K. Short, M. Richard, J. Verhagen, D. Van-riel, E. Schrauwen et al., One health, multiple challenges: The inter-species transmission of influenza A virus, One Health, vol.1, pp.1-13, 2015.
DOI : 10.1016/j.onehlt.2015.03.001

V. Martella, K. Banyai, J. Matthijnssens, C. Buonavoglia, and M. Ciarlet, Zoonotic aspects of rotaviruses, Veterinary Microbiology, vol.140, issue.3-4, pp.246-255, 2010.
DOI : 10.1016/j.vetmic.2009.08.028

URL : https://hal.archives-ouvertes.fr/hal-00556058

N. Adams, L. Byrne, G. Smith, R. Elson, J. Harris et al., Shiga toxin-producing Escherichia coli O157, Emerg Infect Dis, vol.22, pp.1983-2012590, 2016.

E. De-wit, N. Van-doremalen, D. Falzarano, and V. Munster, SARS and MERS: recent insights into emerging coronaviruses, Nature Reviews Microbiology, vol.113, issue.8, pp.523-534, 2016.
DOI : 10.1038/nrmicro.2016.81

P. Singh, T. Teal, T. Marsh, J. Tiedje, R. Mosci et al., Intestinal microbial communities associated with acute enteric infections and disease recovery, Microbiome, vol.18, issue.11, p.45, 2015.
DOI : 10.1186/s40168-015-0109-2

URL : http://doi.org/10.1186/s40168-015-0109-2

B. Stecher, R. Robbiani, A. Walker, A. Westendorf, M. Barthel et al., Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota, PLoS Biology, vol.73, issue.10, pp.2177-2189, 2007.
DOI : 10.1371/journal.pbio.0050244.st002

Y. Taur and E. Pamer, The intestinal microbiota and susceptibility to infection in immunocompromised patients, Current Opinion in Infectious Diseases, vol.26, issue.4, pp.332-337, 2013.
DOI : 10.1097/QCO.0b013e3283630dd3

M. Arrieta, L. Stiemsma, N. Amenyogbe, E. Brown, and B. Finlay, The Intestinal Microbiome in Early Life: Health and Disease, Frontiers in Immunology, vol.486, issue.375????????382, p.427, 2014.
DOI : 10.1038/nature11234

M. Claesson, I. Jeffery, S. Conde, S. Power, O. Connor et al., Gut microbiota composition correlates with diet and health in the elderly, Nature, vol.57, pp.178-184, 2012.
DOI : 10.1038/nature11319

M. Booth and C. , Vomiting Larry: a simulated vomiting system for assessing environmental contamination from projectile vomiting related to norovirus infection, Journal of Infection Prevention, vol.293, issue.15, pp.176-180, 2014.
DOI : 10.1177/1757177414545390

G. Widmer, Y. Lee, P. Hunt, A. Martinelli, M. Tolkoff et al., Comparative genome analysis of two Cryptosporidium parvum isolates with different host range, Infection, Genetics and Evolution, vol.12, issue.6, pp.1213-1221, 2012.
DOI : 10.1016/j.meegid.2012.03.027

J. Cuthbert, Hepatitis A: Old and New, Clinical Microbiology Reviews, vol.14, issue.1, pp.38-58, 2001.
DOI : 10.1128/CMR.14.1.38-58.2001

P. Cheng, D. Wong, L. Tong, S. Ip, A. Lo et al., Viral shedding patterns of coronavirus in patients

V. Corman, A. Albarrak, A. Omrani, M. Albarrak, M. Farah et al., Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection, Clinical Infectious Diseases, vol.62, pp.477-483, 2016.
DOI : 10.1093/cid/civ951

C. Dilantika, E. Sedyaningsih, M. Kasper, M. Agtini, E. Listiyaningsih et al., Influenza virus infection among pediatric patients reporting diarrhea and influenza-like illness, BMC Infectious Diseases, vol.360, issue.1, p.3, 2010.
DOI : 10.1056/NEJMoa0903812

URL : http://doi.org/10.1186/1471-2334-10-3

W. Leung, K. To, P. Chan, H. Chan, A. Wu et al., Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection, Gastroenterology, vol.125, issue.4, pp.1011-1017, 2003.
DOI : 10.1016/S0016-5085(03)01215-0

