Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya.

Many 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.

Geophagia as a risk factor for diarrhoea.

BACKGROUND: Many children under the age of five are exposed to environmental health risks in the home environment. These lead to diseases such as diarrhoea, which along with acute respiratory infections, malaria and intestinal worms, account for 70% of the total health burden to children under five in Kenya. The aim of this study was to investigate whether earth eating within the home environment by children is a risk factor for diarrhoeal disease. METHODOLOGY: A longitudinal study was conducted in 350 households having children aged below five years between April and October, 2005. Questionnaire and observation were used to collect data on participant demographics, earth eating practices in children, incidence of diarrhoea, structure of the home, sanitary facilities available, and presence of faecal matter in the yard. RESULTS: Thirty-seven percent of index children ingest earth occasionally (less than a handful) and 12% ingest a lot (a handful or more). Diarrhoea is positively correlated with earth eating (r = 0.306), presence of human faeces in the yard (r = 0.587), presence of animal faeces in the yard (r = 0.225) and the index child not wearing loincloth (r = 0.471). Chi-square test of independence also indicates that earth eating is significantly related to diarrhoea (p<0.005). CONCLUSION: Earth eating is a risk factor for diarrhoea in the home environment in this region of Kenya.