, Accelerating work to overcome the global impact of neglected tropical diseases: a roadmap for implementation: executive summary. Geneva: World Health Organization, 2012.

S. M. Fletcher, D. Stark, J. Harkness, and J. Ellis, Enteric protozoa in the developed world: a public health perspective, Clin Microbiol Rev, vol.25, issue.3, pp.420-469, 2012.

C. Schrader, A. Schielke, L. Ellerbroek, and R. Johne, PCR inhibitors-occurrence, properties and removal, J Appl Microbiol, vol.113, issue.5, pp.1014-1040, 2012.

Z. Babaei, H. Oormazdi, S. Rezaie, M. Rezaeian, and E. Razmjou, Giardia intestinalis: DNA extraction approaches to improve PCR results, Exp Parasitol, vol.128, issue.2, pp.159-62, 2011.

S. Paulos, M. Mateo, A. De-lucio, M. Hernández-de-mingo, B. Bailo et al., Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp, J Microbiol Methods, vol.127, pp.68-73, 2016.

C. Mary, E. Chapey, E. Dutoit, K. Guyot, L. Hasseine et al., Multicentric evaluation of a new real-time PCR assay for quantification of Cryptosporidium spp. and identification of Cryptosporidium parvum and Cryptosporidium hominis, J Clin Microbiol, vol.51, issue.8, pp.2556-63, 2013.

H. Yoshikawa, F. Dogruman-al, F. Dogruman-ai, S. Turk, S. Kustimur et al., Evaluation of DNA extraction kits for molecular diagnosis of human Blastocystis subtypes from fecal samples, Parasitol Res, vol.109, issue.4, pp.1045-50, 2011.

I. Hamad, A. Abdallah, R. Ravaux, I. Mokhtari, S. Tissot-dupont et al., Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients, PLoS ONE, vol.13, issue.1, p.191913, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01765832

D. Sow, P. Parola, K. Sylla, M. Ndiaye, P. Delaunay et al., Performance of real-time polymerase chain reaction assays for the detection of 20 gastrointestinal parasites in clinical samples from Senegal, Am J Trop Med Hyg, vol.97, issue.1, pp.173-82, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01774347

R. Mejia, Y. Vicuña, N. Broncano, C. Sandoval, M. Vaca et al., A novel, multi-parallel, real-time polymerase chain reaction approach for eight gastrointestinal parasites provides improved diagnostic capabilities to resource-limited at-risk populations, Am J Trop Med Hyg, vol.88, issue.6, pp.1041-1048, 2013.

B. Dridi, M. Henry, A. El-khéchine, D. Raoult, and M. Drancourt, High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol, PLoS ONE, vol.4, issue.9, p.7063, 2009.

J. J. Verweij, R. A. Blange, K. Templeton, J. Schinkel, E. A. Brienen et al., Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR, J Clin Microbiol, vol.42, pp.1220-1223, 2004.

J. Shin, S. Lee, T. S. Kim, D. Ma, J. Chai et al., Multiplex-Touchdown PCR to Simultaneously Detect Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis, the Major Causes of Traveler's Diarrhea, Korean J Parasitol, vol.54, issue.5, pp.631-637, 2016.

S. Persson, R. F. De-boer, A. Kooistra-smid, and K. Olsen, Five commercial DNA extraction systems tested and compared on a stool sample collection, Diagn Microbiol Infect Dis, vol.69, issue.3, pp.240-244, 2011.

S. Khelaifia, P. Ramonet, B. Buffet, M. Drancourt, and M. , A semi-automated protocol for Archaea DNA extraction from stools, BMC Res Notes, vol.7, issue.6, p.186, 2013.
URL : https://hal.archives-ouvertes.fr/inserm-00825513

, Accelerating work to overcome the global impact of neglected tropical diseases : A roadmap for implementation : Executive summary, 2012.

A. Calderaro, Intestinal parasitoses in a tertiary-care hospital located in a non-endemic setting during, BMC Infectious Diseases, vol.14, p.264, 2006.

S. M. Fletcher, Enteric protozoa in the developed world: a public health perspective, Clinical Microbiology Reviews, vol.25, pp.420-449, 2012.

G. A. Holtman, Dientamoeba fragilis colonization is not associated with gastrointestinal symptoms in children at primary care level, Family Practice, vol.34, pp.25-29, 2017.

P. Jokelainen, Dientamoeba fragilis, a commensal in children in Danish day care centers, Journal of Clinical Microbiology, vol.55, pp.1707-1713, 2017.

J. J. Verweij, Application of PCR-based methods for diagnosis of intestinal parasitic infections in the clinical laboratory, Parasitology, vol.141, pp.1863-1872, 2014.

J. J. Verweij and C. R. Stensvold, Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections, Clinical Microbiology Reviews, vol.27, pp.371-418, 2014.

R. J. Ten-hove, Molecular diagnostics of intestinal parasites in returning travellers, European Journal of Clinical Microbiology and Infectious Diseases, vol.28, pp.1045-1053, 2009.

L. Bruijnesteijn-van-coppenraet, Parasitological diagnosis combining an internally controlled real-time PCR assay for the detection of four protozoa in stool samples with a testing algorithm for microscopy, Clinical Microbiology and Infectious Diseases, vol.15, pp.869-874, 2009.

M. Basuni, A pentaplex real-time polymerase chain reaction assay for detection of four species of soil-transmitted helminths, The American Journal of Tropical Medicine and Hygiene, vol.84, pp.338-343, 2011.

R. Mejia, A novel, multi-parallel, real-time polymerase chain reaction approach for eight gastrointestinal parasites provides improved diagnostic capabilities to resource-limited at-risk populations, The American Journal of Tropical Medicine and Hygiene, vol.88, pp.1041-1047, 2013.

S. Mom?ilovi?, Rapid diagnosis of parasitic diseases: current scenario and future needs, Clinical Microbiology and Infection, pp.1198-743, 2018.

U. Ryan, New technologies for detection of enteric parasites, Trends Parasitology, vol.33, pp.532-546, 2017.

L. S. Garcia, Laboratory diagnosis of parasites from the gastrointestinal tract, Clinical Microbiology Reviews, vol.31, pp.25-42, 2018.

E. Menu, Evaluation of two DNA extraction methods for the PCR-based detection of eukaryotic enteric pathogens in fecal samples, BMC Research Notes, vol.11, p.206, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02006222

B. Dridi, High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol, PLoS ONE, vol.4, p.7063, 2009.

D. Sow, Performance of real-time polymerase chain reaction assays for the detection of 20 gastrointestinal parasites in clinical samples from Senegal, The American Journal of Tropical Medicine and Hygiene, vol.97, pp.173-182, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01774347

C. R. Stensvold, Development and evaluation of a genusspecific, probe-based, internal-process-controlled real-time PCR assay for sensitive and specific detection of Blastocystis spp, Journal of Clinical Microbiology, vol.50, pp.1847-1851, 2012.

