ECOPHIP is focusing its research activities on the intestinal parasitic protozoa Blastocystis and Cryptosporidium, which currently represent major socioeconomic and public health problems. Both parasites are responsible for gastrointestinal infections which, in the case of Cryptosporidium, can be serious or even fatal in children and immunocompromised patients. However, these parasites are still poorly studied and generally overlooked by health authorities, while little or no treatment is effective against these parasites. Moreover, these two parasites, presenting a great genetic diversity and being able to colonize many hosts, also represent relevant models to investigate a major biological question in the field of "Ecology of Health": what is the nature of the genetic diversity of these latter parasites and its impact on the circulation and pathogenicity of different species and genotypes? The current and future work of ECOPHIP, which has the particularity of combining “field studies" and "laboratory research", aim to clarify the molecular epidemiology of these parasites, their circulation in human and animal populations as well as in the environment (research of transmission risk factors) and their pathophysiology while identifying molecules and mechanisms involved in the pathogenesis of these parasites. The goal of ECOPHIP is to provide strategies to implement urgent prevention and control measures to significantly reduce the incidence of these parasites.To carry out its activities, ECOPHIP combines molecular epidemiology and phylogeny, comparative genomics, transcriptomics and proteomics, metagenomics and cell and molecular biology approaches together with the development of in vivo, ex vivo and in vitro study models. ECOPHIP has developed a large and well-targeted network of regional, national and international collaborations. Finally, because of its rare expertise in protistology, ECOPHIP is requested for specific collaborations, in particular in the context of the molecular identification of parasitic protozoa of interest in human and animal health or as coordinator / partner of funded projects funded in the fields of parasitology (fish parasites) and environmental parasitology.

Blastocystis & Microbiota

Gut eukaryome: the special role of intestinal protozoa in the gut microbiota

Awareness of the roles that host-associated intestinal microbes play in biology and health has increased in recent years. However, microbiome research has focused essentially on bacteria, and overall, little is known about the role of host-associated eukaryotes outside the field of Parasitology. However, microeukaryotes are common inhabitants of our gut rarely associated with clinical signs of disease. In particular, our team has shown that Blastocystis protozoa, whose pathogenicity is controversial, are associated with positive effect on intestinal bacterial diversity and changes in the composition of the gut microbiome, and would therefore be considered members of a healthy gut microbiota. The study of the diversity and role of these intestinal microeukaryotes on human and animal health is currently supported in the team ECOPHIP by the Hauts-de-France Region (STIMulE 2020 exploratory project funding) as well as by the SATT Nord (co-maturation program).

*  Even G, Lokmer A, Rodrigues J, Audebert C, Viscogliosi E, Ségurel L, Chabé M. Changes in the human gut microbiota associated with colonization by Blastocystis sp. and Entamoeba spp. in non-industrialized populations. Front Microbiol, in revision.
*  Lokmer A, Cian A, Froment A, Gantois N, Viscogliosi E, Chabé M, Ségurel L. Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels. PLoS One. 2019 Feb 6;14(2):e0211139. doi: 10.1371/journal.pone.0211139.
*  Siegwald L, Caboche S, Even G, Viscogliosi E, Audebert C, Chabé M. The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical "Microscope" Affect the Biological Interpretation? Microorganisms. 2019 Sep 26;7(10):393. doi: 10.3390/microorganisms7100393.
*  Chabé M, Lokmer A, Ségurel L. Gut Protozoa: Friends or Foes of the Human Gut Microbiota? Trends Parasitol. 2017 Dec;33(12):925-934. doi: 10.1016/
* Siegwald L, Audebert C, Even G, Viscogliosi E, Caboche S, Chabé M. Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization. Sci Data. 2017 Jun 27;4:170081. doi: 10.1038/sdata.2017.81.
*  Audebert C, Even G, Cian A; Blastocystis Investigation Group, Loywick A, Merlin S, Viscogliosi E, Chabé M. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Sci Rep. 2016 May 5;6:25255. doi: 10.1038/srep25255.

Cryptosporidium and digestive cancer

The Apicomplexan intracellular parasite Cryptosporidium is considered as one of the major causes of mild and severe diarrhea worldwide but less attention has been paid to its tumorigenic potential despite the high exposure of humans and animals to this ubiquitous parasite. Particularly, our team has reported that Cryptosporidium parvum can induce invasive gastrointestinal and biliary adenocarcinoma in a SCID mouse model as soon as 20 days Post-Infection (depending on the virulence of the Cryptosporidium strain) and low grade intraepithelial neoplasia in an intestinal ex vivo model. Moreover, Cryptosporidium infections may induce cell transformation in humans. Indeed, recent epidemiological studies showed a high prevalence of infection in patients with gastrointestinal cancer recently diagnosed and before any treatment. Our research has concentrated on the study of the physiopathology of Cryptosporidium and on the identification of the molecular signature of Cryptosporidium parvum-induced digestive cancer

