Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

Samuel Kariuki, Zoe A. Dyson, Cecilia Mbae, Ronald Ngetich, Susan M. Kavai, Celestine Wairimu, Stephen Anyona, Naomi Gitau, Robert Onsare, Beatrice Ongadi, Sebastian Duchene, Mohamed Ali, John Clemens, Kathryn E. Holt, Gordon Dougan

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17 Citations (Scopus)


Background: Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control. Methods: In a 3 year case-control study, we investigated typhoid among children aged <16 years (4,670 febrile cases and 8,549 age matched controls) living in an informal settlement, Nairobi, Kenya. Results: 148 S. Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1%. Whole-genome sequencing showed 97% of cases and 88% of controls were genotype 4.3.1 (Haplotype 58), with the majority of each (76% and 88%) being multidrug-resistant strains in 3 sublineages of H58 genotype (East Africa 1 (EA1), EA2, and EA3), with sequences from cases and carriers intermingled. Conclusions: The high rate of multidrug-resistant H58 S. Typhi, and the close phylogenetic relationships between cases and controls, provides evidence for the role of carriers as a reservoir for the community spread of typhoid in this setting.

Original languageEnglish
Article numbere67852
Number of pages28
Publication statusPublished - Sept 2021

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