W. Liu, F. Tang, A. Fontanet, L. Zhan, Q. Zhao et al., Long-term SARS Coronavirus Excretion from Patient Cohort, China, Emerging Infectious Diseases, vol.10, issue.10, pp.1841-1843, 2004.
DOI : 10.3201/eid1010.040297

URL : http://doi.org/10.3201/eid1010.040297

Z. Zhu, Y. Liu, L. Xu, W. Guan, X. Zhang et al., Extra-pulmonary viral shedding in H7N9 Avian Influenza patients, Journal of Clinical Virology, vol.69, pp.30-32, 2015.
DOI : 10.1016/j.jcv.2015.05.013

C. Gaudreau, S. Rodrigues-coutlee, P. Pilon, F. Coutlee, and S. Bekal, From 2003 to 2013 in Men Who Have Sex With Men, Quebec, Canada: Figure 1., Clinical Infectious Diseases, vol.61, issue.10, pp.1549-1552, 2015.
DOI : 10.1093/cid/civ570

H. De-man, H. Van-den-berg, E. Leenen, J. Schijven, F. Schets et al., Quantitative assessment of infection risk from exposure to waterborne pathogens in urban floodwater, Water Research, vol.48, pp.90-99, 2014.
DOI : 10.1016/j.watres.2013.09.022

S. Bidawid, J. Farber, and S. Sattar, Survival of hepatitis A virus on modified atmosphere-packaged (MAP) lettuce, Food Microbiology, vol.18, issue.1, pp.95-102, 2001.
DOI : 10.1006/fmic.2000.0380

H. Karch, E. Denamur, U. Dobrindt, B. Finlay, R. Hengge et al., O104:H4 outbreak, EMBO Molecular Medicine, vol.55, issue.9, pp.841-848, 2012.
DOI : 10.1002/emmm.201201662

URL : https://hal.archives-ouvertes.fr/hal-01194805

L. Singletary, J. Karlinsey, S. Libby, J. Mooney, K. Lokken et al., Loss of multicellular behavior in epidemic African nontyphoidal Salmonella enterica serovar Typhimurium ST313 strain D23580, MBio, vol.7, p.2265, 2016.

C. Russell, J. Fonville, A. Brown, D. Burke, D. Smith et al., The Potential for Respiratory Droplet-Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host, Science, vol.336, issue.6088, pp.1541-1547, 2012.
DOI : 10.1126/science.1222526

L. Raman and H. Dalton, Year in Review 2015: Extracorporeal Membrane Oxygenation, Respiratory Care, vol.61, issue.7, pp.986-991, 2016.
DOI : 10.4187/respcare.04985

X. Ye, J. Van, F. Munoz, P. Revell, C. Kozinetz et al., Noroviruses as a Cause of Diarrhea in Immunocompromised Pediatric Hematopoietic Stem Cell and Solid Organ Transplant Recipients, American Journal of Transplantation, vol.365, issue.7, pp.1874-1881, 2015.
DOI : 10.1111/ajt.13227

J. Siebenga, M. Beersma, H. Vennema, P. Van-biezen, N. Hartwig et al., High Prevalence of Prolonged Norovirus Shedding and Illness among Hospitalized Patients: A Model for In Vivo Molecular Evolution, The Journal of Infectious Diseases, vol.198, issue.7, pp.994-1001, 2008.
DOI : 10.1086/591627

J. Murk, A. De-vries, C. Geurtsvankessel, A. G. Osterhaus, A. Wolthers et al., Persistent spiking fever in a child with acute myeloid leukemia and disseminated infection with enterovirus, Journal of Clinical Virology, vol.61, issue.3, pp.453-455, 2014.
DOI : 10.1016/j.jcv.2014.09.006

W. Greendyke, M. Pereira, K. Stittelaar, G. Van-amerongen, V. Kroeze et al., Infectious Complications and Vaccinations in the Posttransplant Population, Medical Clinics of North America, vol.100, issue.3, pp.587-598, 2013.
DOI : 10.1016/j.mcna.2016.01.008

G. Dunn, D. Klapsa, T. Wilton, L. Stone, P. Minor et al., Twenty-Eight Years of Poliovirus Replication in an Immunodeficient Individual: Impact on the Global Polio Eradication Initiative, PLOS Pathogens, vol.88, issue.Suppl 1, p.1005114, 2015.
DOI : 10.1371/journal.ppat.1005114.s001