G. Garcés-sanchez, Evaluation of two methods for quantification of hsp70 mRNA from the waterborne pathogen Cryptosporidium parvum by reverse transcription real-time PCR in environmental samples, Water Research, vol.43, pp.2669-2678, 2009.

J. J. Verweij, Detection of Cyclospora cayetanensis in travellers returning from the tropics and subtropics using microscopy and real-time PCR, International Journal of Medical Microbiology, vol.293, pp.199-202, 2003.

T. Hove and R. , Real-time polymerase chain reaction for detection of Isospora belli in stool samples, Diagnostic Microbiology and Infectious Disease, vol.61, pp.280-283, 2008.

J. J. Verweij, Real-time PCR for the detection of Dientamoeba fragilis in fecal samples, Molecular and Cellular Probes, vol.21, pp.400-404, 2007.

J. Menotti, Development of a real-time PCR assay for quantitative detection of Encephalitozoon intestinalis DNA, Journal of Clinical Microbiology, vol.41, pp.1410-1413, 2003.

S. Roy, Real-time-PCR assay for diagnosis of Entamoeba histolytica infection, Journal of Clinical Microbiology, vol.43, pp.2168-2172, 2005.

J. Menotti, Development of a real-time polymerase-chainreaction assay for quantitative detection of Enterocytozoon bieneusi DNA in stool specimens from immunocompromised patients with intestinal microsporidiosis, The Journal of Infectious Diseases, vol.187, pp.1469-1474, 2003.

J. J. Verweij, Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR, Journal of Clinical Microbiology, vol.42, pp.1220-1223, 2004.

P. Poirier, Development and evaluation of a real-time PCR assay for detection and quantification of blastocystis parasites in human stool samples: prospective study of patients with hematological malignancies, Journal of Clinical Microbiology, vol.49, pp.975-983, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00825471

T. W. Hennessy, Survey of physician diagnostic practices for patients with acute diarrhea: clinical and public health implications, Clinical Infectious Diseases, vol.38, pp.203-211, 2004.

C. G. Clark, Recent developments in Blastocystis research, Advances in Parasitology, vol.82, pp.1-32, 2013.

D. El-safadi, Prevalence, risk factors for infection and subtype distribution of the intestinal parasite Blastocystis sp. from a large-scale multi-center study in France, BMC Infectious Diseases, vol.16, p.451, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01368323

S. Paulos, Occurrence and subtype distribution of Blastocystis sp. in humans, dogs and cats sharing household in northern Spain and assessment of zoonotic transmission risk, Zoonoses and Public Health, vol.65, pp.993-1002, 2018.

A. Lo and C. R. Stensvold, Blastocystis in health and disease: are we moving from a clinical to a public health perspective, Journal of Clinical Microbiology, vol.54, pp.524-528, 2016.

A. Bart, Diagnosis and subtype analysis of Blastocystis sp. in 442 patients in a hospital setting in the Netherlands, BMC Infectious Diseases, vol.13, p.389, 2013.

J. Forsell, Subtype analysis of Blastocystis isolates in Swedish patients, European Journal of Clinical Microbiology and Infectious Diseases, vol.31, pp.1689-1696, 2012.

L. Souppart, Molecular epidemiology of human Blastocystis isolates in France, Parasitology Research, vol.105, pp.413-421, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00527838

C. Noël, Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis, Journal of Clinical Microbiology, vol.43, pp.348-355, 2005.

R. Ten-hove, Detection of diarrhoea-causing protozoa in general practice patients in The Netherlands by multiplex real-time PCR, Clinical Microbiology and Infection, vol.13, pp.1001-1007, 2007.

L. S. Garcia, Dientamoeba fragilis, one of the neglected intestinal Protozoa, Journal of Clinical Microbiology, vol.54, pp.2243-2250, 2016.

L. Maas, Detection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR, Clinical Microbiology and Infectious dieases, vol.20, pp.545-550, 2014.

N. Fournet, Simultaneous increase of Cryptosporidium infections in the Netherlands, the United Kingdom and Germany in late summer season, Euro Surveillance, vol.18, p.20348, 2012.

S. Gupta, Chronic diarrhoea in HIV patients: prevalence of coccidian parasites, Indian Journal of Medical Microbiology, vol.26, pp.172-175, 2008.

M. Bednarska, Occurrence of intestinal microsporidia in immunodeficient patients in Poland, Annals of Agricultural and Environmental Medicine, vol.21, pp.244-248, 2014.

P. C. Döller, Cyclosporiasis outbreak in Germany associated with the consumption of salad, Emerging Infectious Diseases, vol.8, pp.992-994, 2002.

S. G. Vreden, Outbreak of amebiasis in a family in The Netherlands, Clinical Infectious Diseases, vol.31, pp.1101-1104, 2000.

F. L. Schuster and L. Ramirez-avila, Current world status of Balantidium coli, Clinical Microbiology Reviews, vol.21, pp.626-638, 2008.

. Rferences-bibliographiques-1, World Health Organization. Accelerating work to overcome the global impact of neglected tropical diseases : A roadmap for implementation : Executive summary, 2012.

S. L. Becker, Persistent digestive disorders in the tropics: causative infectious pathogens and reference diagnostic tests, BMC Infect. Dis, vol.13, p.37, 2013.

R. Lozano, Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study, Lancet, vol.380, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00827612

D. G. Newell, Food-borne diseases -the challenges of 20 years ago still persist while new ones continue to emerge, Int. J. Food Microbiol, vol.139, pp.3-15, 2010.

S. M. Fletcher, D. Stark, J. Harkness, and J. Ellis, Enteric Protozoa in the Developed World: a Public Health Perspective, Clin. Microbiol. Rev, vol.25, pp.420-449, 2012.

T. W. Hennessy, Survey of physician diagnostic practices for patients with acute diarrhea: clinical and public health implications, Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am, vol.38, pp.203-211, 2004.

J. J. Verweij and C. R. Stensvold, Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections, Clin. Microbiol. Rev, vol.27, pp.371-418, 2014.

S. S. Wong, Molecular diagnosis in clinical parasitology: when and why? Exp

, Biol. Med. Maywood NJ, vol.239, pp.1443-1460, 2014.

D. Sow, Performance of Real-Time Polymerase Chain Reaction Assays for the Detection of 20 Gastrointestinal Parasites in Clinical Samples from Senegal, Am. J. Trop. Med
URL : https://hal.archives-ouvertes.fr/hal-01774347

. Hyg, , vol.97, pp.173-182, 2017.

R. Mejia, A novel, multi-parallel, real-time polymerase chain reaction approach for eight gastrointestinal parasites provides improved diagnostic capabilities to resource-limited at-risk populations, Am. J. Trop. Med. Hyg, vol.88, pp.1041-1047, 2013.

