Molecular diagnosis of Shigella, Salmonella and Campylobacter by multiplex Real-time PCR in stool culture samples in Ouagadougou (Burkina Faso)



Background: Bacteriological diagnosis of Campylobacter spp, Salmonella spp and Shigella spp could be necessary in the case of infectious gastroenteritis syndrome.

The objective of this study was to diagnose concomitantly the three enteropathogenic bacteria by multiplex Real-Time PCR in stool culture samples in Ouagadougou (Burkina Faso).

Materials and Methods: The study was conducted from February 5th to March 9th, 2013. Two hundred stool samples were received during the study period. The bacteria were identified by bacterial culture following by multiplex Real-Time PCR.

Results: Shigella spp and Campylobacter spp were sought by culture in all 200 samples. Enteropathogenic E. coli was sought only in 37 samples from all children under 2 years old. The bacterial culture was positive in 12 stool samples. Shigella spp and Salmonella spp. were isolated respectively in 5 (2.5%) and 3 samples (1.5%). Enteropathogenic E. coli was isolated in 10.8% (4/37) of the samples tested.

The multiplex real-time PCR identified bacteria in 20 patients, including 17 cases of Shigella spp., 1 case of Salmonella spp. and 2 cases of Campylobacter spp.

Conclusions: This study has highlighted the low frequency of 3 sought bacterial genera in stool samples. It has also demonstrated a significant difference between the culture and the multiplex Real-Time PCR method in the diagnosis of Shigella.