T. Lawley, D. Bouley, Y. Hoy, C. Gerke, D. Relman et al., Host Transmission of Salmonella enterica Serovar Typhimurium Is Controlled by Virulence Factors and Indigenous Intestinal Microbiota, Infection and Immunity, vol.76, issue.1, pp.403-416, 2008.
DOI : 10.1128/IAI.01189-07

A. Marzel, P. Desai, A. Goren, Y. Schorr, I. Nissan et al., in Humans: Epidemiology and Genetics, Clinical Infectious Diseases, vol.62, issue.7, pp.879-886, 2016.
DOI : 10.1093/cid/civ1221

H. Dupont, M. Levine, R. Hornick, and S. Formal, Inoculum Size in Shigellosis and Implications for Expected Mode of Transmission, Journal of Infectious Diseases, vol.159, issue.6, pp.1126-1128, 1989.
DOI : 10.1093/infdis/159.6.1126

R. Atmar, A. Opekun, M. Gilger, M. Estes, S. Crawford et al., Norwalk Virus Shedding after Experimental Human Infection, Emerging Infectious Diseases, vol.14, issue.10, pp.1553-1557, 2008.
DOI : 10.3201/eid1410.080117

URL : http://doi.org/10.3201/eid1410.080117

C. Dalton, C. Austin, J. Sobel, P. Hayes, W. Bibb et al., in Milk, New England Journal of Medicine, vol.336, issue.2, pp.100-105, 1997.
DOI : 10.1056/NEJM199701093360204

L. Hu, S. Crawford, R. Czako, N. Cortes-penfield, D. Smith et al., Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen, Nature, vol.77, issue.7397, pp.256-259, 2012.
DOI : 10.1038/nature10996

N. Ruvoen-clouet, G. Belliot, L. Pendu, and J. , Noroviruses and histo-blood groups: the impact of common host genetic polymorphisms on virus transmission and evolution, Reviews in Medical Virology, vol.19, issue.7, pp.355-366, 2013.
DOI : 10.1002/rmv.1757

R. Purcell and S. Emerson, Hepatitis E: An emerging awareness of an old disease, Journal of Hepatology, vol.48, issue.3, pp.494-503, 2008.
DOI : 10.1016/j.jhep.2007.12.008

D. Cao and X. Meng, Molecular biology and replication of hepatitis E virus, Emerging Microbes & Infections, vol.16, issue.8, p.17, 2012.
DOI : 10.1038/emi.2012.7

H. Nguyen, P. Shukla, U. Torian, K. Faulk, and S. Emerson, Hepatitis E Virus Genotype 1 Infection of Swine Kidney Cells In Vitro Is Inhibited at Multiple Levels, Journal of Virology, vol.88, issue.2, pp.868-877, 2014.
DOI : 10.1128/JVI.02205-13

S. Caccio and R. Chalmers, Human cryptosporidiosis in Europe, Clinical Microbiology and Infection, vol.22, issue.6, pp.471-480, 2016.
DOI : 10.1016/j.cmi.2016.04.021

B. Speich, D. Croll, T. Furst, J. Utzinger, and J. Keiser, Effect of sanitation and water treatment on intestinal protozoa infection: a systematic review and meta-analysis, The Lancet Infectious Diseases, vol.16, issue.1, pp.87-99, 2016.
DOI : 10.1016/S1473-3099(15)00349-7

C. Zhou, M. Li, K. Yuan, S. Deng, and W. Peng, Pig Ascaris: An important source of human ascariasis in China, Infection, Genetics and Evolution, vol.12, issue.6, pp.1172-1177, 2012.
DOI : 10.1016/j.meegid.2012.04.016

P. Nejsum, M. Betson, R. Bendall, S. Thamsborg, and J. Stothard, Assessing the zoonotic potential of Ascaris suum and Trichuris suis: looking to the future from an analysis of the past, Journal of Helminthology, vol.88, issue.02, pp.148-155, 2012.
DOI : 10.1007/s00436-002-0640-5

M. Betson, P. Nejsum, and J. Stothard, From the Twig Tips to the Deeper Branches, pp.265-285
DOI : 10.1016/B978-0-12-396978-1.00010-0

J. Rocha-pereira, D. Jochmans, and J. Neyts, Prophylactic treatment with the nucleoside analogue 2'-C-methylcytidine completely prevents transmission of norovirus, Journal of Antimicrobial Chemotherapy, vol.70, issue.1, pp.190-197, 2015.
DOI : 10.1093/jac/dku363