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

Abstract

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.

Keywords: Children; Co-infections; Enteropathogens; Epidemiology; Kenya; RVA; Taqman array card; Vaccination.

Fig. 1

The configuration of the GASTRO v4.0 K TaqMan Array Card used for screening 28 enteropathogens. Some of the enteropathogens had multiple spots (targets) on the card

Fig. 2

Prevalence of enteropathogens in stool samples from 718 children hospitalised at KCH at different PCR cycle threshold (Ct) cut-offs. The bars represent organism type and include 95% confidence interval errors bars for the proportions. Panel (a) prevalence of the detected enteropathogens when applying a Ct cut-off of ≤ 40 to define positives. Panel (b) prevalence of the detected enteropathogens when applying a Ct cut-off ≤ 35 to define positives. Panel (c) prevalence of detected the enteropathogens when applying a Ct cut-off ≤ 30 to define positives

Fig. 3

Boxplots examining the relationship between the observed RVA detection cycle threshold (Ct) from TAC assay and (a) previous enzyme-linked immunosorbent assay (ELISA) result on the same samples, (b) period of sample collection, (c) rotavirus vaccination status, and (d) age group in stool samples from 718 children at KCH. P-values are derived from an independent t-test, one-way ANOVA, and where applicable Kruskal Wallis was used