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. 2024;1(3):18-27.
doi: 10.14302/issn.2690-4721.ijcm-24-5195. Epub 2024 Sep 16.

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

Susan Mutile Kavai  1   2 , Julius Oyugi  2   3 , Cecilia Mbae  1 , Celestine Wairimu  1 , Kelvin Kering  1 , Collins Kebenei  1 , Peter Muturi  1 , Sylvia Omulo  3   4   5 , Samuel Kariuki  1   6   7
Affiliations

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

Susan Mutile Kavai et al. Int J Clin Microbiol. 2024.

Abstract

The persistence of multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) is a challenge especially in regions where typhoid is endemic. Surveillance of circulating genotypes of MDR S. Typhi is crucial in typhoid acute cases and carriers. This study aimed to investigate genotypic diversity of S. 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 S. Typhi isolates were subjected to antibiotic susceptibility testing to investigate multidrug resistance. The MDR S. Typhi isolates' DNA was extracted and illumina sequenced. Raw reads were de novo assembled and analyzed by pathogen-watch. From the 90 sequenced isolates, 60 (67%) were confirmed to be S. Typhi (sequence Type 1 and genotype 4.3.1). Out of the 60 S. Typhi strains; 39 (65%) had plasmids, from these 38 (97%) had IncHI1 plasmids alone. Out of the 60, 59 (98%) S. Typhi isolates had bla TEM-1D . Point mutations conferring reduced susceptibility to quinolones were detected in 42 (70%) of S. Typhi isolates, from these; 14 (33%) had gyrA S83Y, and 28 (67%) gyrB S464F genes, respectively. This study reports 4.3.1 (H58) as the most dominant S. Typhi genotype responsible for spread of MDR phenotypes carried on IncHI1 plasmids. Presence of MDR S. Typhi with resistance genes such as bla TEM-1D 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.

Keywords: Haplotype 58; S. Typhi; antimicrobial resistance; asymptomatic; genetic diversity; informal settlements; symptomatic.

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Figures

Figure 1.
Figure 1.
Phylogenetic tree comparing S. Typhi genotypes from our study with those from other countries in Africa and Asia. We selected 208 S. Typhi isolates distributed across 11 African and Asian countries. All S. Typhi isolates belonging to genotype 4.3.1 appear to originate from the same branch.
Figure 2.
Figure 2.
Antimicrobial resistance genes from S. Typhi isolated from children ≤16 years of age from Mukuru and Kibera informal settlements, Nairobi, Kenya
See this image and copyright information in PMC

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References

    1. World Health Organization. Typhoid; 2018. Available from: https://www.who.int/news-room/fact-sheets/detail/typhoid. Accessed May 6, 2021.
    1. Kim JH, Choi J, Kim C, Pak GD, Parajulee P, Haselbeck A, et al. Mapping the incidence rate of typhoid fever in sub-Saharan Africa. PLoS Negl Trop Dis. 2024. Feb 26;18(2): e0011902. doi: 10.1371/journal.pntd.0011902. Epub ahead of print. - DOI - PMC - PubMed
    1. Breiman RF, Cosmas L, Njuguna H, Audi A, Olack B, Ochieng JB, et al. Population-based incidence of typhoid fever in an urban informal settlement and a rural area in Kenya: Implications for typhoid vaccine use in Africa. PLoS One 2012;7. doi: 10.1371/journal.pone.0029119 - DOI - PMC - PubMed
    1. Mengo D, Kariuki S, and Muigai A. Salmonella enteric serovar Typhi in Nairobi, Kenya from 2004 to 2006. The Journal Of Infection In Developing Countries, 2010; 6: 393–396. - PubMed
    1. Kavai S, Kangogo M, Muigai A and Kariuki S (2018) Analysis of Trends in Resistance to Fluoroquinolones and Extended Spectrum Beta-Lactams among Salmonella Typhi Isolates Obtained from Patients at Four Outpatient Clinics in Nairobi County, Kenya. Advances in Microbiology, 8, 578–588. doi: 10.4236/aim.2018.87038. - DOI

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