Adenocarcinoma in the ileocaecal region induced by Cryptosporidium parvum. A: Macroscopic aspects of the lesion; B and C: Microscopic aspects of the lesion (Hematoxylin & Eosin). D: Electron micrograph of C. parvum infecting epithelial cell. Bar (µm) = A: 1000; B: 400; C: 25; D: 0.4. From Benamrouz et al. 2012.b

Current projects:

* Exploring the role of Cryptosporidium in the epigenetics of cancer (Funding†: Plan cancer INSERM)

* Study of the signalling pathways involved in cancer induction by the Cryptosporidium parvum parasite (Funding: Bonus H CHU of Lille)

* Discovering new inhibitors targeting Cryptosporidium (ApiHDACi) (Funding: Inter-team program CIIL)

* Involvement of protozoa of the genus Cryptosporidium in the occurrence of colorectal cancer in humans (Funding: Groupement des Hôpitaux de l'Institut Catholique de Lille-GHICL)


* Sawant M, Baydoun M, Creusy C, ChabÈ M, Viscogliosi E, Certad G, Benamrouz-Vanneste S. Cryptosporidium and Colon Cancer: Cause or Consequence? Microorganisms. 2020; 8 (11):E1665. doi: 10.3390/microorganisms8111665.
* Osman M, Benamrouz S, Guyot K, Baydoun M, Frealle E, Chabe M, Gantois N, Delaire B, Goffard A, Aoun A, Jurdi N, Dabboussi F, Even G, Slomianny C, Gosset P, Hamze M, Creusy C, Viscogliosi E, Certad G. High association of Cryptosporidium spp. infection with colon adenocarcinoma in Lebanese patients. PLoS One. 2017; 12(12):e0189422. doi: 10.1371/journal.pone.0189422.
* Baydoun M, Vanneste SB, Creusy C, Guyot K, Gantois N, Chabe M, Delaire B, Mouray A, Baydoun A, Forzy G, Chieux V, Gosset P, Senez V, Viscogliosi E, Follet J, Certad G. Three-dimensional (3D) culture of adult murine colon as an in vitro model of cryptosporidiosis: Proof of concept. Sci Rep. 2017; 7(1):17288. doi: 10.1038/s41598-017-17304-2.

* Cheeseman K, Certad G, Weitzman JB. Parasites and cancer: is there a causal link? Med Sci (Paris). 2016; 32(10):867-873. doi: 10.1051/medsci/20163210020.
* Benamrouz S, Conseil V, ChabÈ M, Praet M, Audebert C, Blervaque R, Guyot K, Gazzola S, Mouray A, Chassat T, Delaire B, Goetinck N, Gantois N, Osman M, Slomianny C, Dehennaut V, Lefebvre T, Viscogliosi E, Cuvelier C, Dei-Cas E, Creusy C, Certad G. Cryptosporidium parvum-induced ileo-caecal adenocarcinoma and Wnt signaling in a mouse model. Dis Model Mech. 2014;7(6):693-700. doi: 10.1242/dmm.013292.
* Benamrouz S, Guyot K, Gazzola S, Mouray A, Chassat T, Delaire B, ChabÈ M, Gosset P, Viscogliosi E, Dei-Cas E, Creusy C, Conseil V, Certad G. Cryptosporidium parvum infection in SCID mice infected with only one oocyst: qPCR assessment of parasite replication in tissues and development of digestive cancer. PLoS One. 2012; 7(12):e51232. doi: 10.1371/journal.pone.0051232.
* Benamrouz S, Conseil V, Creusy C, Calderon E, Dei-Cas E, Certad G. Parasites and malignancies, a review, with emphasis on digestive cancer induced by Cryptosporidium parvum (Alveolata: Apicomplexa). Parasite. 2012;19(2):101-15. doi: 10.1051/parasite/2012192101.
* Certad G, Benamrouz S, Guyot K, Mouray A, Chassat T, Flament N, Delhaes L, Coiteux V, Delaire B, Praet M, Cuvelier C, Gosset P, Dei-Cas E, Creusy C Fulminant cryptosporidiosis after near-drowning: a human Cryptosporidium parvum strain implicated in invasive gastrointestinal adenocarcinoma and cholangiocarcinoma in an experimental model. Appl Environ Microbiol. 2012;78(6):1746-51. doi: 10.1128/AEM.06457-11.

* Certad G, Creusy C, Guyot K, Mouray A, Chassat T, Delaire B, Pinon A, Sitja-Bobadilla A, Alvarez-Pellitero P, Praet M, Cuvelier C, Dei-Cas E. Fulminant cryptosporidiosis associated with digestive adenocarcinoma in SCID mice infected with Cryptosporidium parvum TUM1 strain. Int J Parasitol. 2010; 40(13):1469-75. doi: 10.1016/j.ijpara.2010.07.007.

