Browsing by Author "Shivoga, William A."
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Publication Influences of land use/cover on water quality in the upper and middle reaches of River Njoro, Kenya(Blackwell Publishing Asia Pty Ltd, 2007-04-20) Muchiri, Mucai; Shivoga, William A.; Kibichi, Samuel; Odanga, Jethro; Miller, Scott N.; Baldyga, Tracy J.; Enanga, Eric M.; Gichaba, Maina C.Data from 10 sampling sites along the River Njoro are used to examine the contribution of nutrients from upstream land uses draining each of the sampling sites. The data also are used to assess whether both the proportion of land uses and the size of the subwatersheds account for the variability in water quality in the River Njoro watershed. Geographical Information System analysis was used to determine the spatial distribution of land-cover types and subwatersheds contributing run-off to the sampling sites in the River Njoro. Standard Digital Elevation Model-based routines were used to establish the watershed area contributing run-off to each sampling site. Water and sediment samples were collected for chemical analysis, and the nutrient levels were related to the upstream land-use types and the size of the subwatersheds. The mid-stream portion of the River Njoro (near Egerton University) accounts for the highest nutrient contributions. The percentage contribution is magnified by additions from industrial, human settlements and agricultural land uses around the University. There is a significant decrease in nutrient levels downstream, however, indicating natural purification as the river flows through an area of large-scale farming with intense, well-preserved riparian and in-stream vegetation. Steep slopes of the land upstream of Egerton University enhance erosion and nutrient losses from those subwatersheds. Mixed small-scale agricultural and bare lands contribute over 55% of the phosphorus load to the upper and mid-reaches of the River Njoro. The size of the subwatershed accounts for about 53% of the variability in the soluble phosphorus in the river. The land-use subwatershed proportions are important for characterizing and modelling water quality in the River Njoro watershed. Upland land uses are as important as near-stream land uses. We suggest that conservation of intact riparian corridor along the river and its tributaries contributes significantly to natural purification processes and recovery of the ecological integrity of the River Njoro ecosystemPublication Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya(Elsevier, 2021-02-27) Wawire, Sifuna Anthony; Reva, Oleg N.; O'Brien, Thomas J.; Figueroa, Wendy; Dinda, Victor; Shivoga, William A.; Welch, MartinMany low-middle income countries in Africa have poorly-developed infectious disease monitoring systems. Here, we employed whole genome sequencing (WGS) to investigate the presence/absence of antimicrobial resistance (AMR) and virulence-associated (VA) genes in a collection of clinical and municipal wastewater Escherichia coli isolates from Kakamega, west Kenya. We were particularly interested to see whether, given the association between infection and water quality, the isolates from these geographically-linked environments might display similar genomic signatures. Phylogenetic analysis based on the core genes common to all of the isolates revealed two broad divisions, corresponding to the commensal/enterotoxigenic E. coli on the one hand, and uropathogenic E. coli on the other. Although the clinical and wastewater isolates each contained a very similar mean number of antibiotic resistance-encoding genes, the clinical isolates were enriched in genes required for in-host survival. Furthermore, and although the chromosomally encoded repertoire of these genes was similar in all sequenced isolates, the genetic composition of the plasmids from clinical and wastewater E. coli was more habitat-specific, with the clinical isolate plasmidome enriched in AMR and VA genes. Intriguingly, the plasmid-borne VA genes were often duplicates of genes already present on the chromosome, whereas the plasmid-borne AMR determinants were more specific. This reinforces the notion that plasmids are a primary means by which infection-related AMR and VA-associated genes are acquired and disseminated among these strains.