L. Liu, H. Johnson, S. Cousens, J. Perin, S. Scott et al., Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000, The Lancet, vol.379, issue.9832, pp.2151-61, 2000.
DOI : 10.1016/S0140-6736(12)60560-1

F. Walker, C. Perin, J. Aryee, M. Boschi-pinto, C. Black et al., Diarrhea incidence in low-and middle-income countries in 1990 and 2010: a systematic review, BMC Public Health. 2012, vol.12, p.22436130

E. Sanchez-padilla, R. Grais, P. Guerin, A. Steele, M. Burny et al., Burden of disease and circulating serotypes of rotavirus infection in sub-Saharan Africa: systematic review and meta-analysis, The Lancet Infectious Diseases, vol.9, issue.9, pp.567-76, 2009.
DOI : 10.1016/S1473-3099(09)70179-3

Z. Waggie, A. Hawkridge, and G. Hussey, Review of Rotavirus Studies in Africa: 1976???2006, The Journal of Infectious Diseases, vol.202, issue.S1, pp.23-33, 2010.
DOI : 10.1086/653554

J. Mwenda, K. Ntoto, A. Abebe, C. Enweronu-laryea, I. Amina et al., Burden and Epidemiology of Rotavirus Diarrhea in Selected African Countries: Preliminary Results from the African Rotavirus Surveillance Network, The Journal of Infectious Diseases, vol.202, issue.S1, pp.5-11, 2010.
DOI : 10.1086/653557

C. Walker, I. Rudan, L. Liu, H. Nair, E. Theodoratou et al., Global burden of childhood pneumonia and diarrhoea. Lancet, Apr, vol.20, issue.381987513, pp.1405-1421, 2013.

K. Kotloff, J. Nataro, W. Blackwelder, D. Nasrin, T. Farag et al., Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study, The Lancet, vol.382, issue.9888, pp.209-231, 2013.
DOI : 10.1016/S0140-6736(13)60844-2

J. Sire, B. Garin, L. Chartier, N. Fall, A. Tall et al., Community-acquired infectious diarrhoea in children under 5 years of age in Dakar, Senegal. Paediatr Int Child Health, pp.139-183, 2013.

I. Bonkoungou, K. Haukka, M. Österblad, A. Hakanen, A. Traoré et al., Bacterial and viral etiology of childhood diarrhea in Ouagadougou, Burkina Faso, BMC Pediatrics, vol.10, issue.1, p.23506294
DOI : 10.1016/j.ijid.2005.05.009

T. Phan, N. Vo, I. Bonkoungou, A. Kapoor, N. Barro et al., Acute Diarrhea in West African Children: Diverse Enteric Viruses and a Novel Parvovirus Genus, Journal of Virology, vol.86, issue.20, pp.11024-11054, 2012.
DOI : 10.1128/JVI.01427-12

L. Nitiema, J. Nordgren, D. Ouermi, D. Dianou, A. Traore et al., Burden of rotavirus and other enteropathogens among children with diarrhea in Burkina Faso, International Journal of Infectious Diseases, vol.15, issue.9, pp.646-52, 2011.
DOI : 10.1016/j.ijid.2011.05.009

S. Moyo, N. Gro, M. Matee, J. Kitundu, H. Myrmel et al., Age specific aetiological agents of diarrhoea in hospitalized children aged less than five years in Dar es Salaam, Tanzania. BMC Pediatr, p.19, 2011.

C. Lanata, C. Fischer-walker, A. Olascoaga, C. Torres, M. Aryee et al., Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review, PLoS ONE, vol.380, issue.1, p.24023773
DOI : 10.1371/journal.pone.0072788.s001

R. Guerrant, R. Oriá, S. Moore, M. Oriá, and A. Lima, Malnutrition as an enteric infectious disease with long-term effects on child development, Nutrition Reviews, vol.66, issue.9, pp.487-505, 2008.
DOI : 10.1111/j.1753-4887.2008.00082.x

J. Opintan, M. Newman, P. Ayeh-kumi, R. Affrim, R. Gepi-attee et al., Pediatric Diarrhea in Southern Ghana: Etiology and Association with Intestinal Inflammation and Malnutrition, American Journal of Tropical Medicine and Hygiene, vol.83, issue.4, pp.936-979, 2010.
DOI : 10.4269/ajtmh.2010.09-0792

C. Tabu, R. Breiman, B. Ochieng, A. B. Cosmas, L. Audi et al., Differing burden and epidemiology of non-Typhi Salmonella bacteremia in rural and urban Kenya, PLoS One. 2012, vol.7, issue.2, p.22363591, 2006.

