Epidemiological patterns and antimicrobial resistance of bacterial diarrhea among children in Nairobi City, Kenya
Gastroenterology and Hepatology from Bed to Bench,
2 June 2020
Aim: Determine the prevalence of enteric bacterial pathogens and their antimicrobial resistance among diarrheic children in Nairobi City, Kenya.
Background: Regardless of enteric bacterial pathogens being a major cause of gastroenteritis in children, their occurrence and antimicrobial resistance patterns reveals regional spatial and temporal variation.
Methods: In a cross-sectional study, a total of 374 children below five years presenting with diarrhea at Mbagathi County Hospital were recruited. Stool microbiology test was used to detect enteric bacterial infection. Antimicrobial resistance was determined using the disk diffusion method.
Results: Diarrheagenic E. coli (36.4%) was the leading species followed by Shigella (3.2%), Salmonella (2.4%), Campylobacter (1.6%), Yersinia (1.3%) and Aeromonas (1.1%) species. Escherichia coli pathotyping revealed that 20.9%, 4.0%, 10.2% and 0.5% of the study participants were infected with enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC) and enteroinvasive E. coli (EIEC) pure isolates while the prevalence of mixed pathotype infections was 0.3% for EAEC/EPEC/ETEC and 0.5% for EAEC/ETEC. Shigella sero-grouping revealed that 0.5%, 0.3%, 1.9%, and 0.5% were infected with Shigella boydii, Shigella dysentriae, Shigella flexneri and Shigella sonnei pure isolates. Shigella species and E. coli co-infection was detected in 2.4% of the children, specifically, 1.1% for EAEC/Shigella boydii, 0.5% for EAEC/Shigella dysentriae and 0.3% in each case of EAEC/Shigella sonnei, EPEC/Shigella flexneri and ETEC/Shigella flexneri co-infections. Most of the isolates were resistant to commonly prescribed antibiotics.
Conclusion: There was a high prevalence of enteric bacterial pathogens and co-infection alters epidemiological dynamics of bacterial diarrhea in children. Continuous antibiotic resistance surveillance is justified because the pathogens were highly resistant to commonly prescribed antimicrobials.
Keywords: Epidemiology; antimicrobial resistance; bacterial diarrhea.
(Please cite as: Kilongosi Webale M, Wanjala C, Guyah B, Shaviya N, Munyekenye GO, Lokamar Nyanga P, et al. Epidemiological patterns and antimicrobial resistance of bacterial diarrhea among children in Nairobi city,Kenya. Gastroenterol Hepatol Bed Bench 2020; 12(3):238-246).
- antimicrobial resistance
- bacterial diarrhea.
Global Burden of Disease (2016) Diarrhoeal Diseases Collaborators, Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect Dis 2018;18:1211-28.
The United Nations Children's Fund, The State of the World's Children 2016. A fair chance for every child. UNICEF, 2016. ISBN:978-92-806-4838-6
Njuguna CI, Njeru E, Mgamb D, Langat A, Makokha D, Ongore et al. Enteric pathogens and factors associated with acute bloody diarrhoea, Kenya. BMC Infect Dis 2016;16:477.
Swierczewski BE, Odundo MC, Koech JN, Ndonye RK, Kirera CP, Odhiambo et al. Surveillance for enteric pathogens in a case-control study of acute diarrhea in Western Kenya. Trans R Soc Trop Med Hyg 2013;107:83-90.
Bundgaard-Nielsen C, Hagstrøm S, Sørensen S.Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions. Sci Rep 2018;8:17367.
Gupta VK, Paul S, Dutta C. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity. Front Microbiol 2017;8:1162.
Singh P, Teal TK, Marsh TL, Tiedje JM, Mosci R, Jernigan K, et al. Intestinal microbial communities associated with acute enteric infections and disease recovery. Microbiome 2015;3:45.
Mosites E, Sammons M, Otiang E, Eng A, Noecker C, Manor O, et al. Microbiome sharing between children, livestock and household surfaces in western Kenya. PLoS One 2017;12:e0171017.
van Eijk AM, Brooks JT, Adcock PM, Garrett V, Eberhard M, Rosen DH, et al. Diarrhea in children less than two years of age with known HIV status in Kisumu, Kenya. Int J Infect Dis 2010;14:e220-5.