1. Farthing M, Salam MA, Lindberg G, Dite P, Khalif I, Salazar-Lindo E, et al. Acute diarrhea in adults and children: a global perspective. Journal of clinical gastroenterology. 2013;47(1):12-20.
2. Liu L, Johnson HL, Cousens S, Perin J, Scott S, Lawn JE, et al. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012;379(9832):2151-61.
3. AFSSA. Appréciation des risques alimentaires liés aux campylobacters, application au couple poulet/Campylobacter jejuni. 2004.
4. Senok AC, Botta GA. Campylobacter enteritis in the Arabian Gulf. Journal of infection in developing countries. 2009;3(2):74-82.
5. Burucoa C. Campylobacter. In : Bactériologie médicale, Paris: Masson; 2011. p.429-434
6. Chimalizeni Y, Kawaza K, Molyneux E. The epidemiology and management of non typhoidal salmonella infections. Advances in experimental medicine and biology. 2010;659:33-46.
7. Sansonetti P. Des microbes et des hommes. Guerre et Paix aux surfaces muqueuses Paris: Collège de France.; 2009.
8. Khan E, Jabeen K, Ejaz M, Siddiqui J, Shezad MF, Zafar A. Trends in antimicrobial resistance in Shigella species in Karachi, Pakistan. Journal of infection in developing countries. 2009;3(10):798-802.
9. Mengo DM, Kariuki S, Muigai A, Revathi G. Trends in Salmonella enteric serovar Typhi in Nairobi, Kenya from 2004 to 2006. Journal of infection in developing countries. 2010;4(6):393-6.
10. Beyene G, Nair S, Asrat D, Mengistu Y, Engers H, Wain J. Multidrug resistant Salmonella Concord is a major cause of salmonellosis in children in Ethiopia. Journal of infection in developing countries. 2011;5(1):23-33.
11. Afzal A, Sarwar Y, Ali A, Maqbool A, Salman M, Habeeb MA, et al. Molecular evaluation of drug resistance in clinical isolates of Salmonella enterica serovar Typhi from Pakistan. Journal of infection in developing countries. 2013;7(12):929-40.
12. Remic. Référentiel en microbiologie médicale. Groupe Remic de la Société française de microbiologie (éd), 2e édition. Montmorency, 2004 : 27-32.
13. Sanou I, Kam KL, Tougouma A, Sangare L, Nikiema JHP, Sanou I, et al. Diarrhées aigues de l’enfant : Aspects épidémiologiques, cliniques et évolutifs en milieu hospitalier pediatrique à ouagadougou. Médecine d'Afrique Noire. 1999;46(1):21-6.
14. Ouermi D, Simpore J, Belem AM, Sanou DS, Karou DS, Ilboudo D, et al. Co-infection of Toxoplasma gondii with HBV in HIV-infected and uninfected pregnant women in Burkina Faso. Pakistan journal of biological sciences: PJBS. 2009;12(17):1188-93.
15. Simpore J, Ouermi D, Ilboudo D, Kabre A, Zeba B, Pietra V, et al. Aetiology of acute gastro-enteritis in children at Saint Camille Medical Centre, Ouagadougou, Burkina Faso. Pakistan journal of biological sciences : PJBS. 2009;12(3):258-63.
16. Nitiema LW, Nordgren J, Ouermi D, Dianou D, Traore AS, Svensson L, et al. Burden of rotavirus and other enteropathogens among children with diarrhea in Burkina Faso. International journal of infectious. 2011;15(9):e646-52.
17. Bonkoungou IJ, Haukka K, Osterblad M, Hakanen AJ, Traore AS, Barro N, et al. Bacterial and viral etiology of childhood diarrhea in Ouagadougou, Burkina Faso. BMC pediatrics. 2013;13:36.
18. Agence Nationale d'Accréditation et d'Evaluation en Santé. [Indications for stool tests in adults]. Gastroenterologie clinique et biologique. 2003;27(6-7):627-42.
19. Orlandi PP, Magalhaes GF, Matos NB, Silva T, Penatti M, Nogueira PA, et al. Etiology of diarrheal infections in children of Porto Velho (Rondonia, Western Amazon region, Brazil). Brazilian journal of medical and biological research. 2006;39(4):507-17.
20. Mariani-Kurkdjian P, Bingen E. Analyse bactériologique des selles. In: Bactériologie médicale, techniques usuelles. Masson ed. Paris: Masson; 2011.
21. Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic acids research. 2005;33(19):6445-58.
22. Qu M, Zhang X, Liu G, Huang Y, Jia L, Liang W, et al. An eight-year study of Shigella species in Beijing, China: serodiversity, virulence genes, and antimicrobial resistance. Journal of infection in developing countries. 2014;8(7):904-8.
23. van den Beld MJ, Reubsaet FA. Differentiation between Shigella, enteroinvasive Escherichia coli (EIEC) and noninvasive Escherichia coli. European journal of clinical microbiology & infectious diseases. 2012;31(6):899-904.
24. Vu DT, Sethabutr O, Von Seidlein L, Tran VT, Do GC, Bui TC, et al. Detection of Shigella by a PCR assay targeting the ipaH gene suggests increased prevalence of shigellosis in Nha Trang, Vietnam. Journal of clinical microbiology. 2004;42(5):2031-5.
25. Dutta S, Chatterjee A, Dutta P, Rajendran K, Roy S, Pramanik KC, et al. Sensitivity and performance characteristics of a direct PCR with stool samples in comparison to conventional techniques for diagnosis of Shigella and enteroinvasive Escherichia coli infection in children with acute diarrhoea in Calcutta, India. Journal of medical microbiology. 2001;50(8):667-74.
26. Sethabutr O, Echeverria P, Hoge CW, Bodhidatta L, Pitarangsi C. Detection of Shigella and enteroinvasive Escherichia coli by PCR in the stools of patients with dysentery in Thailand. Journal of diarrhoeal diseases research. 1994;12(4):265-9.
27. Cunningham SA, Sloan LM, Nyre LM, Vetter EA, Mandrekar J, Patel R. Three-hour molecular detection of Campylobacter, Salmonella, Yersinia, and Shigella species in feces with accuracy as high as that of culture. Journal of clinical microbiology. 2010;48(8):2929-33.
28. Weber P, Laudat P, EPIVILLE. R. Bactéries entéropathogènes isolées des coprocultures en médecine de ville : enquête «EPICOP» 1999-2000 Bulletin Epidémiologique Hebdomadaire. 2003;8:45-6.
29. Bessede E, Delcamp A, Sifre E, Buissonniere A, Megraud F. New methods for detection of campylobacters in stool samples in comparison to culture. Journal of clinical microbiology. 2011;49(3):941-4.