* Certad G, Creusy C, Ngouanesavanh T, Guyot K, Gantois N, Mouray A, Chassat T, Flament N, Fleurisse L, Pinon A, Delhaes L, Dei-Cas E. Development of Cryptosporidium parvum-induced gastrointestinal neoplasia in severe combined immunodeficiency (SCID) mice: severity of lesions is correlated with infection intensity. Am J Trop Med Hyg. 2010 Feb;82(2):257-65. doi: 10.4269/ajtmh.2010.09-0309.

* Certad G, Ngouanesavanh T, Guyot K, Gantois N, Chassat T, Mouray A, Fleurisse L, Pinon A, Cailliez JC, Dei-Cas E, Creusy C. Cryptosporidium parvum, a potential cause of colic adenocarcinoma. Infect Agent Cancer. 2007 Nov 21;2:22. doi: 10.1186/1750-9378-2-22.

Publications 2015-2020

Audebert C, Bonardi F, Caboche S, Guyot K, Touzet H, Merlin S, Gantois N, Creusy C, Meloni D, Mouray A, Viscogliosi E, Certad G, Benamrouz-Vanneste S, Chabé M (2020) Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates. Sci Rep 10: 7316

Baydoun M, Treizeibre A, Follet J, Benamrouz-Vanneste S, Creusy C, Delaire B, Mouray A, Viscogliosi E, Certad G, Senez V (2020) An interphase microfluidic culture system for the study of ex vivo intestinal tissue. Micromachines 11, 150

Certad G, Zahedi A, Gantois N, Sawant M, Creusy C, Duval E, Benamrouz-Vanneste S, Ryan U, Viscogliosi E (2020) Molecular characterization of novel Cryptosporidium fish genotypes in edible marine fish. Microorganisms submitted.

Costa D, Razakandrainibe R, Valot S, Vannier M, Sautour M, Basmaciyan L, Gargala G, Viller V, Lemeteil D, Ballet JJ; French National Network on Surveillance of Human Cryptosporidiosis, Dalle F, Favennec L (2020) Epidemiology of cryptosporidiosis in France from 2017 to 2019. Microorganisms 8: 1358

Even G, Lokmer A, Rodrigues J, Audebert C, Viscogliosi E, Segurel L, Chabé M (2020) Changes in the human gut microbiota associated with colonization by Blastocystis sp. and Entamoeba spp. in non-industrialized populations. Front Microbiol in revision

Gantois N, Lamot A, Seesao Y, Creusy C, Li L-L, Monchy S, Benamrouz-Vanneste S, Karpouzopoulos J, Bourgain J-L, Rault C, Demaret F, Baydoun M, Chabé M, Fréalle E, Aliouat-Denis CM, Gay M, Certad G, Viscogliosi E (2020) First report on the prevalence and subtype distribution of Blastocystis sp. in edible marine fish and marine mammals: a large scale-study conducted in Atlantic Northeast and on the coasts of northern France. Microorganisms 8: 460

Gantois N, Lesaffre A, Durand-Joly I, bautin N, Le Rouzic O, Nseir S, Sendid B, Reboux G, Scherer E, Aliouat EM, Fry S, Gosset P, Fréalle E. Circulation of Pneumocystis jirovecii between COPD patients and their domestic environment. Clin Microbiol Infect submitted

Khaled S, Gantois N, Tidjany Ly A, Senghor S, Even G, Dautel E, Dejager R, Sawant M, Baydoun M, Benamrouz-Vanneste S, Chabé M, Ndiaye S, Schacht AM, Certad G, Riveau G, Viscogliosi E (2020) Prevalence and subtype distribution of Blastocystis sp. in Senegalese school children. Microorganisms 8: 1408

Khaled S, Gantois N, Even G, Sawant M, Benamrouz-Vanneste S, Chabé M, Certad G, El Safadi D, Daboussy F, Viscogliosi E. Blastocystis sp. prevalence and subtypes distribution in Syrian refugee camps located in North Lebanon. Microorganisms submitted.