J. T. Nazeer, Use of multiplex real-time PCR for detection of common diarrhea causing protozoan parasites in Egypt, Parasitol. Res, vol.112, pp.595-601, 2013.

D. Klein, Quantification using real-time PCR technology: applications and limitations

, Trends Mol. Med, vol.8, pp.257-260, 2002.

I. G. Wilson, Inhibition and facilitation of nucleic acid amplification, Appl. Environ

. Microbiol, , vol.63, pp.3741-3751, 1997.

C. Schrader, A. Schielke, L. Ellerbroek, and R. Johne, PCR inhibitors -occurrence, properties and removal, J. Appl. Microbiol, vol.113, pp.1014-1026, 2012.

R. N. Incani, Diagnosis of intestinal parasites in a rural community of Venezuela: Advantages and disadvantages of using microscopy or RT-PCR, Acta Trop, vol.167, pp.64-70, 2016.

L. E. Bruijnesteijn-van-coppenraet, J. A. Wallinga, G. J. Ruijs, and M. J. Bruins,

J. J. Verweij, Parasitological diagnosis combining an internally controlled real-time PCR

, Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis, vol.15, pp.869-874, 2009.

M. Basuni, A pentaplex real-time polymerase chain reaction assay for detection of four species of soil-transmitted helminths, Am. J. Trop. Med. Hyg, vol.84, pp.338-343, 2011.

A. Calderaro, Contribution of the FilmArray® Gastrointestinal Panel in the laboratory diagnosis of gastroenteritis in a cohort of children: a two-year prospective study

, J. Med. Microbiol. IJMM, vol.308, pp.514-521, 2018.

C. Stockmann, Detection of 23 Gastrointestinal Pathogens Among Children Who Present With Diarrhea, J. Pediatr. Infect. Dis. Soc, vol.6, pp.231-238, 2017.

G. Dirani, Easyscreen TM Enteric Protozoa Assay For the Detection of Intestinal Parasites: A Retrospective Bi-Center Study, J. Parasitol, vol.105, pp.58-63, 2019.

N. Singhal, M. Kumar, J. S. Virdi, . Maldi-tof, and . Ms, clinical parasitology: applications, constraints and prospects, vol.143, pp.1491-1500, 2016.

S. M. Adl, Revisions to the Classification, Nomenclature, and Diversity of

, Eukaryotes. J. Eukaryot. Microbiol, vol.66, pp.4-119, 2019.

J. C. Swartzwelder and . Balantidiasis, Am. J. Dig. Dis, vol.17, pp.173-179, 1950.

C. Mcleod, P. Smith, S. L. Mcguinness, J. R. Francis, and R. W. Baird, Human case of Balantidium infection in Australia, Pathology (Phila.), vol.47, pp.603-604, 2015.

F. L. Schuster and L. Ramirez-avila, Current world status of Balantidium coli

, Microbiol. Rev, vol.21, pp.626-638, 2008.

P. Karanis, C. Kourenti, and H. Smith, Waterborne transmission of protozoan parasites: a worldwide review of outbreaks and lessons learnt, J. Water Health, vol.5, pp.1-38, 2007.

S. Yazar, F. Altuntas, I. Sahin, and M. Atambay, Dysentery caused by Balantidium coli in a patient with non-Hodgkin's lymphoma from Turkey, World J. Gastroenterol, vol.10, pp.458-459, 2004.

S. Kaur and A. Gupta, Urinary balantidiasis: A rare incidental finding in a patient with chronic obstructive pulmonary disease, J. Cytol, vol.33, pp.169-171, 2016.

K. Anargyrou, Pulmonary Balantidium coli infection in a leukemic patient, Am. J

. Hematol, , vol.73, pp.180-183, 2003.

F. Cakir, M. Cicek, and I. H. Yildirim, Determination the Subtypes of Blastocystis sp. and Evaluate the Effect of These Subtypes on Pathogenicity, Acta Parasitol, 2019.

D. El-safadi, Prevalence, risk factors for infection and subtype distribution of the intestinal parasite Blastocystis sp. from a large-scale multi-center study in France
URL : https://hal.archives-ouvertes.fr/hal-01368323

. Dis, , vol.16, p.451, 2016.

C. Noël, Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis, J. Clin. Microbiol, vol.43, pp.348-355, 2005.

L. O. Andersen and C. R. Stensvold, Blastocystis in Health and Disease: Are We Moving from a Clinical to a Public Health Perspective?, J. Clin. Microbiol, vol.54, pp.524-528, 2016.

S. S. Ajjampur and K. S. Tan, Pathogenic mechanisms in Blastocystis spp. -Interpreting results from in vitro and in vivo studies, Parasitol. Int, vol.65, pp.772-779, 2016.

K. S. Tan, New insights on classification, identification, and clinical relevance of Blastocystis spp, Clin. Microbiol. Rev, vol.21, pp.639-665, 2008.

J. Forsell, Subtype analysis of Blastocystis isolates in Swedish patients, Eur. J

, Clin. Microbiol. Infect. Dis. Off. Publ. Eur. Soc. Clin. Microbiol, vol.31, pp.1689-1696, 2012.

S. Paulos, Occurrence and subtype distribution of Blastocystis sp. in humans, dogs and cats sharing household in northern Spain and assessment of zoonotic transmission risk

, Zoonoses Public Health, vol.65, pp.993-1002, 2018.

J. ?lapeta, Cryptosporidium: Identification and Genetic Typing

S. Pedraza-díaz, C. Amar, A. M. Iversen, P. J. Stanley, and J. Mclauchlin, Unusual cryptosporidium species recovered from human faeces: first description of Cryptosporidium felis and Cryptosporidium 'dog type' from patients in England, J. Med. Microbiol, vol.50, pp.293-296, 2001.

F. Leoni, C. Amar, G. Nichols, S. Pedraza-díaz, and J. Mclauchlin, Genetic analysis of Cryptosporidium from 2414 humans with diarrhoea in England between 1985 and 2000, J. Med. Microbiol, vol.55, pp.703-707, 2006.

P. R. Hunter and R. C. Thompson, The zoonotic transmission of Giardia and Cryptosporidium, Int. J. Parasitol, vol.35, pp.1181-1190, 2005.

L. Xiao and Y. Feng, Zoonotic cryptosporidiosis, FEMS Immunol. Med. Microbiol, vol.52, pp.309-323, 2008.

D. P. Casemore, R. L. Sands, and A. Curry, Cryptosporidium species a 'new' human pathogen, J. Clin. Pathol, vol.38, pp.1321-1336, 1985.

S. Glaberman, Three drinking-water-associated cryptosporidiosis outbreaks, Northern Ireland. Emerg. Infect. Dis, vol.8, pp.631-633, 2002.

