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. 2020 Aug 3;14(8):e0008440.
doi: 10.1371/journal.pntd.0008440. eCollection 2020 Aug.

High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya

Affiliations

High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya

Samuel Kariuki et al. PLoS Negl Trop Dis. .

Abstract

Invasive Non-typhoidal Salmonella (iNTS) disease is a major public health challenge, especially in Sub-Saharan Africa (SSA). In Kenya, mortality rates are high (20-25%) unless prompt treatment is instituted. The most common serotypes are Salmonella enterica serotype Typhimurium (S. Typhimurium) and Salmonella enterica serotype Enteritidis (S. Enteritidis). In a 5 year case-control study in children residing in the Mukuru informal settlement in Nairobi, Kenya, a total of 4201 blood cultures from suspected iNTS cases and 6326 fecal samples from age-matched controls were studied. From the laboratory cultures we obtained a total of 133 S. Typhimurium isolates of which 83(62.4%) came from cases (53 blood and 30 fecal) and 50(37.6%) from controls (fecal). A total of 120 S. Enteritidis consisted of 70(58.3%) from cases (43 blood and 27 fecal) and 50(41.7%) from controls (fecal). The S. Typhimurium population fell into two distinct ST19 lineages constituting 36.1%, as well as ST313 lineage I (27.8%) and ST313 lineage II (36.1%) isolates. The S. Enteritidis isolates fell into the global epidemic lineage (46.6%), the Central/Eastern African lineage (30.5%), a novel Kenyan-specific lineage (12.2%) and a phylogenetically outlier lineage (10.7%). Detailed phylogenetic analysis revealed a high level of relatedness between NTS from blood and stool originating from cases and controls, indicating a common source pool. Multidrug resistance was common throughout, with 8.5% of such isolates resistant to extended spectrum beta lactams. The high rate of asymptomatic carriage in the population is a concern for transmission to vulnerable individuals and this group could be targeted for vaccination if an iNTS vaccine becomes available.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Mapped villages constituting Mukuru informal settlement study site.
The image was acquired from Google Earth to create the map of structures/buildings of the study area as the first step of creating the GIS database. The images were geometrically rectified to a known coordinate system (Universal Transverse Mercator (UTM) 37S on the basis of a number of Ground Control Points (GCPs), selected from the periphery of the study area so that possible errors would converge towards middle of the area. Images were converted into TIFF files in ArcGIS10x software.
Fig 2
Fig 2. Phylogenetic tree of S. Typhimurium isolates from this study.
Maximum likelihood phylogenetic tree based on the 130 S. Typhimurium genome sequences from this study. Sequencing reads were mapped to S. Typhimurium ST313 lineage II reference strain D23580, and S. Typhi 10040_15 was added as an outgroup to root the tree. The tree is based on 61161 chromosomal SNPs. Patient state (case/control) and the source (blood/stool) is visualized as indicated in the legend. Presence of multidrug resistance markers (MDR; bla, dfrA, sul, cat), blaCTX-M/blaOXA antimicrobial resistance markers and SNPs in gyr are annotated. Branch lengths represent numbers of SNPs as indicated in the scale bar.
Fig 3
Fig 3. Phylogenetic tree of S. Enteritidis isolates from this study.
Maximum likelihood phylogenetic tree based on the 120 S. Enteritidis genome sequences from this study. Sequencing reads were mapped against S. Enteritidis reference strain P125109, and S. Typhi 10040_15 was added as an outgroup to root the tree. The tree is based on 60302 chromosomal SNPs. Patient state (case/control) and the source (blood/stool) is visualized as indicated in the legend. Presence of multidrug resistance markers (MDR; bla, dfrA, sul, cat) and SNPs in gyr are annotated. Branch lengths represent numbers of SNPs as indicated in the scale bar.

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