Ma L, Chen Z, Huang D, Cisse O, Rothenburger J, Latinne A, Bishop L, Blair R, Brenchley J, Chabé M, Deng X, Hirsch V, Keesler R, Kutty G, Liu Y, Margolis D, Morand S, Pahar B, Peng L, Rompay KV, Song X, Song J, Sukura A, Thapar S, Wang H, Weissenbacher-Lang C, Xu J, Lee CH, Jardine C, Lempicki R, Cushion M, Cuomo C, Kovacs J (2020) Diversity and complexity of the large surface protein family in the compacted genomes of multiple Pneumocystis species. mBio 3: 11

Sawant M, Benamrouz S, Chabé M, Guyot K, Costa D, Favennec L, Gargala G, Viscogliosi E, Certad G (2020) La cryptosporidiose et son impact en santé publique. Rev Biol Med 352: 53-68

Sawant M, Baydoun M, Creusy C, Chabé M, Viscogliosi E, Certad G, Benamrouz-Vanneste S (2020) Cryptosporidium and colon cancer: cause or consequence? Microorganisms 8: e1665

Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, The Mucofong Investigation Group, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiébaut R, Delhaes L (2020) Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep 10: 3589

Ahangari D, Gillard M, Certad G, Bataille M, Lasek A, Modiano P (2019) Scurvy presenting as pseudo-scleroderma of the leg. JAAD Case Rep 5: 831-833

Bello-Gil D, Audebert C, Olivera-Ardid S, Pérez-Cruz M, Even G, Khasbiullina N, Gantois N, Shilova N, Merlin S, Costa C, Bovin N, Mañez R (2019) The formation of glycan-specific natural antibodies repertoire in GalT-KO mice is determined by gut microbiota. Front Immunol 10: 342

Certad G, Follet J, Gantois N, Hammouma-Ghelboun O, Guyot K, Benamrouz-Vanneste S, Fréalle E, Seesao Y, Delaire B, Creusy C, Even G, Verrez-Bagnis V, Ryan U, Gay M, Aliouat-Denis CM, Viscogliosi E (2019) Prevalence, molecular identification, and risk factors for Cryptosporidium infection in edible marine fish: a survey across sea areas surrounding France. Front Microbiol 10: 1037

Demanche C, Guillot J, Chabé M (2019) Pneumocystis species co-evolution: state-of-the-art review. OBM Genetics 3: 13

Greige S, El Safadi D, Khaled S, Gantois N, Baydoun M, Chemaly M, Benamrouz-Vanneste S, Chabé M, Osman M, Certad G, Hamze M, Viscogliosi E (2019) First report on the prevalence and subtype distribution of Blastocystis sp. in dairy cattle in Lebanon and assessment of zoonotic transmission risk. Acta Trop 194, 23-29

Greige S, Rivoal K, Osman M, El Safadi D, Dabboussi F, El Hage R, Viscogliosi E, Hamze M, Chemaly M (2019) Prevalence and genetic diversity of Campylobacter spp. in the production chain of broiler chickens in Lebanon and its association with the intestinal protozoan Blastocystis sp. Poultry Sci 98: 5883-5891

Landman WJM, Gantois N, van Eck JHH, van der Heijden HMJF, Viscogliosi E (2019) Tetratrichomonas gallinarum granuloma disease in a flock of free range layers. Vet Q 39: 153-160

Lokmer A, Cian A, Froment A, Gantois N, Viscogliosi E, Chabé M, Ségurel L (2019) Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels. PLoS ONE 14: e0211139

Siegwald L, Caboche S, Even G, Viscogliosi E, Audebert C, Chabé M (2019) The impact of bioinformatics pipelines on microbiota studies: does the analytical “microscope” affect the biological interpretation? Microorganisms 7: 393

Aliouat EM, Dei-Cas E, Gantois N, Pottier M, Pinçon C, Hawser S, Lier A, Huang DB (2018) In Vitro and in Vivo Activity of iclaprim, a diaminopyrimidine compound, a potential therapeutic alternative against Pneumocystis pneumonia. Eur J Clin Microb Infect Dis 37: 409-415

Dauchy C, Bautin N, Nseir S, Reboux G, Wintjens R, Le Rouzic O, Sendid B, Viscogliosi E, Le Pape P, Arendrup MC, Gosset P, Fry S, Fréalle E (2018) Emergence of Aspergillus fumigatus azole-resistance in azole-naïve COPD patients and their homes. Indoor Air 28, 298-306

Greige S, El Safadi D, Becu N, Gantois N, Pereira B, Chabé M, Certad G, Chemaly M, El Hage R, Monzer H, Viscogliosi E (2018) Prevalence, subtype distribution and zoonotic potential of Blastocystis sp. isolates from poultry in Lebanon. Parasit Vectors 11, 389

Latinne A, Bezé F, Delhaes L, Pottier M, Gantois N, Nguyen J, Blasdell K, Dei-Cas E, Morand S, Chabé M (2018) Genetic diversity and evolution of Pneumocystis fungi infecting wild Southeast Asian murid rodents. Parasitology 145: 885-900

Osman M, Benamrouz S, Guyot K, El Safadi D, Mallat H, Dabboussi F, Hamze M, Viscogliosi E, Certad G (2018) Molecular epidemiology of Cryptosporidium spp. in North Lebanon. J Infect Dev Ctries 12: 34S

