It is interesting to note that although Escherichia coli is the most comprehensively characterized prokaryotic model organism and one of the most dominant indicator organism for food and water quality testing, relatively little is known about the structure of E. coli populations compared to other species. Limited studies however shown that diversity of E. coli is highly polyclonal and that strain diversity may be lower in human hosts than in other animals including cows and horses. Related studies have also shown that despite their low diversity in the human host, E.coli populations are likely to experience a rapid and substantial shift from a multiply antibiotic-resistant to a relatively antibiotic-susceptible phenotype depending on the antimicrobial use patterns of the host.

The high genetic diversity of E. coli populations, differences in diversity among hosts, and temporal variability all indicate complex population dynamics that influence the usefulness of E. coli as an environmental indicator (water and food quality) and as indicator in microbial source tracking. This organism is also ideal as a study model to assess strain relatedness and transfer between humans, animals and the environment. Pathogenic subtypes of E. coli are known to cause illness around the world, and an increased understanding of the genetic variability of populations in animal reservoirs can inform epidemiological studies

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The aim of the current study is to obtain E. coli isolates from different households in Nairobi, an urban setting, and compare their phenotypic and genetic diversity with those obtained from animals and environmental samples collected in the same households. Fecal samples from humans and animals will be enriched in buffered peptone water (BPW) and isolations done on MacConkey’s or Eosin Methylene Blue agar (EMBA). From each primary plate, 5 colonies per specimen will be picked and purified in MacConkey’s agar. Confirmation of species identity will be done using standard biochemical tests. The antimicrobial susceptibility profiles will then be determined against a panel of antimicrobials carefully selected to identify unique resistance phenotypes such as Extended Spectrum β-Lactamase –producers (ESBL) and those showing co-resistance to important classes of antimicrobials such as fluoroquinolones and aminoglycosides. Based on the antimicrobial resistance (AMR) profiles, a maximum of 3 isolates from each specimen will be subjected to a low-resolution genotyping protocol such as ERIC/BOX or (GTG)₅-fingerprinting PCRs. Based on a combination of the AMR and the fingerprinting data, a set of strains will be selected for full genome sequencing.

The figure to the left summarises the workflow of the laboratory procedures.

Article by Dr. John Kiiru