Diversity and distribution of Escherichia coli genotypes and antibiotic resistance phenotypes in feces of humans, cattle, and horses

Abstract

Escherichia coli is the most completely characterized prokaryotic model organism and one of the dominant indicator organisms for food and water quality testing, yet comparatively little is known about the structure of E. coli populations in their various hosts. The diversities of E. coli populations isolated from the feces of three host species (human, cow, and horse) were compared by two subtyping methods: ribotyping (using HindIII) and antibiotic resistance analysis (ARA). The sampling effort required to obtain a representative sample differed by host species, as E. coli diversity was consistently greatest in horses, followed by cattle, and was lowest in humans. The diversity of antibiotic resistance patterns isolated from individuals was consistently greater than the diversity of ribotypes. E. coli populations in individuals sampled monthly, over a 7- to 8-month period, were highly variable in terms of both ribotypes and ARA phenotypes. In contrast, E. coli populations in cattle and humans were stable over an 8-h period. Following the cessation of antibiotic therapy, the E. coli population in the feces of one human experienced a rapid and substantial shift, from a multiply antibiotic-resistant phenotype associated with a particular ribotype to a relatively antibiotic-susceptible phenotype associated with a different ribotype. 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 a water quality indicator and its use in microbial source tracking studies.

FIG. 1.

Experimental design. Letter designations A, B, C, D, E, and X refer to the individual sampled.

FIG. 2.

Accumulation curves representing the average number of unique patterns observed per host individual by ribotyping (A) and antibiotic resistance analysis (B) during the 1-day experiment.

FIG. 3.

The temporal persistence of E. coli subtypes isolated from individual cattle, horses, and humans as determined by ribotyping (A) and ARA (B). Each bar represents the number of different subtypes sampled from one individual over 7 to 8 months, and the shading designates the number of months in which the subtypes were observed.

FIG. 4.

The abundance and persistence of subtypes within human X over 1 month as determined by ribotyping (A) and ARA (B). Each bar represents the number of isolates typed for each sampling date. Each different subtype is designated by a number and a color.