Armengaud J, Pible O, Gaillard JC, Cian A, Gantois N, Tan KSW, Chabé M, Viscogliosi E (2017) Proteogenomic insights from the intestinal parasite Blastocystis sp. subtype 4 isolate WR1. Proteomics 17: doi: 10.1002/pmic.201700211

Baydoun M, Benamrouz-Vanneste S, Creusy C, Guyot K, Gantois N, Chabé M, Delaire B, Mouray A, Baydoun A, Forzy G, Chieux V, Gosset P, Senez V, Viscogliosi E, Follet J, Certad G (2017) Three-dimensional (3D) culture of adult murine colon as an in vitro model of cryptosporidiosis: proof of concept. Sci Rep 7: 17288

Ben Abda I, Maatoug N, Ben Romdhane R, Bouhelmi N, Zallegua N, Aoun K, Viscogliosi E, Bouratbine A (2017) Prevalence and subtype identification of Blastocystis sp. in healthy individuals in the Tunis area, Tunisia, North Africa. Am J Trop Med Hyg 96: 202-204

Certad G, Viscogliosi E, Chabé M, Caccio S (2017) Pathogenic patterns of Cryptosporidium and Giardia. Trends Parasitol 33: 561-576

Chabé M, Lokmer A, Ségurel L (2017) Gut protozoa: friends or foes of the human gut microbiota? Trends Parasitol 33: 925-934

Cian A, El Safadi D, Osman M, Moriniere R, Gantois N, Benamrouz-Vanneste S, Delgado-Viscogliosi P, Guyot K, Li LL, Monchy S, Noël C, Poirier P, Nourrisson C, Wawrzyniak I, Delbac F, Bosc S, Chabé M, Petit T, Certad G, Viscogliosi E (2017) Molecular epidemiology of Blastocystis sp. in various animal groups from two French zoos and evaluation of potential zoonotic risk. PLoS ONE 12: e0169659

Fréalle E, Valade S, Guigue N, Hamane S, Chabé M, Le Gal S, Damiani C, Totet A, Aliouat EM, Nevez G, Menotti J (2017) Diffusion of Pneumocystis jirovecii in the surrounding air of patients with Pneumocystis colonization: frequency and risk factors. Med Mycol 55: 568-572

Osman M, El Safadi D, Benamrouz-Vanneste S, Morinière R, Gantois N, Delgado-Viscogliosi P, Guyot K, Bosc S, Chabé M, Petit T, Viscogliosi E, Certad G (2017) Prevalence, transmission and host-specificity of Cryptosporidium spp. in various animal groups from two French Zoos. Parasitol Res 116: 3419-3422

Osman M, Benamrouz S, Guyot K, Baydoun M, Fréalle E, Chabé M, Gantois N, Delaire B, Goffard A, Aoun A, Jurdi N, Dabboussi F, Even G, Slomianny C, Gosset P, Hamze M, Creusy C, Viscogliosi E, Certad G (2017) High association of Cryptosporidium spp. infection with colon adenocarcinoma in Lebanese patients. PloS ONE 12: e0189422

Osman M (2017) Genetic and phenotypic characterization of Cryptosporidium. In DNA laboratory, 392 p. Lambert Acad. Publishing

Pocaterra L, Ferrara G, Peñaranda R, Pérez-Chacón G, Certad G, Rojas E, Hernán A, Goldstein C, Núñez L (2017) Improved detection of Strongyloides stercoralis in modified agar plate cultures. Am J Trop Med Hyg 96: 863-865

Ponce CA, Chabé M, George C, Cárdenas A, Duran L, Guerrero J, Bustamante R, Matos O, Huang L, Miller RF, Vargas SL (2017) High prevalence of Pneumocystis jirovecii dihydropteroate synthase gene mutations in patients with a first episode of Pneumocystis pneumonia in Santiago, Chile, and clinical response to trimethoprim-sulfamethoxazole therapy. Antimicrob Agents Chemother 61: pii: e01290-16. doi: 10.1128/AAC.01290-16

Seesao Y, Gay M, Merlin S, Viscogliosi E, Aliouat-Denis CM, Audebert C (2017) A review of methods for nematode identification. J Microbiol Meth 138: 37-49

Siegwald L, Audebert C, Even G, Viscogliosi E, Caboche S, Chabé M (2017) Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis sp. colonization. Sci Data 4: 170081

Aliouat EM, Demanche C, Chabé M (2016) Partie Parasites. In La guerre secrète des microbes. Eds. F Pinaud and S Kiehl (eds). Actes Sud Junior

Audebert C, Even G, Cian A, The Blastocystis Investigation Group, Loywick A, Merlin S, Viscogliosi E, Chabé M (2016) Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Sci Rep 6 : 25255

Certad G, Osman M, Benamrouz S (2016) Pathogenesis of Cryptosporidium in humans. In Emerging and Re-Emerging Human Infections, pp 371-392. John Wiley & Sons/Wiley Blackwell Press