R. L. Guerrant, Cryptosporidiosis: an emerging, highly infectious threat

. Dis, , vol.3, pp.51-57, 1997.

M. Bouzid, P. R. Hunter, R. M. Chalmers, and K. M. Tyler, Cryptosporidium Pathogenicity and Virulence, Clin. Microbiol. Rev, vol.26, pp.115-134, 2013.

M. H. Kramer, First reported outbreak in the United States of cryptosporidiosis associated with a recreational lake, Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am, vol.26, pp.27-33, 1998.

W. R. Mackenzie, Massive outbreak of waterborne cryptosporidium infection in

. Milwaukee, Wisconsin: recurrence of illness and risk of secondary transmission, Clin. Infect

, Dis. Off. Publ. Infect. Dis. Soc. Am, vol.21, pp.57-62, 1995.

M. Egger, D. Mäusezahl, P. Odermatt, H. P. Marti, and M. Tanner, Symptoms and transmission of intestinal cryptosporidiosis, Arch. Dis. Child, vol.65, pp.445-447, 1990.

P. T. Monis and R. C. Thompson, Cryptosporidium and Giardia-zoonoses: fact or fiction?, Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis, vol.3, pp.233-244, 2003.

L. Xiao and R. Fayer, Molecular characterisation of species and genotypes of

, Cryptosporidium and Giardia and assessment of zoonotic transmission, Int. J. Parasitol, vol.38, pp.1239-1255, 2008.

S. M. Cacciò, Molecular epidemiology of human cryptosporidiosis, Parassitologia, vol.47, pp.185-192, 2005.

W. L. Current, L. S. Garcia, and . Cryptosporidiosis, Clin. Microbiol. Rev, vol.4, pp.325-358, 1991.

W. L. Current, Human cryptosporidiosis in immunocompetent and immunodeficient persons. Studies of an outbreak and experimental transmission, N. Engl. J. Med, vol.308, pp.1252-1257, 1983.

B. T. Mmbaga, E. R. Houpt, and G. Cryptosporidium, Children: A Review. Pediatr. Clin. North Am, vol.64, pp.837-850, 2017.

W. Checkley, Asymptomatic and symptomatic cryptosporidiosis: their acute effect on weight gain in Peruvian children, Am. J. Epidemiol, vol.145, pp.156-163, 1997.

R. M. Chalmers and A. P. Davies, Minireview: clinical cryptosporidiosis, Exp. Parasitol, vol.124, pp.138-146, 2010.

Y. R. Ortega and R. Sanchez, Update on Cyclospora cayetanensis, a food-borne and waterborne parasite, Clin. Microbiol. Rev, vol.23, pp.218-234, 2010.

U. Aksoy, First reported waterborne outbreak of cryptosporidiosis with Cyclospora co-infection in Turkey. Wkly. Releases, vol.12, p.3142, 1997.

J. G. Rabold, Cyclospora outbreak associated with chlorinated drinking water

, Lancet Lond. Engl, vol.344, pp.1360-1361, 1994.

P. S. Mead, Food-related illness and death in the United States, Emerg. Infect. Dis, vol.5, pp.607-625, 1999.

C. A. Fleming, D. Caron, J. E. Gunn, and M. A. Barry, A foodborne outbreak of

, Cyclospora cayetanensis at a wedding: clinical features and risk factors for illness, Arch. Intern. Med, vol.158, pp.1121-1125, 1998.

B. L. Herwaldt and M. L. Ackers, An outbreak in 1996 of cyclosporiasis associated with imported raspberries. The Cyclospora Working Group, N. Engl. J. Med, vol.336, pp.1548-1556, 1997.

C. Paschke, Controlled study on enteropathogens in travellers returning from the tropics with and without diarrhoea, Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis, vol.17, pp.1194-1200, 2011.

H. L. García-lópez, L. E. Rodríguez-tovar, and C. E. Medina-de-la-garza, Identification of Cyclospora in poultry, Emerg. Infect. Dis, vol.2, pp.356-357, 1996.

R. Zerpa, N. Uchima, and L. Huicho, Cyclospora cayetanensis associated with watery diarrhoea in Peruvian patients, J. Trop. Med. Hyg, vol.98, pp.325-329, 1995.

L. E. Yai, A. R. Bauab, M. P. Hirschfeld, M. L. De-oliveira, and J. T. Damaceno, The first two cases of Cyclospora in dogs, Brazil. Rev. Inst. Med. Trop. Sao Paulo, vol.39, pp.177-179, 1997.

Y. R. Ortega, Pathologic and clinical findings in patients with cyclosporiasis and a description of intracellular parasite life-cycle stages, J. Infect. Dis, vol.176, pp.1584-1589, 1997.

D. R. Shlim, An alga-like organism associated with an outbreak of prolonged diarrhea among foreigners in Nepal, Am. J. Trop. Med. Hyg, vol.45, pp.383-389, 1991.

J. Sifuentes-osornio, Cyclospora cayetanensis infection in patients with and without AIDS: biliary disease as another clinical manifestation, Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am, vol.21, pp.1092-1097, 1995.

M. De-górgolas, J. Fortés, and M. L. Fernández-guerrero, Cyclospora cayetanensis Cholecystitis in a patient with AIDS, Ann. Intern. Med, vol.134, p.166, 2001.

R. F. Richardson, B. F. Remler, B. Katirji, and M. H. Murad, Guillain-Barré syndrome after Cyclospora infection, Muscle Nerve, vol.21, pp.669-671, 1998.

B. A. Connor, E. J. Johnson, and R. Soave, Reiter syndrome following protracted symptoms of Cyclospora infection, Emerg. Infect. Dis, vol.7, pp.453-454, 2001.

D. S. Lindsay, J. P. Dubey, and B. L. Blagburn, Biology of Isospora spp. from humans, nonhuman primates, and domestic animals, Clin. Microbiol. Rev, vol.10, pp.19-34, 1997.

E. Pozio, Foodborne and waterborne parasites, Acta Microbiol. Pol, vol.52, pp.83-96, 2003.

P. Legua, C. Seas, . Cystoisospora, and . Cyclospora, Curr. Opin. Infect. Dis, vol.26, pp.479-483, 2013.

U. Ghoshal, Identification of opportunistic enteric parasites among immunocompetent patients with diarrhoea from Northern India and genetic characterisation of Cryptosporidium and Microsporidia, Indian J. Med. Microbiol, vol.34, pp.60-66, 2016.

M. Noor, Unexpectedly High Prevalence of Cystoisospora belli Infection in

, Acalculous Gallbladders of Immunocompetent Patients, Am. J. Clin. Pathol, vol.151, pp.100-107, 2019.