N. Feasey, G. Dougan, R. Kingsley, R. Heyderman, and M. Gordon, Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa, The Lancet, vol.379, issue.9835, pp.2489-99, 2012.
DOI : 10.1016/S0140-6736(11)61752-2

A. Page, N. De-rekeneire, S. Sayadi, S. Aberrane, A. Janssens et al., Infections in Children Admitted with Complicated Severe Acute Malnutrition in Niger, PLoS ONE, vol.56, issue.7, p.23874731
DOI : 10.1371/journal.pone.0068699.s001

R. Laxminarayan, A. Duse, C. Wattal, A. Zaidi, H. Wertheim et al., Antibiotic resistance???the need for global solutions, The Lancet Infectious Diseases, vol.13, issue.12, pp.1057-98
DOI : 10.1016/S1473-3099(13)70318-9

I. Okeke, R. Laxminarayan, Z. Bhutta, A. Duse, P. Jenkins et al., Antimicrobial resistance in developing countries. Part I: recent trends and current status, The Lancet Infectious Diseases, vol.5, issue.8, pp.481-93, 2005.
DOI : 10.1016/S1473-3099(05)70189-4

E. Vlieghe, M. Phoba, J. Tamfun, and J. Jacobs, Antibiotic resistance among bacterial pathogens in Central Africa: a review of the published literature between, Int J Antimicrob Agents, 1955.
URL : https://hal.archives-ouvertes.fr/hal-00556348

A. Ahmed, H. Osman, A. Mansour, H. Musa, A. Ahmed et al., Antimicrobial agent resistance in bacterial isolates from patients with diarrhea and urinary tract infection in the Sudan, Am J Trop Med Hyg, vol.63, pp.5-6259, 2000.

R. Bercion, S. Njuimo, P. Boudjeka, and A. Manirakiza, Distribution and antibiotic susceptibility of Shigella isolates in Bangui, Central African Republic, Tropical Medicine & International Health, vol.55, issue.4, pp.468-71, 2008.
DOI : 10.1111/j.1365-3156.2008.02023.x

J. Brooks, J. Ochieng, L. Kumar, G. Okoth, R. Shapiro et al., Surveillance for Bacterial Diarrhea and Antimicrobial Resistance in Rural Western Kenya, 1997-2003, Clinical Infectious Diseases, vol.43, issue.4, pp.393-401, 1997.
DOI : 10.1086/505866

A. Djie-maletz, K. Reither, S. Danour, L. Anyidoho, E. Saad et al., High rate of resistance to locally used antibiotics among enteric bacteria from children in Northern Ghana, Journal of Antimicrobial Chemotherapy, vol.61, issue.6, pp.1315-1323, 2008.
DOI : 10.1093/jac/dkn108

R. Bercion, D. Mossoro-kpinde, A. Manirakiza, L. Faou, and A. , Increasing prevalence of antimicrobial resistance among Enterobacteriaceae uropathogens in Bangui, Central African Republic, The Journal of Infection in Developing Countries, vol.3, issue.03, pp.187-90, 2009.
DOI : 10.3855/jidc.34

M. Raji, W. Jamal, O. Ojemhen, and R. Vo, Point-surveillance of antibiotic resistance in Enterobacteriaceae isolates from patients in a Lagos Teaching Hospital, Nigeria, Journal of Infection and Public Health, vol.6, issue.6, pp.431-438
DOI : 10.1016/j.jiph.2013.05.002

D. Harrois, S. Breurec, A. Seck, A. Delauné, L. Hello et al., Prevalence and characterization of extended-spectrum ??-lactamase-producing clinical Salmonella enterica isolates in Dakar, Senegal, from 1999 to 2009, Clinical Microbiology and Infection, vol.20, issue.2, pp.109-125, 1999.
DOI : 10.1111/1469-0691.12339

G. Tansarli, P. Poulikakos, A. Kapaskelis, and M. Falagas, Proportion of extended-spectrum ??-lactamase (ESBL)-producing isolates among Enterobacteriaceae in Africa: evaluation of the evidence--systematic review, Journal of Antimicrobial Chemotherapy, vol.69, issue.5, pp.1177-84, 2014.
DOI : 10.1093/jac/dkt500

J. Das, A. Tripathi, A. Ali, A. Hassan, C. Dojosoeandy et al., Vaccines for the prevention of diarrhea due to cholera, Shigella, ETEC and rotavirus, BMC Public Health. 2013, vol.13, p.24564510

Y. Kim, S. Yeo, J. Park, and H. Ko, Shigella Vaccine Development: Prospective Animal Models and Current Status, Current Pharmaceutical Biotechnology, vol.14, issue.10, pp.903-915, 2014.
DOI : 10.2174/1389201014666131226123900

A. Page, V. Jusot, A. Mamaty, L. Adamou, J. Kaplon et al., Rotavirus Surveillance in Urban and Rural Areas of Niger, April 2010???March 2012, Emerging Infectious Diseases, vol.20, issue.4, pp.573-80
DOI : 10.3201/eid2004.131328

. Comité, Antibiogramme de la Société Française de Microbiologie, 2010.