Cheeseman K, Certad G, Weitzman JB (2016) Parasites et cancer: existe-il un lien? Med Sci (Paris) 32 : 867-873

Cian A, El Safadi D, Nourrisson C, Fréalle E, Dutoit E, Wawrzyniak I, Gantois N, Delbac F, Chabé M, Certad G, Poirier P, Viscogliosi E (2016) Blastocystis, un protozoaire entérique émergent. Feuillets de Biologie 331: 55-68

El Safadi D, Cian A, Nourrisson C, Pereira B, Morelle C, Bastien P, Bellanger A, Botterel F, Candolfi E, Desoubeaux G, Lachaud L, Morio F, Pomares C, Rabodonirina M, Wawrzyniak I, Delbac F, Gantois N, Certad G, Delhaes L, Poirier P, Viscogliosi E (2016) Prevalence, risk factors for infection and subtype distribution of the intestinal parasite Blastocystis sp. from a large scale multi-center study in France. BMC Infect Dis 16: 451

Fréalle E, Gay M, Touabet N, Seesao Y, Dutoit E, Yera H, Certad G, Dupouy-Camet J, Viscogliosi E, Aliouat-Denis CM (2016) L’anisakidose, une helminthose humaine aux manifestations allergiques émergentes. Feuillets de Biologie 328 : 27-38

Genitsaris S, Monchy S, Denonfoux J, Ferreira S, Kormas KA, Sime-Ngando T, Viscogliosi E, Christaki U (2016) Marine microbial community structure assessed from combined metagenomic analysis and ribosomal tag pyrosequencing. Mar Biol Res 12: 30-42

Khalife S, Chabé M, Gantois N, Audebert C, Pottier M, Hlais S, Pinçon C, Chassat T, Pierrot C, Khalife J, Aliouat-Denis CM, Aliouat EM (2016) Relationship between Pneumocystis carinii burden and the degree of host immunosuppression in an airborne transmission experimental model. J Eukaryot Microbiol 63: 309-317

Landman WJM, Molenaar RJ, Cian A, Van der Heijden HMJF, Viscogliosi E (2016) Granuloma disease in flocks of productive layers caused by Tetratrichomonas gallinarum. Avian Pathol 45: 465-477

Le Govic Y, Guyot K, Certad G, Dehennault M, Deschildre A, Mary C, Sendid B, Viscogliosi E, Favennec L, Dei-Cas E, Fréalle E, Dutoit E, The ANOFEL Cryptosporidium National Network (2016) Optimization of Cryptosporidium DNA extraction from human stools and evaluation of Cryptosporidium qPCR for the diagnosis and follow-up of intestinal cryptosporidiosis. Eur J Clin Microbiol Infect Dis 35: 137-148

Nguyen LDN, Deschaght P, Merlin S, Loywick A, Audebert C, Viscogliosi E, Vaneechoutte M, Delhaes L (2016) Effects of propidium monoazide (PMA) treatment on cystic fibrosis airway mycobiome and bacteriome analysis. PLoS ONE 11 : e0168860

Nobre LS, Meloni D, Teixeira M, Viscogliosi E, Saraiva LM (2016) Trichomonas vaginalis repair of iron centres proteins: the different role of two paralogs. Protist 167 : 222-233

Nourrisson C, Wawrzyniak I, Cian A, Livrelli V, Viscogliosi E, Delbac F, Poirier P (2016) On Blastocystis secreted cysteine proteases: a legumain-activated cathepsin B increases paracellular permeability of intestinal Caco-2 cell monolayers. Parasitology 143: 1713-1722

Osman M, El Safadi D, Cian A, Benamrouz S, Nourrisson C, Poirier P, Pereira B, Razakandrainibe R, Pinon A, Lambert C, Wawrzyniak I, Dabboussi F, Delbac F, Favennec L, Hamze M, Viscogliosi E, Certad G (2016) Prevalence and risk factors for intestinal protozoan infections with Cryptosporidium, Giardia, Blastocystis and Dientamoeba among schoolchildren in Tripoli, Lebanon. PLoS Negl Trop Dis 10 : e0004643

Tellier G, Lenne A, Cailliau-Maggio K, Cabezas-Cruz A, Valdés JJ, Martoriati A, Aliouat el M, Gosset P, Delaire B, Fréville A, Pierrot C, Khalife J (2016) Identification of Plasmodium falciparum translation initiation eIF2ß subunit: direct interaction with protein phosphatase type 1. Front Microbiol 7: 777

Travaille E, La Carbona S, Aubert D, Guyot K, Gargala G, Dumetre A, Villena I, Houssin M (2016) Development of qRT-PCR method to assess viability of Giardia intestinalis cysts, and Cryptosporidium spp. and Toxoplasma gondii oocysts. Food Control 59: 359-365

