Differences in epidemiology of enteropathogens in children pre- and post-rotavirus vaccine introduction in Kilifi, coastal Kenya

Charles N. Agoti*, Martin D. Curran, Nickson Murunga, Moses Ngari, Esther Muthumbi, Arnold W. Lambisia, Simon D.W. Frost, Barbara A. Blacklaws, D. James Nokes, Lydia N. Drumright

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Background: Kenya introduced Rotarix® (GlaxoSmithKline Biologicals, Rixensart, Belgium) vaccination into its national immunization programme beginning July 2014. The impact of this vaccination program on the local epidemiology of various known enteropathogens is not fully understood. Methods: We used a custom TaqMan Array Card (TAC) to screen for 28 different enteropathogens in 718 stools from children aged less than 13 years admitted to Kilifi County Hospital, coastal Kenya, following presentation with diarrhea in 2013 (before vaccine introduction) and in 2016–2018 (after vaccine introduction). Pathogen positivity rate differences between pre- and post-Rotarix® vaccination introduction were examined using both univariate and multivariable logistic regression models. Results: In 665 specimens (92.6%), one or more enteropathogen was detected, while in 323 specimens (48.6%) three or more enteropathogens were detected. The top six detected enteropathogens were: enteroaggregative Escherichia coli (EAggEC; 42.1%), enteropathogenic Escherichia coli (EPEC; 30.2%), enterovirus (26.9%), rotavirus group A (RVA; 24.8%), parechovirus (16.6%) and norovirus GI/GII (14.4%). Post-rotavirus vaccine introduction, there was a significant increase in the proportion of samples testing positive for EAggEC (35.7% vs. 45.3%, p = 0.014), cytomegalovirus (4.2% vs. 9.9%, p = 0.008), Vibrio cholerae (0.0% vs. 2.3%, p = 0.019), Strongyloides species (0.8% vs. 3.6%, p = 0.048) and Dientamoeba fragilis (2.1% vs. 7.8%, p = 0.004). Although not reaching statistical significance, the positivity rate of adenovirus 40/41 (5.8% vs. 7.3%, p = 0.444), norovirus GI/GII (11.2% vs. 15.9%, p = 0.089), Shigella species (8.7% vs. 13.0%, p = 0.092) and Cryptosporidium spp. (11.6% vs. 14.7%, p = 0.261) appeared to increase post-vaccine introduction. Conversely, the positivity rate of sapovirus decreased significantly post-vaccine introduction (7.8% vs. 4.0%, p = 0.030) while that of RVA appeared not to change (27.4% vs. 23.5%, p = 0.253). More enteropathogen coinfections were detected per child post-vaccine introduction compared to before (mean: 2.7 vs. 2.3; p = 0.0025). Conclusions: In this rural Coastal Kenya setting, childhood enteropathogen infection burden was high both pre- and post-rotavirus vaccination introduction. Children who had diarrheal admissions post-vaccination showed an increase in coinfections and changes in specific enteropathogen positivity rates. This study highlights the utility of multipathogen detection platforms such as TAC in understanding etiology of childhood acute gastroenteritis in resource-limited regions.

Original languageEnglish
Article number32
JournalGut Pathogens
Issue number1
Publication statusPublished - Dec 2022

Bibliographical note

Funding Information:
This study was funded by the Cambridge-Africa ALBORADA Research Fund. Dr Charles Agoti was supported by the Initiative to Develop African Research Leaders (IDeAL) through the DELTAS Africa Initiative [DEL-15-003]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)’s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa’s Development Planning and Coordinating Agency (NEPAD Agency). Dr Lydia Drumright was supported by the following funding sources during this study: Medical Research Council (award # MR/S013164/1), the Alan Turing Institute through a Research Fellowship, the National Institutes for Health Research (award # CDF-2011-04-017) and the Cambridge Biomedical Research Center, the Economic and Social Science Research Council (award # AH/R001952/1), and an Isaac Newton/Wellcome Trust ISSF award to understand gastrointestinal infection epidemiology through use of this TAC. The views expressed in this report are those of the authors and not necessarily those of AAS, NEPAD Agency, The Wellcome, the UK government.

Funding Information:
We thank the study participants who provided the samples and members of the Virus Epidemiology and Control (VEC) group at KEMRI-Wellcome Trust Programme who collected the samples and performed the laboratory processing. We thank Prof. Philip Bejon for stimulating discussions about the work and comments provided on the initial draft manuscript. This study is published with permission of the from Director of KEMRI. The views expressed in this article are solely those of the authors and not of the funders or affiliated institutions.

Publisher Copyright:
© 2022, The Author(s).


  • Children
  • Co-infections
  • Enteropathogens
  • Epidemiology
  • Kenya
  • RVA
  • Taqman array card
  • Vaccination


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