H. Takahashi, G. A. Falk, M. Cruise, and G. Morris-stiff, Chronic cholecystitis with Cystoisospora belli in an immunocompetent patient, BMJ Case Rep, 2015.

A. Marathe and K. Parikh, Severe diarrhoea due to Cystoisospora belli in renal transplant patient on immunosuppressive drugs, Indian J. Med. Microbiol, vol.31, pp.185-187, 2013.

L. Post, Uncommon and fatal case of cystoisosporiasis in a non HIVimmunosuppressed patient from a non-endemic country, Parasitol. Int, vol.67, pp.1-3, 2018.

Z. Walther and M. D. Topazian, Isospora cholangiopathy: case study with histologic characterization and molecular confirmation, Hum. Pathol, vol.40, pp.1342-1346, 2009.

J. Farman, AIDS-related cholangiopancreatographic changes, Abdom. Imaging, vol.19, pp.417-422, 1994.

N. Ud-din, Severe Isospora (Cystoisospora) belli Diarrhea Preceding the Diagnosis of Human T-Cell-Leukemia-Virus-1-Associated T-Cell Lymphoma. Case Rep, Infect. Dis, vol.2012, p.640104, 2012.

R. Shafiei, M. Najjari, A. Kargar-kheirabad, G. Hatam, and . Severe,

, Diarrhea Due To Cystoisospora belli Infection in an HTLV-1 Woman, Iran. J. Parasitol, vol.11, pp.121-125, 2016.

M. W. Jepps and C. Dobell, Dientamoeba fragilis n. g., n. sp., a new Intestinal Amoeba from Man, Parasitology, vol.10, pp.352-367, 1918.

D. Stark, J. Barratt, D. Chan, and J. T. Ellis, Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel, Clin. Microbiol. Rev, vol.29, pp.553-580, 2016.

J. L. Barratt, J. Harkness, D. Marriott, J. T. Ellis, and D. Stark, The ambiguous life of Dientamoeba fragilis: the need to investigate current hypotheses on transmission, Parasitology, vol.138, pp.557-572, 2011.

D. J. Stark, N. Beebe, D. Marriott, J. T. Ellis, and J. Harkness, Dientamoebiasis: clinical importance and recent advances, Trends Parasitol, vol.22, pp.92-96, 2006.

V. S. Munasinghe, N. G. Vella, J. T. Ellis, P. A. Windsor, and D. Stark, Cyst formation and faecal-oral transmission of Dientamoeba fragilis--the missing link in the life cycle of an emerging pathogen, Int. J. Parasitol, vol.43, pp.879-883, 2013.

D. Stark, Description of Dientamoeba fragilis Cyst and Precystic Forms from Human Samples, J. Clin. Microbiol, vol.52, pp.2680-2683, 2014.

S. M. Cacciò, Molecular epidemiology of Dientamoeba fragilis, Acta Trop, vol.184, pp.73-77, 2018.

S. M. Cacciò, Pigs as Natural Hosts of Dientamoeba fragilis Genotypes Found in Humans, Emerg. Infect. Dis, vol.18, pp.838-841, 2012.

D. Chan, Detection of Dientamoeba fragilis in animal faeces using species specific real time PCR assay, Vet. Parasitol, vol.227, pp.42-47, 2016.

D. Stark, Gorillas are a host for Dientamoeba fragilis: an update on the life cycle and host distribution, Vet. Parasitol, vol.151, pp.21-26, 2008.

S. Fletcher, Epidemiology and geographical distribution of enteric protozoan infections in sydney, australia, J. Public Health Res, vol.3, p.298, 2014.

J. Ögren, Dientamoeba fragilis prevalence coincides with gastrointestinal symptoms in children less than 11 years old in Sweden, Eur. J. Clin. Microbiol. Infect. Dis. Off

. Publ, Eur. Soc. Clin. Microbiol, vol.34, 1995.

J. L. Barratt, J. Harkness, D. Marriott, J. T. Ellis, and D. Stark, A review of Dientamoeba fragilis carriage in humans: several reasons why this organism should be considered in the diagnosis of gastrointestinal illness, Gut Microbes, vol.2, 2011.

D. Stark, A review of the clinical presentation of dientamoebiasis, Am. J. Trop

, Med. Hyg, vol.82, pp.614-619, 2010.

M. J. Jong and . De, Dientamoeba fragilis and chronic abdominal pain in children: a case-control study, Arch. Dis. Child, vol.99, pp.1109-1113, 2014.

G. A. Holtman, Dientamoeba fragilis colonization is not associated with gastrointestinal symptoms in children at primary care level, Fam. Pract, vol.34, pp.25-29, 2017.

P. Jokelainen, Dientamoeba fragilis, a Commensal in Children in Danish Day Care Centers, J. Clin. Microbiol, vol.55, pp.1707-1713, 2017.

D. Röser, Metronidazole therapy for treating dientamoebiasis in children is not associated with better clinical outcomes: a randomized, double-blinded and placebo-controlled clinical trial, Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am, vol.58, pp.1692-1699, 2014.

M. Espinosa-cantellano and A. Martínez-palomo, Pathogenesis of Intestinal Amebiasis: From Molecules to Disease, Clin. Microbiol. Rev, vol.13, pp.318-331, 2000.

S. Saidin, N. Othman, and R. Noordin, Update on laboratory diagnosis of amoebiasis

, Eur. J. Clin. Microbiol. Infect. Dis. Off. Publ. Eur. Soc. Clin. Microbiol, vol.38, pp.15-38, 2019.

L. R. Rivero, F. A. Fernández, and L. J. Robertson, Cuban parasitology in review: a revolutionary triumph, Trends Parasitol, vol.24, pp.440-448, 2008.

C. Hung, Increased risk for Entamoeba histolytica infection and invasive amebiasis in HIV seropositive men who have sex with men in Taiwan, PLoS Negl. Trop. Dis, vol.2, p.175, 2008.

K. S. Ralston and W. A. Petri, Tissue destruction and invasion by Entamoeba histolytica, Trends Parasitol, vol.27, pp.254-263, 2011.

D. Eichinger, Encystation of entamoeba parasites, BioEssays News Rev. Mol. Cell. Dev

, Biol, vol.19, pp.633-639, 1997.

J. A. Walsh, Problems in recognition and diagnosis of amebiasis: estimation of the global magnitude of morbidity and mortality, Rev. Infect. Dis, vol.8, pp.228-238, 1986.

R. Fotedar, Laboratory diagnostic techniques for Entamoeba species, Clin Microbiol Rev, vol.20, 2007.

W. A. Petri and U. Singh, Diagnosis and management of amebiasis, Clin. Infect. Dis. Off

, Publ. Infect. Dis. Soc. Am, vol.29, pp.1117-1125, 1999.