Pavlinac PB, John-Stewart GC, Naulikha JM, Onchiri FM, Denno DM, Odundo EA, et al. High-risk enteric pathogens associated with HIV infection and HIV exposure in Kenyan children with acute diarrhoea. AIDS 2014;28:2287-96.
Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, et al. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms 2019;7.
Zilberman-Schapira G, Zmora N, Itav S, Bashiardes S, Elinav H, Elinav E. The gut microbiome in human immunodeficiency virus infection. BMC Med 2016;14:83.
Boru WG, Kikuvi G, Omollo J, Abade A, Amwayi S, Ampofo W, et al. Aetiology and factors associated with bacterial diarrhoeal diseases amongst urban refugee children in Eastleigh, Kenya: A case control study. Afr J Lab Med 2013;2:63.
Karambu S, Matiru V, Kiptoo M, Oundo J. 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 Afr Med J 2013;16:37.
Brooks JT, Ochieng JB, Kumar L, Okoth G, Shapiro RL, Wells JG, et al. Surveillance for bacterial diarrhea and antimicrobial resistance in rural western Kenya, 1997-2003. Clin Infect Dis 2006;43:393-401.
Brooks JT, Shapiro RL, Kumar L, Wells JG, Phillips-Howard PA, Shi YP, et al. Epidemiology of sporadic bloody diarrhea in rural Western Kenya. Am J Trop Med Hyg 2003;68:671-7.
Sang WK, Oundo V, Schnabel D. Prevalence and antibiotic resistance of bacterial pathogens isolated from childhood diarrhoea in four provinces of Kenya. J Infect Dev Ctries, 2012;6:572-8.
Shah M, Kathiiko C, Wada A, Odoyo E, Bundi M, Miringu G, et al. Prevalence, seasonal variation, and antibiotic resistance pattern of enteric bacterial pathogens among hospitalized diarrheic children in suburban regions of central Kenya. Trop Med Health 2016;44:39.
Shah ME, Odoyo E, Wandera C, Kathiiko M, Bundi G, Miringu et al. Burden of Rotavirus and Enteric Bacterial Pathogens among Children under 5 Years of Age Hospitalized with Diarrhea in Suburban and Rural Areas in Kenya. Jpn J Infect Dis 2017;70:442-7.
Swierczewski BE, Odundo EA, Koech MC, Ndonye JN, Kirera RK, Odhiambo CP, et al. Enteric pathogen surveillance in a case-control study of acute diarrhoea in the town of Kisii, Kenya. J Med Microbiol 2013;62:1774-6.
Brogan DM, Mossialos E. A critical analysis of the review on antimicrobial resistance report and the infectious disease financing facility. Global Health 2016;12:8.
Brander RL, Walson JL, John-Stewart GC, Naulikha JM, Ndonye J, Kipkemoi N, et al. Correlates of multi-drug non-susceptibility in enteric bacteria isolated from Kenyan children with acute diarrhea. PLoS Negl Trop Dis 2017;11:e0005974.
Nyanga PL, Onyuka J, Webale MK, Were T, Budambula V. Escherichia coli pathotypes and Shigella sero-groups in diarrheic children in Nairobi city, Kenya. Gastroenterol Hepatol Bed Bench, 2017;10:220-8.
Muloi D, Fevre EM, Bettridge J, Rono R, Ong'are D, Hassell JM, et al. A cross-sectional survey of practices and knowledge among antibiotic retailers in Nairobi, Kenya. J Glob Health 2019;9:010412.
Rhee C, Aol G, Ouma A, Audi A, Muema S, Auko J, et al. Inappropriate use of antibiotics for childhood diarrhea case management -Kenya, 2009-2016. BMC Public Health 2019;19:468.
World Health Organization, Antibacterial agents in clinical development – an analysis of the antibacterial clinical development pipeline, including tuberculosis. 2017.
Cole ST. Who will develop new antibacterial agents? Philos Trans R Soc Lond B Biol Sci 2014;369:20130430.
World Health Organization. The treatment of diarrhoea: A manual for physicians and other senior health workers. 4 revision 2005.
World Health Organization, Manual for the laboratory identification and antimicrobial susceptibility testing of bacterial pathogens of public health concern in the developing world. 2003.
Humphries RM, Ambler J, Mitchell SL, Castanheira M, Dingle T, Hindler JA, et al. CLSI Methods Development and Standardization Working Group Best Practices for Evaluation of Antimicrobial Susceptibility Tests. J Clin Microbiol 2018;56.
