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.

Genomic epidemiology of human adenovirus F40 and F41 in coastal Kenya: A retrospective hospital-based surveillance study (2013–2022)

“…The samples were collected as part of a prospective hospital-based rotavirus surveillance study at Kilifi County Hospital paediatric ward in Kilifi, Kenya ( Agoti et al. 2022 ).…”

“…The positives had been identified either by conventional real-time reverse transcription polymerase chain reaction (RT-PCR) approach or by custom TaqMan Array cards as previously described ( Lambisia et al. 2020 ; Agoti et al. 2022 ).…”

“…Briefly, the samples were extracted from 0.2 g of the specimen (or 200 µl if liquid) using the QIAamp Fast DNA Stool Mini kit (Qiagen, Manchester, UK) as per the manufacturer’s instructions and screened using the TaqMan Fast Virus 1-Step Master Mix and adenovirus 40/41 specific primers (forward primer: 5’-CACTTAATGCTGACACGGGC-3’; probe: ‘FAM-TGCACCTCTTGGACTAGT-MGBNFQ’; and Reverse primer: 5’-ACTGGATAGAGCTAGCGGGC-3’). The thermocycling conditions were 95°C for 20 seconds and 35 cycles of 94°C for 15 seconds and 60°C for 30 seconds ( Agoti et al. 2022 ).…”

“…In the HAdV-F positives, Group A rotavirus was screened using a conventional real-time RT-PCR approach or by custom TaqMan Array cards as previously described ( Lambisia et al. 2020 ; Agoti et al. 2022 ).…”

“…2021 ). In Kenya, the positivity rate of HAdV-F40/41 in diarrhoeal stools from hospitalized under 13-year olds was estimated at 5.8 per cent (95 per cent CI: 3.2–9.6) and 7.3 per cent (95 per cent CI: 5.2–10.1) pre- and post-rotavirus vaccine introduction, respectively ( Agoti et al. 2022 ).…”