R. Haque, C. D. Huston, M. Hughes, E. Houpt, and W. A. Petri, Amebiasis. N. Engl. J. Med, vol.348, pp.1565-1573, 2003.

A. Cheepsattayakorn and R. Cheepsattayakorn, Parasitic pneumonia and lung involvement, BioMed Res. Int, p.874021, 2014.
DOI : 10.1155/2014/874021

URL : http://downloads.hindawi.com/journals/bmri/2014/874021.pdf

D. P. Kotler and J. Orenstein, Clinical syndromes associated with microsporidiosis

, Adv. Parasitol, vol.40, pp.321-349, 1998.

B. Han, L. M. Weiss, and . Microsporidia, Obligate Intracellular Pathogens Within the Fungal Kingdom. Microbiol. Spectr, vol.5, 2017.

A. Sapir, Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea, Front. Microbiol, vol.5, 2014.

J. Favet, Microbial hitchhikers on intercontinental dust: catching a lift in Chad

, ISME J, vol.7, pp.850-867, 2013.

C. Franzen, Microsporidia: how can they invade other cells?, Trends Parasitol, vol.20, pp.275-279, 2004.

A. Mathis, R. Weber, and P. Deplazes, Zoonotic potential of the microsporidia, Clin. Microbiol. Rev, vol.18, pp.423-445, 2005.

B. Sak, Unapparent microsporidial infection among immunocompetent humans in the Czech Republic, J. Clin. Microbiol, vol.49, pp.1064-1070, 2011.

A. Nagpal, Disseminated microsporidiosis in a renal transplant recipient: case report and review of the literature, Transpl. Infect. Dis. Off. J. Transplant. Soc, vol.15, pp.526-532, 2013.

L. Cernikova, C. Faso, and A. B. Hehl, Five facts about Giardia lamblia, PLoS Pathog, vol.14, 2018.

U. Ryan and S. M. Cacciò, Zoonotic potential of Giardia, Int. J. Parasitol, vol.43, pp.943-956, 2013.

A. Efstratiou, J. E. Ongerth, and P. Karanis, Waterborne transmission of protozoan parasites: Review of worldwide outbreaks -An update 2011-2016, Water Res, vol.114, pp.14-22, 2017.

R. D. Adam, Biology of Giardia lamblia, Clin. Microbiol. Rev, vol.14, pp.447-475, 2001.

J. E. Painter, J. W. Gargano, S. A. Collier, and J. S. Yoder, & Centers for Disease Control and Prevention. Giardiasis surveillance --United States, MMWR Suppl, vol.64, pp.15-25, 2015.

N. Tejman-yarden and L. Eckmann, New approaches to the treatment of giardiasis, Curr. Opin. Infect. Dis, vol.24, pp.451-456, 2011.

E. Einarsson, S. Ma'ayeh, and S. G. Svärd, An up-date on Giardia and giardiasis, Curr. Opin. Microbiol, vol.34, pp.47-52, 2016.

L. A. Bartelt and R. B. Sartor, Advances in understanding Giardia: determinants and mechanisms of chronic sequelae, 2015.

I. H. Mchardy, M. Wu, R. Shimizu-cohen, M. R. Couturier, and R. M. Humphries, Detection of intestinal protozoa in the clinical laboratory, J. Clin. Microbiol, vol.52, pp.712-720, 2014.

R. A. Hiatt, E. K. Markell, and E. Ng, How many stool examinations are necessary to detect pathogenic intestinal protozoa?, Am. J. Trop. Med. Hyg, vol.53, pp.36-39, 1995.

I. I. Bogoch, G. Raso, E. K. N'goran, H. P. Marti, and J. Utzinger, Differences in microscopic diagnosis of helminths and intestinal protozoa among diagnostic centres, Eur. J

, Clin. Microbiol. Infect. Dis. Off. Publ. Eur. Soc. Clin. Microbiol, vol.25, pp.344-347, 2006.

S. J. Lewis and K. W. Heaton, Stool form scale as a useful guide to intestinal transit time

, Scand. J. Gastroenterol, vol.32, pp.920-924, 1997.

, WHO | Basic laboratory methods in medical parasitology (archived), p.24, 2019.

D. Baxby, N. Blundell, and C. A. Hart, The development and performance of a simple, sensitive method for the detection of Cryptosporidium oocysts in faeces, J. Hyg, vol.93, pp.317-323, 1984.

K. Patil, A. De, and M. Mathur, Comparison of Weber Green and Ryan Blue modified trichrome staining for the diagnosis of microsporidial spores from stool samples of HIVpositive patients with diarrhoea, Indian J. Med. Microbiol, vol.26, p.407, 2008.

D. Van-den-bossche, L. Cnops, J. Verschueren, and M. Van-esbroeck, Comparison of four rapid diagnostic tests, ELISA, microscopy and PCR for the detection of Giardia lamblia, Cryptosporidium spp. and Entamoeba histolytica in feces, J. Microbiol. Methods, vol.110, pp.78-84, 2015.

U. Ryan, A. Paparini, and C. Oskam, New Technologies for Detection of Enteric Parasites, Trends Parasitol, vol.33, pp.532-546, 2017.

D. A. Zaglool, A. Mohamed, Y. A. Khodari, and M. U. Farooq, Crypto-Giardia antigen rapid test versus conventional modified Ziehl-Neelsen acid fast staining method for diagnosis of cryptosporidiosis. Asian Pac, J. Trop. Med, vol.6, pp.212-215, 2013.

T. Weitzel, S. Dittrich, I. Möhl, E. Adusu, and T. Jelinek, Evaluation of seven commercial antigen detection tests for Giardia and Cryptosporidium in stool samples

. Microbiol, Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis, vol.12, pp.656-659, 2006.

P. Agnamey, Evaluation of Four Commercial Rapid Immunochromatographic Assays for Detection of Cryptosporidium Antigens in Stool Samples: a Blind Multicenter Trial

, J. Clin. Microbiol, vol.49, pp.1605-1607, 2011.

S. L. Becker, PCR-based verification of positive rapid diagnostic tests for intestinal protozoa infections with variable test band intensity, Acta Trop, vol.174, pp.49-55, 2017.

N. Oster, Evaluation of the immunochromatographic CORIS Giardia-Strip test for rapid diagnosis of Giardia lamblia, Eur. J. Clin. Microbiol. Infect. Dis. Off. Publ. Eur. Soc. Clin. Microbiol, vol.25, pp.112-115, 2006.

J. Minak, Evaluation of Rapid Antigen Point-of-Care Tests for Detection of Giardia and Cryptosporidium Species in Human Fecal Specimens, J. Clin. Microbiol, vol.50, pp.154-156, 2012.

S. P. Johnston, M. M. Ballard, M. J. Beach, L. Causer, and P. P. Wilkins, Evaluation of three commercial assays for detection of Giardia and Cryptosporidium organisms in fecal specimens, J. Clin. Microbiol, vol.41, pp.623-626, 2003.