Andréjak C, Delhaes L (2015) The lung microbiome in 2015: a window on chronic lung diseases. Med Sci (Paris) 31: 971-978

Certad G, Dupuy-Camet J, Gantois N, Hamouna-Gelboun O, Pottier M, Guyot K, Benamrouz S, Osman M, Delaire B, Creusy C, Viscogliosi E, Dei-Cas E, Aliouat CM, Follet J (2015) Identification of Cryptosporidium species in fish from Lake Geneva (Lac Léman) in France. PLoS ONE 10 : e0133047

Demanche C, Deville M, Michaux J, Barriel V, Pincon C, Aliouat-Denis CM, Pottier M, Noël C, Viscogliosi E, Aliouat EM, Dei-Cas E, Morand S, Guillot J (2015) What do Pneumocystis organisms tell us about the phylogeography of their hosts? The case of the woodmouse Apodemus sylvaticus in continental Europe and western Mediterranean islands. PLoS ONE 10: e0120839

Filisetti D, Yera H, Villard O, Escande B, Wafo E, Houfflin-Debarge V, Delhaes L, Bastien P (2015) Contribution of neonatal amniotic fluid testing to diagnosis of congenital toxoplasmosis. J Clin Microbiol 53: 1719-1721

Filisetti D, Sterkers Y, Brenier-Pinchart MP, Cassaing S, Dalle F, Delhaes L, Pelloux H, Touafek F, Varlet-Marie E, Yera H, Candolfi E, Bastien P (2015) Multicentric comparative assessment of the bio-evolution Toxoplasma gondii detection kit with eight laboratory-developed PCR assays for molecular diagnosis of congenital toxoplasmosis. J Clin Microbiol 53: 29-34

Fréalle E, El Safadi D, Cian A, Aubry E, Certad G, Osman M, Wacrenier A, Dutoit E, Creusy C, Dubos F, Viscogliosi E (2015) Acute Blastocystis-associated appendicular peritonitis in a child, Casablanca, Morocco. Emerg Infect Dis 21: 91-94

Fréalle E, Gantois N, Aliouat-Denis CM, Leroy S, Zawadzki C, Perkhofer S, Aliouat EM, Dei-Cas E (2015) Comparison of different blood compartments for the detection of circulating DNA using a rat model of Pneumocystis pneumonia. Med Mycol 53: 754-759

Genitsaris S, Monchy S, Viscogliosi E, Sime-Ngando T, Ferreira S, Christaki U (2015) Seasonal variations of marine protist community structure based on taxon-specific traits using the eastern English Channel as a model coastal system. FEMS Microbiol Ecol 91: pii: fiv068. doi: 10.1093/femsec/fiv068

Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand AC, Giraldo A, da Cunha KC, Sandoval-Denis M, Hendrickx M, Nishikaku AS, de Azevedo Melo AS, Merseguel KB, Khan A, Parente Rocha JA, Sampaio P, da Silva Briones MR, e Ferreira RC, de Medeiros Muniz M, Castañón-Olivares LR, Estrada-Barcenas D, Cassagne C, Mary C, Duan SY, Kong F, Sun AY, Zeng X, Zhao Z, Gantois N, Botterel F, Robbertse B, Schoch C, Gams W, Ellis D, Halliday C, Chen S, Sorrell TC, Piarroux R, Colombo AL, Pais C, de Hoog S, Zancopé-Oliveira RM, Taylor ML, Toriello C, de Almeida Soares CM, Delhaes L, Stubbe D, Dromer F, Ranque S, Guarro J, Cano-Lira JF, Robert V, Velegraki A, Meyer W (2015) International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Med Mycol 53: 313-337

Khalife S, Aliouat EM, Aliouat-Denis CM, Gantois N, Devos P, Mallat H, Dei-Cas E, Dabboussi F, Hamze M, Fréalle E. 2015. First data on Pneumocystis jirovecci colonization in patients with respiratory diseases in North Lebanon. New Microbes New Infect 6: 11

Nguyen DNL, Delhaes L (2015) The emerging concept of lung mycobiome. Med Sci (Paris) 31: 945-947

Nguyen DNL, Viscogliosi E, Delhaes L (2015) The lung mycobiome or the forgotten component of the human respiratory microbiome. Front Microbiol 6: 89

Osman M, El Safadi D, Benamrouz S, Guyot K, Dei-Cas E, Aliouat EM, Creusy C, Hlais S, Mallat H, Hamze M, Dabboussi F, Viscogliosi E, Certad G (2015) Initial data on the molecular epidemiology of cryptosporidiosis in Lebanon. PLoS ONE 10: e0125129

Osman M, Bories J, El Safadi D, Poirel MT, Gantois N, Benamrouz-Vanneste S, Delhaes L, Hugonnard M, Certad G, Zenner L, Viscogliosi E (2015) Prevalence and genetic diversity of the intestinal parasites Blastocystis sp. and Cryptosporidium spp. in household dogs in France and evaluation of zoonotic transmission risk. Vet Parasitol 214: 167-170