P. Grimont and F. Weill, Antigenic formulae of the Salmonella serotypes, WHO Collaborating Center for Reference and Research on Salmonella, 2007.

L. Hello, S. Hendriksen, R. Doublet, B. Fisher, I. Nielsen et al., International Spread of an Epidemic Population of Salmonella enterica Serotype Kentucky ST198 Resistant to Ciprofloxacin, Journal of Infectious Diseases, vol.204, issue.5, pp.675-84, 2011.
DOI : 10.1093/infdis/jir409

URL : https://hal.archives-ouvertes.fr/pasteur-01121157

A. Bej, J. Dicesare, L. Haff, and R. Atlas, Detection of Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for uid, Appl Environ Microbiol, vol.57, issue.4, pp.1013-1020, 1991.

M. Beaudry, C. Zhu, J. Fairbrother, and J. Harel, Genotypic and phenotypic characterization of Escherichia coli isolates from dogs manifesting attaching and effacing lesions, J Clin Microbiol, vol.34, issue.1, pp.144-152, 1996.

S. Gunzburg, N. Tornieporth, and L. Riley, Identification of enteropathogenic Escherichia coli by PCRbased detection of the bundle-forming pilus gene, J Clin Microbiol, vol.33, issue.5, pp.1375-1382, 1995.

Z. Lin, H. Kurazono, S. Yamasaki, and Y. Takeda, by Polymerase Chain Reaction, Microbiology and Immunology, vol.3, issue.7, pp.543-551, 1993.
DOI : 10.1111/j.1348-0421.1993.tb01675.x

D. Pollard, W. Johnson, H. Lior, S. Tyler, and K. Rozee, Rapid and specific detection of verotoxin genes in Escherichia coli by the polymerase chain reaction, J Clin Microbiol, vol.28, issue.3, pp.540-545, 1990.

A. Paton and J. Paton, Detection and characterization of Shiga toxigenic Escherichia coli by using multiplex PCR assays for stx1, stx2, eaeA, enterohemorrhagic E. coli hlyA, rfbO111, and rfbO157, J Clin Microbiol. Feb, vol.36, issue.2, pp.598-602, 1998.

N. Boisen, C. Struve, F. Scheutz, K. Krogfelt, and J. Nataro, New Adhesin of Enteroaggregative Escherichia coli Related to the Afa/Dr/AAF Family, Infection and Immunity, vol.76, issue.7, pp.3281-92, 2008.
DOI : 10.1128/IAI.01646-07

S. Moseley, J. Hardy, M. Hug, P. Echeverria, and S. Falkow, Isolation and nucleotide sequence determination of a gene encoding a heat-stable enterotoxin of Escherichia coli, Infect Immun, vol.39, issue.3, pp.1167-74, 1983.

M. Woodward, P. Carroll, and C. Wray, Detection of entero- and verocyto-toxin genes in Escherichia coli from diarrhoeal disease in animals using the polymerase chain reaction, Veterinary Microbiology, vol.31, issue.2-3, pp.2-3, 1992.
DOI : 10.1016/0378-1135(92)90083-6

G. Frankel, J. Giron, J. Valmassoi, and G. Schoolnik, Multi-gene amplification: simultaneous detection of three virulence genes in diarrhoeal stool, Molecular Microbiology, vol.257, issue.12, pp.1729-1763, 1989.
DOI : 10.1084/jem.167.1.225

R. Coimbra, F. Grimont, P. Lenormand, P. Burguière, L. Beutin et al., Identification of Escherichia coli O-serogroups by restriction of the amplified O-antigen gene cluster (rfb-RFLP) Res Microbiol, 2000.

K. Lewis, Vesikari Clinical Severity Scoring System Manual. PATH website Available: http://www.path. org/publications/files/VAD_vesikari_scoring_manual.pdf. Accessed, pp.2015-2027

C. Meng, B. Smith, L. Bodhidatta, S. Richard, K. Vansith et al., Etiology of Diarrhea in Young Children and Patterns of Antibiotic Resistance in Cambodia, The Pediatric Infectious Disease Journal, vol.30, issue.4, pp.331-336
DOI : 10.1097/INF.0b013e3181fb6f82

B. Swierczewski, E. Odundo, M. Koech, J. Ndonye, R. Kirera et al., Surveillance for enteric pathogens in a case-control study of acute diarrhea in Western Kenya, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.107, issue.2, pp.83-90, 2013.
DOI : 10.1093/trstmh/trs022

J. Sire, E. Macondo, J. Perrier-gros-claude, T. Siby, I. Bahsoun et al., Antimicrobial resistance in Shigella species isolated in, Jpn J Infect Dis, vol.61, issue.4, pp.307-316, 2004.

