Genotypic and phenotypic characterization of Escherichia coli isolates from feces, hands, and soils in rural Bangladesh via the Colilert Quanti-Tray System

Abstract

The increased awareness of the role of environmental matrices in enteric disease transmission has resulted in the need for rapid, field-based methods for fecal indicator bacteria and pathogen detection. Evidence of the specificity of β-glucuronidase-based assays for detection of Escherichia coli from environmental matrices relevant to enteric pathogen transmission in developing countries, such as hands, soils, and surfaces, is limited. In this study, we quantify the false-positive rate of a β-glucuronidase-based E. coli detection assay (Colilert) for two environmental reservoirs in Bangladeshi households (hands and soils) and three fecal composite sources (cattle, chicken, and humans). We investigate whether or not the isolation source of E. coli influences phenotypic and genotypic characteristics. Phenotypic characteristics include results of biochemical assays provided by the API-20E test; genotypic characteristics include the Clermont phylogroup and the presence of enteric and/or environmental indicator genes sfmH, rfaI, and fucK. Our findings demonstrate no statistically significant difference in the false-positive rate of Colilert for environmental compared to enteric samples. E. coli isolates from all source types are genetically diverse, representing six of the seven phylogroups, and there is no difference in relative frequency of phylogroups between enteric and environmental samples. We conclude that Colilert, and likely other β-glucuronidase-based assays, is appropriate for detection of E. coli on hands and in soils with low false-positive rates. Furthermore, E. coli isolated from hands and soils in Bangladeshi households are diverse and indistinguishable from cattle, chicken, and human fecal isolates, using traditional biochemical assays and phylogrouping.

FIG 1

Linear discriminant analysis results for estimating the probability that an E. coli isolate is from cattle feces, P(Cattle), chicken feces, P(Chicken), or human feces, P(Human), based on the isolates' biochemical assay results and Clermont phylogroup. The ternary plots are used to visualize the fecal source probabilities for E. coli isolates collected from cattle feces (A), chicken feces (B), human feces (C), hands (D), and soil (E). (F) Ternary plot overlays of all of the samples together, with annotations (1 to 5) indicating clusters of isolates with similar biochemical and phylogroup profiles. Each marker represents one isolate. The sample locations in the plot are shifted slightly by the addition of random noise for visualization to avoid sample overlap. Density gradients were estimated using linear interpolation to visualize relative sample densities at locations within the ternary plots, with levels used to describe the relative local sample density at a given spatial location.