World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects. J Am Coll Dent 2014;81:14-8.
Bublitz DC, PC Wright, JR Bodager, FT Rasambainarivo, JB Bliska, Gillespie TR. Epidemiology of pathogenic enterobacteria in humans, livestock, and peridomestic rodents in rural Madagascar. PLoS One 2014;9:e101456.
Chekabab SM, Paquin-Veillette J, Dozois CM, Harel J. The ecological habitat and transmission of Escherichia coli O157:H7. FEMS Microbiol Lett 2013;341:1-12.
Parvez SM, Azad R, Pickering AJ, Kwong LH, Arnold BF, Rahman MJ, et al. Microbiological contamination of young children's hands in rural Bangladesh: Associations with child age and observed hand cleanliness as proxy. PLoS One 2019;14:e0222355.
Gomes TA, Elias WP, Scaletsky IC, Guth BE, Rodrigues JF, Piazza RM, et al. Diarrheagenic Escherichia coli. Braz J Microbiol 2016;47:3-30.
Olivo G, Lucas TM, Borges AS, Silva RO, Lobato FC, Siqueira AK, et al. Enteric Pathogens and Coinfections in Foals with and without Diarrhea. Biomed Res Int 2016;2016:1512690.
Qu M, Lv B, Zhang X, Yan H, Huang Y, Qian H, et al. Prevalence and antibiotic resistance of bacterial pathogens isolated from childhood diarrhea in Beijing, China (2010-2014). Gut Pathog 2016;8:31.
Andersson M, Kabayiza JC, Elfving K, Nilsson S, Msellem MI, Martensson A, et al. Coinfection with Enteric Pathogens in East African Children with Acute Gastroenteritis-Associations and Interpretations. Am J Trop Med Hyg 2018;98:1566-70.
Sang WK, Kariuki SM, Schnabel D, Boga HI, Waiyaki PG, Wamae CN. Antibiotic susceptibility of Enteric pathogens from the Maasai community, Narok and Kajiado Districts, Kenya. Afr J Health Sci 2011;19:74-9.
Kimondo J, Miaron J, Mutai P, Njogu P. Ethnobotanical survey of food and medicinal plants of the Ilkisonko Maasai community in Kenya. J Ethnopharmacol 2015;175:463-9.
Chiyangi H, Muma JB, Malama S, Manyahi J, Abade A, Kwenda G, et al. Identification and antimicrobial resistance patterns of bacterial enteropathogens from children aged 0-59 months at the University Teaching Hospital, Lusaka, Zambia: a prospective cross sectional study. BMC Infect Dis 2017;17:117.
Tafa B, Sewunet T, Tassew H, Asrat D. Isolation and Antimicrobial Susceptibility Patterns of Campylobacter Species among Diarrheic Children at Jimma, Ethiopia. Int J Bacteriol, 2014;2014:560617.
Tian L, Zhu X, Chen Z, Liu W, Li S, Yu W, et al. Characteristics of bacterial pathogens associated with acute diarrhea in children under 5 years of age: a hospital-based cross-sectional study. BMC Infect Dis 2016;16:253.
Andualem B, Geyid A. Antimicrobial responses of Yersinia enterocolitica isolates in comparison to other commonly encountered bacteria that causes diarrhoea. East Afr Med J 2005;82:241-6.
Novoa-Farias O, Frati-Munari AC, Peredo MA, Flores-Juarez S, Novoa-Garcia O, Galicia-Tapia J, et al. Susceptibility to rifaximin and other antimicrobials of bacteria isolated in patients with acute gastrointestinal infections in Southeast Mexico. Rev Gastroenterol Mex 2017;82:226-33.
Prediger KD, Pereira Rda S, Winckler Neto CH, Santos RC, Fadel-Picheth CM, Vizzotto BS. A prospective study on Aeromonas in outpatients with diarrhea in the central region of Rio Grande do Sul State. Braz J Microbiol 2012;43:966-8.
Van Boeckel TP, Gandra S, Ashok A, Caudron Q, Grenfell BT, Levin SA, et al. Global antibiotic consumption 2000 to 2010: an analysis of national pharmaceutical sales data. Lancet Infect Dis 2014;14:742-50.
- Abstract Viewed: 47 times
- PDF Downloaded: 0 times