H. A. Sadaka, M. R. Gaafar, R. F. Mady, and N. N. Hezema, Evaluation of ImmunoCard STAT test and ELISA versus light microscopy in diagnosis of giardiasis and cryptosporidiosis, Parasitol. Res, vol.114, pp.2853-2863, 2015.

M. K. Bouyou-akotet, Low sensitivity of the ImmunocardSTAT® Crypto/Giardia Rapid Assay test for the detection of Giardia and Cryptosporidium in fecal samples from children living in Libreville, Central Africa. J. Parasit. Dis. Off. Organ Indian Soc. Parasitol, vol.40, pp.1179-1183, 2016.

T. Shimelis and E. Tadesse, Performance evaluation of point-of-care test for detection of Cryptosporidium stool antigen in children and HIV infected adults, Parasit. Vectors, vol.7, p.227, 2014.

P. S. Korpe, Evaluation of a Rapid Point-of-Care Fecal Antigen Detection Test for Entamoeba histolytica, Am. J. Trop. Med. Hyg, vol.86, pp.980-981, 2012.

H. P. Verkerke, Multisite Clinical Evaluation of a Rapid Test for Entamoeba histolytica in Stool, J. Clin. Microbiol, vol.53, pp.493-497, 2015.

A. Calderaro, Diagnostic performances of antigen detection compared to conventional and nucleic acid detection of Entamoeba histolytica in a non-endemic setting, New Microbiol, vol.39, pp.153-155, 2016.

C. L. Alexander, M. Niebel, and B. Jones, The rapid detection of Cryptosporidium and Giardia species in clinical stools using the Quik Chek immunoassay, Parasitol. Int, vol.62, pp.552-553, 2013.

M. Nooshadokht, Stool antigen immunodetection for diagnosis of Giardia duodenalis infection in human subjects with HIV and cancer, J. Microbiol. Methods, vol.141, pp.35-41, 2017.

D. Stark, Comparison of Stool Antigen Detection Kits to PCR for Diagnosis of Amebiasis, J. Clin. Microbiol, vol.46, pp.1678-1681, 2008.

A. A. El-moamly, . .-r, and M. A. El-sweify, ImmunoCard STAT! cartridge antigen detection assay compared to microplate enzyme immunoassay and modified Kinyoun's acidfast staining technique for detection of Cryptosporidium in fecal specimens, Parasitol. Res, vol.110, pp.1037-1041, 2012.

A. M. Vidal and W. R. Catapani, Enzyme-linked immunosorbent assay (ELISA) immunoassaying versus microscopy: advantages and drawbacks for diagnosing giardiasis, Sao Paulo Med. J. Rev. Paul. Med, vol.123, pp.282-285, 2005.

L. S. Garcia and R. Y. Shimizu, Evaluation of nine immunoassay kits (enzyme immunoassay and direct fluorescence) for detection of Giardia lamblia and Cryptosporidium parvum in human fecal specimens, J. Clin. Microbiol, vol.35, pp.1526-1529, 1997.

K. Mullis, Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction, Cold Spring Harb. Symp. Quant. Biol. 51 Pt, vol.1, pp.263-273, 1986.

W. M. Freeman, S. J. Walker, and K. E. Vrana, Quantitative RT-PCR: pitfalls and potential, BioTechniques, vol.26, pp.124-125, 1999.

U. E. Gibson, C. A. Heid, and P. M. Williams, A novel method for real time quantitative RT-PCR, Genome Res, vol.6, pp.995-1001, 1996.

R. Hove, L. Van-lieshout, E. A. Brienen, M. A. Perez, and J. J. Verweij, Realtime polymerase chain reaction for detection of Isospora belli in stool samples

. Microbiol, Infect. Dis, vol.61, pp.280-283, 2008.

G. Garcés-sanchez, P. A. Wilderer, J. C. Munch, H. Horn, and M. Lebuhn, Evaluation of two methods for quantification of hsp70 mRNA from the waterborne pathogen Cryptosporidium parvum by reverse transcription real-time PCR in environmental samples, Water Res, vol.43, pp.2669-2678, 2009.

J. J. Verweij, Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR, J Clin Microbiol, vol.42, 2004.

R. Hove, Detection of diarrhoea-causing protozoa in general practice patients in The Netherlands by multiplex real-time PCR, Clin. Microbiol. Infect. Off. Publ. Eur. Soc

, Clin. Microbiol. Infect. Dis, vol.13, pp.1001-1007, 2007.

R. J. Ten-hove, Molecular diagnostics of intestinal parasites in returning travellers

, Eur J Clin Microbiol Infect Dis, vol.28, 2009.

S. Lee, Multiplex PCR Detection of Waterborne Intestinal Protozoa

C. Microsporidia and C. , Korean J. Parasitol, vol.48, pp.297-301, 2010.

D. Stark, Evaluation of multiplex tandem real-time PCR for detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in clinical stool samples, J. Clin. Microbiol, vol.49, pp.257-262, 2011.

M. Taniuchi, Multiplex PCR method to detect Cyclospora, Cystoisospora, and Microsporidia in stool samples, Diagn. Microbiol. Infect. Dis, vol.71, pp.386-390, 2011.

L. Maas, Detection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR, Clin. Microbiol. Infect. Off. Publ. Eur

. Soc, Clin. Microbiol. Infect. Dis, vol.20, pp.545-550, 2014.

J. Yoo, Comparative Evaluation of Seegene Allplex Gastrointestinal, Luminex xTAG Gastrointestinal Pathogen Panel, and BD MAX Enteric Assays for Detection of Gastrointestinal Pathogens in Clinical Stool Specimens, Arch. Pathol. Lab. Med, 2019.

S. Oikarinen, PCR inhibition in stool samples in relation to age of infants, J. Clin

, Virol. Off. Publ. Pan Am. Soc. Clin. Virol, vol.44, pp.211-214, 2009.

R. A. Barrett and M. Alexander, Resistance of Cysts of Amoebae to Microbial Decomposition, Appl. Environ. Microbiol, vol.33, pp.670-674, 1977.

B. Bowers and E. D. Korn, The fine structure of Acanthamoeba castellanii (Neff strain)

, II. Encystment. J. Cell Biol, vol.41, pp.786-805, 1969.

Z. Babaei, H. Oormazdi, S. Rezaie, M. Rezaeian, and E. Razmjou, Giardia intestinalis: DNA extraction approaches to improve PCR results, Exp. Parasitol, vol.128, pp.159-162, 2011.

A. Zimmermann, J. Lüthy, and U. Pauli, Quantitative and qualitative evaluation of nine different extraction methods for nucleic acids on soya bean food samples, Z. Für Leb. -Forsch. A, vol.207, pp.81-90, 1998.