H. Njuguna, L. Cosmas, J. Williamson, D. Nyachieo, B. Olack et al., Use of populationbased surveillance to define the high incidence of shigellosis in an urban slum in Nairobi, Kenya. PLoS One, p.23505506, 2013.

W. Zhang, Y. Luo, J. Li, L. Lin, Y. Ma et al., Wide dissemination of multidrug-resistant Shigella isolates in China, Journal of Antimicrobial Chemotherapy, vol.66, issue.11, pp.2527-2562, 2011.
DOI : 10.1093/jac/dkr341

K. Holt, T. Nga, T. Thanh, D. Vinh, H. Kim et al., Tracking the establishment of local endemic populations of an emergent enteric pathogen, Proceedings of the National Academy of Sciences, vol.110, issue.43, pp.17522-17529, 2013.
DOI : 10.1073/pnas.1308632110

K. Kotloff, J. Winickoff, B. Ivanoff, J. Clemens, D. Swerdlow et al., Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull World Health Organ, pp.651-66, 1999.

A. Ud-din, S. Wahid, H. Latif, M. Shahnaij, M. Akter et al., Changing Trends in the Prevalence of Shigella Species: Emergence of Multi-Drug Resistant Shigella sonnei Biotype g in Bangladesh, PLoS ONE, vol.18, issue.12, p.24367527, 2013.
DOI : 10.1371/journal.pone.0082601.t002

H. Vinh, N. Nhu, T. Nga, P. Duy, J. Campbell et al., A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation, BMC Infectious Diseases, vol.134, issue.6, pp.204-214, 1471.
DOI : 10.1016/0264-410X(95)00102-7

A. Bangtrakulnonth, A. Vieira, L. Wong, D. Pornreongwong, S. Pulsrikarn et al., from Humans in Thailand During 1993 to 2006: Spatial-Time Trends in Species and Serotype Distribution, Foodborne Pathogens and Disease, vol.5, issue.6, pp.773-84, 2008.
DOI : 10.1089/fpd.2008.0109

M. Tiruneh, Serodiversity and antimicrobial resistance pattern of Shigella isolates at Gondar University teaching hospital, Northwest Ethiopia, Jpn J Infect Dis, vol.62, issue.2, pp.93-100, 2009.

R. Bercion, M. Demartin, C. Recio, P. Massamba, T. Frank et al., Molecular epidemiology of multidrug-resistant Shigella dysenteriae type 1 causing dysentery outbreaks in Central African Republic, 2003???2004, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.100, issue.12, pp.1151-1159, 2003.
DOI : 10.1016/j.trstmh.2006.02.007

S. Karambu, V. Matiru, M. Kiptoo, and J. Oundo, Characterization and factors associated with diarrhoeal diseases caused by enteric bacterial pathogens among children aged five years and below attending Igembe District Hospital, Kenya, Pan African Medical Journal, vol.16, p.24570797
DOI : 10.11604/pamj.2013.16.37.2947

P. Woerther, C. Angebault, H. Jacquier, H. Hugede, A. Janssens et al., Massive Increase, Spread, and Exchange of Extended Spectrum ??-Lactamase-Encoding Genes Among Intestinal Enterobacteriaceae in Hospitalized Children With Severe Acute Malnutrition in Niger, Clinical Infectious Diseases, vol.53, issue.7, pp.677-85, 2011.
DOI : 10.1093/cid/cir522

L. Trabulsi, R. Keller, T. Gomes, and T. , Typical and atypical enteropathogenic Escherichia coli. Emerg Infect Dis, pp.508-521, 2002.

S. Morpeth, H. Ramadhani, and J. Crump, Invasive non-Typhi Salmonella disease in Africa, Clin Infect Dis. Aug, vol.15, issue.494, pp.606-617, 2009.

C. Okoro, R. Kingsley, T. Connor, S. Harris, C. Parry et al., Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa, Nature Genetics, vol.4, issue.11, pp.1215-1236, 2012.
DOI : 10.1093/bioinformatics/btn529

S. Kariuki, G. Revathi, N. Kariuki, J. Kiiru, J. Mwituria et al., Characterisation of community acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal infections in children admitted to hospital in Nairobi, BMC Microbiology, vol.6, issue.1, pp.101-17173674, 2006.
DOI : 10.1186/1471-2180-6-101

L. Hello, S. Harrois, D. Bouchrif, B. Sontag, L. Elhani et al., Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study, The Lancet Infectious Diseases, vol.13, issue.8, pp.672-681, 2013.
DOI : 10.1016/S1473-3099(13)70124-5

URL : https://hal.archives-ouvertes.fr/pasteur-01109890