis on resource-poor settings), Cochrane Database Syst Rev, issue.3, pp.5420-16856096, 2006.

G. Beraud, S. Pierre-francois, A. Foltzer, D. Smadja, and A. Cabié, Cotrimoxazole pour la toxoplasmose c??r??brale : moins cher et moins toxique ?, M??decine et Maladies Infectieuses, vol.38, issue.208, pp.94-100, 2008.
DOI : 10.1016/S0399-077X(08)73005-1

S. Lucas, A. Hounnou, C. Peacock, A. Beaumel, G. Djomand et al., The mortality and pathology of HIV infection in a West African city, AIDS, vol.7, issue.12, pp.1569-79, 1993.
DOI : 10.1097/00002030-199312000-00005

M. Nacher, F. Huber, E. Guedj, M. Vaz, T. Magnien et al., Risk factors for death among patients in French Guiana, HIV Med, vol.8, issue.7, pp.1996-2005472, 2007.

. Unaids and . Junpoha, Global report: UNAIDS report on the global AIDS epidemic 2013, 2013.

C. Lewden, M. Sobesky, A. Cabié, P. Couppie, F. Boulard et al., Causes de d??c??s des adultes infect??s par le VIH dans les d??partements fran??ais d'Am??rique ?? l'??re des traitements antir??troviraux hautement actifs, M??decine et Maladies Infectieuses, vol.34, issue.7, pp.286-92, 2004.
DOI : 10.1016/S0399-077X(04)00146-5

M. Brenier-pinchart, E. Capderou, R. Bertini, S. Bailly, H. Fricker-hidalgo et al., Molecular diagnosis of toxoplasmosis: value of the buffy coat for the detection of circulating Toxoplasma gondii, Diagnostic Microbiology and Infectious Disease, vol.82, issue.4, pp.289-91, 2015.
DOI : 10.1016/j.diagmicrobio.2015.04.004

URL : https://hal.archives-ouvertes.fr/hal-01262441

Y. Sterkers, E. Varlet-marie, S. Cassaing, M. Brenier-pinchart, S. Brun et al., Multicentric Comparative Analytical Performance Study for Molecular Detection of Low Amounts of Toxoplasma gondii from Simulated Specimens, Journal of Clinical Microbiology, vol.48, issue.9, pp.3216-3238, 2010.
DOI : 10.1128/JCM.02500-09

P. Bastien, G. Procop, and U. Reischl, Quantitative Real-Time PCR Is Not More Sensitive than "Conventional" PCR, Journal of Clinical Microbiology, vol.46, issue.6, pp.1897-900, 2008.
DOI : 10.1128/JCM.02258-07

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2446855

P. Bastien, Molecular diagnosis of toxoplasmosis, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.96, issue.1, pp.205-220, 2002.
DOI : 10.1016/S0035-9203(02)90078-7

URL : https://hal.archives-ouvertes.fr/hal-01262441

D. Ajzenberg, H. Yera, P. Marty, L. Paris, F. Dalle et al., Isolates Associated with Toxoplasmosis in Immunocompromised Patients and Correlation with Clinical Findings, The Journal of Infectious Diseases, vol.199, issue.8, pp.1155-67, 2009.
DOI : 10.1086/597477

URL : https://hal.archives-ouvertes.fr/hal-00374813

C. Bourdin, A. Busse, E. Kouamou, F. Touafek, B. Bodaghi et al., PCR-Based Detection of Toxoplasma gondii DNA in Blood and Ocular Samples for Diagnosis of Ocular Toxoplasmosis, Journal of Clinical Microbiology, vol.52, issue.11, pp.3987-91, 2014.
DOI : 10.1128/JCM.01793-14

A. Fekkar, D. Ajzenberg, B. Bodaghi, F. Touafek, L. Hoang et al., Direct Genotyping of Toxoplasma gondii in Ocular Fluid Samples from 20 Patients with Ocular Toxoplasmosis: Predominance of Type II in France, Journal of Clinical Microbiology, vol.49, issue.4, pp.1513-1520, 2011.
DOI : 10.1128/JCM.02196-10

URL : https://hal.archives-ouvertes.fr/hal-00677558

A. Khan, C. Jordan, C. Muccioli, A. Vallochi, L. Rizzo et al., Genetic Divergence of Toxoplasma gondii Strains Associated with Ocular Toxoplasmosis, Brazil, Emerging Infectious Diseases, vol.12, issue.6, pp.942-951, 2006.
DOI : 10.3201/eid1206.060025

I. Ferreira, J. Vidal, C. De-mattos-cde, L. De-mattos, D. Qu et al., Toxoplasma gondii isolates: Multilocus RFLP???PCR genotyping from human patients in Sao Paulo State, Brazil identified distinct genotypes, Experimental Parasitology, vol.129, issue.2, pp.190-195, 2011.
DOI : 10.1016/j.exppara.2011.06.002

URL : http://doi.org/10.1016/j.exppara.2011.06.002

C. Silveira, A. Vallochi, R. Da-silva, U. Muccioli, C. Holland et al., Toxoplasma gondii in the peripheral blood of patients with acute and chronic toxoplasmosis, British Journal of Ophthalmology, vol.95, issue.3, pp.396-400, 2011.
DOI : 10.1136/bjo.2008.148205

R. Sonneville, M. Schmidt, J. Messika, A. Hssain, A. Da-silva et al., Neurologic outcomes and adjunctive steroids in HIV patients with severe cerebral toxoplasmosis, Neurology, vol.79, issue.17, pp.1762-1768, 2012.
DOI : 10.1212/WNL.0b013e3182704040