K. Elwin, H. V. Fairclough, S. J. Hadfield, and R. M. Chalmers, Giardia duodenalis typing from stools: a comparison of three approaches to extracting DNA, and validation of a probe-based real-time PCR typing assay, J. Med. Microbiol, vol.63, pp.38-44, 2014.

M. A. Efunshile, Molecular Detection of the Carriage Rate of Four Intestinal Protozoa with Real-Time Polymerase Chain Reaction: Possible Overdiagnosis of Entamoeba histolytica in Nigeria, Am. J. Trop. Med. Hyg, vol.93, pp.257-262, 2015.

S. Kuk, S. Yazar, and U. Cetinkaya, Stool sample storage conditions for the preservation of Giardia intestinalis DNA, Mem. Inst. Oswaldo Cruz, vol.107, pp.965-968, 2012.

S. Paulos, Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp, J. Microbiol. Methods, vol.127, pp.68-73, 2016.

C. Mary, Multicentric evaluation of a new real-time PCR assay for quantification of Cryptosporidium spp. and identification of Cryptosporidium parvum and Cryptosporidium hominis, J. Clin. Microbiol, vol.51, pp.2556-2563, 2013.

H. Yoshikawa, Evaluation of DNA extraction kits for molecular diagnosis of human Blastocystis subtypes from fecal samples, Parasitol. Res, vol.109, pp.1045-1050, 2011.

K. Nagamine, T. Hase, and T. Notomi, Accelerated reaction by loop-mediated isothermal amplification using loop primers, Mol. Cell. Probes, vol.16, pp.223-229, 2002.

G. N. Hartmeyer, S. V. Hoegh, M. N. Skov, and M. Kemp, Use of Loop-Mediated Isothermal Amplification in a Resource-Saving Strategy for Primary Malaria Screening in a Non-Endemic Setting, Am. J. Trop. Med. Hyg, vol.100, pp.566-571, 2019.

M. Tambo, M. Mwinga, and D. R. Mumbengegwi, Loop-mediated isothermal amplification (LAMP) and Polymerase Chain Reaction (PCR) as quality assurance tools for Rapid Diagnostic Test (RDT) malaria diagnosis in Northern Namibia, PloS One, vol.13, p.206848, 2018.

C. Huang, Exploration of fluorescence-based real-time loop-mediated isothermal amplification (LAMP) assay for detection of Isospora suis oocysts, Exp. Parasitol, vol.165, pp.1-6, 2016.

Y. Arimatsu, S. Kaewkes, T. Laha, S. Hong, and B. Sripa, Rapid detection of Opisthorchis viverrini copro-DNA using loop-mediated isothermal amplification (LAMP)

, Parasitol. Int, vol.61, pp.178-182, 2012.

A. Calderaro, MALDI-TOF mass spectrometry for the detection and differentiation of Entamoeba histolytica and Entamoeba dispar, PloS One, vol.10, p.122448, 2015.

C. G. Clark, M. Van-der-giezen, M. A. Alfellani, and C. R. Stensvold, Recent developments in Blastocystis research, Adv. Parasitol, vol.82, pp.1-32, 2013.

A. Bart, Diagnosis and subtype analysis of Blastocystis sp. in 442 patients in a hospital setting in the Netherlands, BMC Infect. Dis, vol.13, p.389, 2013.

L. Souppart, Molecular epidemiology of human Blastocystis isolates in France, Parasitol. Res, vol.105, pp.413-421, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00527838

L. S. Garcia, Dientamoeba fragilis, One of the Neglected Intestinal Protozoa, J. Clin. Microbiol, vol.54, pp.2243-2250, 2016.

N. Fournet, Simultaneous increase of Cryptosporidium infections in the

T. Netherlands, United Kingdom and Germany in late summer season, Euro Surveill, 2012.

, Bull. Eur. Sur Mal. Transm. Eur. Commun. Dis. Bull, vol.18, 2013.

S. Gupta, S. Narang, V. Nunavath, and S. Singh, Chronic diarrhoea in HIV patients: prevalence of coccidian parasites, Indian J. Med. Microbiol, vol.26, pp.172-175, 2008.

P. Beaudeau, Lessons learned from ten investigations of waterborne gastroenteritis outbreaks, J. Water Health, vol.6, pp.491-503, 1998.

M. Bednarska, Occurrence of intestinal microsporidia in immunodeficient patients in Poland, Ann. Agric. Environ. Med. AAEM, vol.21, pp.244-248, 2014.

P. C. Döller, Cyclosporiasis outbreak in Germany associated with the consumption of salad, Emerg. Infect. Dis, vol.8, pp.992-994, 2002.

S. G. Vreden, Outbreak of amebiasis in a family in The Netherlands, Clin. Infect

, Dis. Off. Publ. Infect. Dis. Soc. Am, vol.31, pp.1101-1104, 2000.

J. H. Christensen and O. B. Christensen, Climate modelling: Severe summertime flooding in Europe, Nature, vol.421, pp.805-806, 2003.

S. L. Harper, V. L. Edge, C. J. Schuster-wallace, O. Berke, and S. A. Mcewen,

, Weather, water quality and infectious gastrointestinal illness in two Inuit communities in Nunatsiavut, Canada: potential implications for climate change, EcoHealth, vol.8, pp.93-108, 2011.

, France, à l'aide d'un diagnostic basé sur la détection de l'ADN de ces parasites par la PCR en temps réel, p.643

S. Prélèvements-de, adressées au laboratoire de parasitologiemycologie du Centre Hospitalo-Universitaire de Marseille sur une période de 6 mois a été inclus. La moyenne d'âge des patients était de 44 ans

, A l'issu de cette étude préliminaire, nous avons choisi d'extraire L'ADN en utilisant la méthode semiautomatisée EZ1 ® (Qiagen). Les parasites d'intérêt ont été détectés à l'aide de PCR « singleplex » quantitatives (qPCR). Le choix des amorces pour chaque protozoaire a été réalisé à partir d'une recherche bibliographique dans pubmed, En amont de cette étude nous avons comparé le kit manuel le plus représenté dans la littérature QIAmp ® DNA Stool Mini Kit

, Au cours de l'étude, la prévalence globale des protozoaires entériques était de 17%. Blastocystis spp. a été l'espèce la plus fréquente (10,5%), suivie par Dientamoeba fragilis (2,3%) et Giardia intestinalis (2,3%). La prévalence des autres protozoaires était inférieure à 1% chacun

, les sous types (ST) retrouvés ont été les suivants : le sous-type 3 (ST3) prédominant (43,6%) et les autres sous-types ST1, vol.2, pp.4-6

, A notre connaissance, c'est la première fois qu'un diagnostic basé sur la qPCR est utilisé pour étudier la prévalence de dix protozoaires entériques dans un hôpital universitaire français