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 antibioticresistant 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.The structure of Escherichia coli populations influences several aspects of public health. Pathogenic subtypes of E. coli are known to cause illness around the world (18), and an increased understanding of the genetic variability of populations in animal reservoirs can inform epidemiological studies. E. coli is also one of the standard indicator organisms for fecal pollution in environmental waters (1). The natural host range of E. coli includes all warm-blooded animals, some cold-blooded animals (12), and environmental reservoirs, such as sediments (2, 32) and free-living strains (24); therefore, the source of fecal pollution in water bodies is often ambiguous. Knowledge of indicator organism source is necessary for risk assessment and remediation of polluted waters, including application, such as total maximum daily load assessment. Consequently, the field of microbial source tracking (MST), which seeks to determine the origin of fecal material in water, has emerged (4, 7, 10, 14, 23, 31, 35).Many microbial source tracking methods rely on the premise that, in their gastrointestinal tracts, animal species contain distinct subtypes of E. coli that are shed in their feces. Matching the subtypes of E. coli identified in polluted watersheds to those isolated from known sources would hypothetically allow the identification of the source of the pollution (28). Many MST methods require a library of E. coli subtypes isolated fr...

Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping

“…Others have used a 2-enzyme digest (Meays et al 2006), or separate ribotyping analyses with 2 different enzymes (Harwood et al 2003, Jenkins et al 2003, Jones et al 2006, to increase the potential diversity in ribopatterns. However, studies where DNA profiles from many isolates from an individual animal have been compared show saturations of diversity, or richness, at different numbers of profiles (Carson et al 2001, Johnson et al 2004, McLellan 2004, Anderson et al 2006. Myoda et al (2003) suggested DNA banding patterns produced by ribotyping and other genotypic methods are probably random with respect to what makes individual and hostspecific strains of target bacteria unique, so the added cost of using a second enzyme may not be necessary.…”

“…Direct comparisons of Escherichia coli populations in various host animals are rare in the literature, as most studies have focused on one host species (Anderson et al 2006). No prior studies have specifically compared E. coli isolates between gull species or between more than one gull species and multiple environmental sources.…”

“…The observed frequency and distribution of E. coli subtypes, determined by ribotype, were compared within and between hosts and sources. Four different indices from the Hill family of diversity indices were used (following Anderson et al 2006): (1) a richness estimator (S) was calculated as the number of different subtypes; (2) Shannon-Wiener diversity index (H') was calculated as H' = −Σp i ln(p i ) where p i is (number of isolates with pattern [i])/total isolates; (3) Simpson's index (D) was calculated as Σ[n i (n i -1)]/[n(n -1)] where n i is the number of isolates with subtype [i] and n is the total number of isolates; and (4) Pielou's evenness (J') was calculated as H' lnS −1…”

Bacterial indicators and antibiotic resistance of Escherichia coli in groundwater

“…On the other hand, the percentages of resistance for cephalothin observed in this research were relevant. All these aspects should be highlighted, since few authors have investigated the presence of resistant bacteria in groundwater [19]. …”

Source tracking faecal contamination in an urbanised and a rural waterway in the Nelson-Tasman region, New Zealand

“…Library-dependent methods rely on the collection of FIB isolates from a known source for comparison of genetic or phenotypic patterns (fingerprints) of isolates from environmental samples. Such libraries are relatively location specific, and their utility is greatly hampered by the diversity and temporal variability of faecal organisms (Gordon 2001;Wiggins et al 2003;Anderson et al 2006).…”