Robert-Gangneux F, Sterkers Y, Yera H, Accoceberry I, Menotti J, Cassaing S, Brenier-Pinchart MP, Hennequin C, Delhaes L, Bonhomme J, Villena I, Scherer E, Dalle F, Touafek F, Filisetti D, Varlet-Marie E, Pelloux H, Bastien P (2015) Molecular diagnosis of toxoplasmosis in immunocompromised patients: a 3-year multicenter retrospective study. J Clin Microbiol 53: 1677-1684

Standaert-Vitse A, Aliouat-Denis CM, Martinez A, Khalife S, Pottier M, Gantois N, Dei-Cas E, Aliouat EM (2015) SYTO-13, a viability marker as a new tool to monitor in vitro pharmacodynamic parameters of anti-Pneumocystis drugs. PLoS One 10: e0130358

Wawrzyniak I, Courtine D, Osman M, Hubans-Pierlot C, Cian A, Nourrisson C, Chabé M, Poirier P, Bart A, Polonais V, Delgado-Viscogliosi P, El Alaoui H, Belkorchia A, Van Gool T, Tan KSW, Ferreira S, Delbac F, Viscogliosi E (2015) Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1. Genom Data 4: 22-23



As part of its research activities, ECOPHIP has established a dense network of collaborations at local and regional (CIIL platforms and teams, Lille Hospital and University, PEGASE, BiLille, Genes Diffusion, Genoscreen), national (VetAgro Sup, ANSES, IFREMER, CEA, Hospitals, MNHN Paris, CNRS and Inserm units) and international level in Europe (Belgium, the Netherlands, Italy), Africa (Tunisia, Egypt, Senegal, Guinea), South America (French Guyana), Caribbean (Cuba), Asia (Thailand, Vietnam, Japan, India) and Middle East (Lebanon) and Australia (Murdoch University, Melbourne).


* ANR. ANR ALIA 09 PROTOFOOD (ANR 09 ALIA 009-04) 2010-2013 Partner
* ANR. ANR 2010 ALIA FISH PARASITES (ANR 2010 ALIA 004-01) 2010-2013 Coordinator
* ANSES. ANSES 2011 PNEUMAIR (EST 2011/1/053) 2011-2013 Partner
* Region Hauts-de-France - CHU of Lille. CP PSER CHRU – FUNGICOPD (n°11003705) 2011-2014 Coordinator
* CHU of Lille. MFIP (n°12-11-808) 2012-2013 Coordinator
* University of Lille. Programme Orientations Stratégiques BlastoGeDiPath 2012-2015 Coordinator
* Pfizer. ATCF Azole Therapy in Cystic Fibrosis EudraCT 2011-005799-41 2012-2015 Partner
* Genoscreen Lille. Collaboration contract 2013-2014 Coordinator
* Region Hauts-de-France - FRB. DEMO 2013-2015 Partner
* Association Vaincre la Mucoviscidose. MUCO-BAC-MYCO (C-20120-600697) 2013-2015 Coordinator
* ANR. ANR BLANC ROME 2012 (ANR-12-BSV7-0019-02) 2013-2016 Partner
* Region Hauts-de-France. Action de Recherche Concerté d’Initiative Régionale (ARCIR) ABC FISH (n°13003283) 2013-2016 Coordinator
* PEGASE Lille. Collaboration contract 2014 Coordinator
* CHU of Lille. Fonds Hospitalier d’Aide à l’Emergence 2014-2015 Coordinator
* MAE and MESR. Partenariats Hubert Curien (PHC) Programme CEDRE France - Liban 2015-2016 Coordinator
* University of Lille. Equipement scientifique innovant 2015-2017 Partner
* Inserm. Plan Cancer 2014-2019 ITMO Cancer Inserm (n°EPIG201510 ) AAP Epigénétique et Cancer PARA-CAN 2016-2019 Partner
* SF3i Lille. Collaborative project between scientists from CIIL and LIRIC (UMR995) 2016-2017 Coordinator
* Bioinformatic Platform BiLille. Call for projects Engineers missions 2018-2019 Coordinator
* CHU of Lille. Bonus H 2019-2020 Coordinator
* Catholic University of Lille. GHICL Crypto-K 2019-2021 Coordinator
* French Ambassy in Vietnam. Call for projects Scientific Cooperation 2020-2021 Coordinator
* CIIL. Intra-CIIL collaborative projects 2020 Coordinator
* Region Hauts-de-France. Programme STIMulE - Volet "Recherche Exploratoire" AGRIMARK 2020-2022 Coordinator
* Société d’Accélération de Transfert Technologique (SATT) Nord 2020-2022 Coordinator