Genotypic Diversity among Typhi Isolated from Children Living in Informal Settlements in Nairobi, Kenya.

The persistence of multidrug-resistant (MDR) Typhi (. Typhi) is a challenge especially in regions where typhoid is endemic. Surveillance of circulating genotypes of MDR . Typhi is crucial in typhoid acute cases and carriers. This study aimed to investigate genotypic diversity of . Typhi from symptomatic and asymptomatic children in endemic settings in Nairobi, Kenya. Symptomatic and asymptomatic individuals' ≤ 16 years were recruited at four health facilities and tested for typhoid through stool cultures. The . Typhi isolates were subjected to antibiotic susceptibility testing to investigate multidrug resistance. The MDR . Typhi isolates' DNA was extracted and illumina sequenced. Raw reads were assembled and analyzed by pathogen-watch. From the 90 sequenced isolates, 60 (67%) were confirmed to be . Typhi (sequence Type 1 and genotype 4.3.1). Out of the 60 . Typhi strains; 39 (65%) had plasmids, from these 38 (97%) had plasmids alone. Out of the 60, 59 (98%) . Typhi isolates had . Point mutations conferring reduced susceptibility to quinolones were detected in 42 (70%) of . Typhi isolates, from these; 14 (33%) had , and 28 (67%) genes, respectively. This study reports 4.3.1 (H58) as the most dominant . Typhi genotype responsible for spread of MDR phenotypes carried on plasmids. Presence of MDR . Typhi with resistance genes such as and reduced susceptibility to ciprofloxacin especially among asymptomatic individuals, reiterates the need for use of typhoid conjugate vaccine among vulnerable children as a control and prevention measure against typhoid.