Putative temporal variability of Escherichia coli ribotypes from yearling steers.

Escherichia coli is a ubiquitous component of the intestinal microflora of warm-blooded animals, and is an indicator of fecal contamination of surface waters. Ribotype profiling of E. coli is one of several genotypic methods that has been developed to determine the host origin of fecal bacteria. Like most genotypic methods of source tracking, ribotyping requires a host origin database to identify environmental isolates. To determine the extent of temporal variability of ribotypes and its effect on a host origin database, E. coli isolates were obtained from fecal samples of two herds of Black Angus steers at a long-term experimental site at four sampling times from October 1999 to July 2000. Fecal samples were taken from six randomly chosen steers at each time. At a similarity index of 90% as calculated by unweighted pair-group method using arithmetic averages (UPGMA), 240 ribotypes were identified from 451 E. coli isolates. Only 20 ribotypes (8.3%), comprising 33% of the total isolates, were shared among sampling times and were considered resident ribotypes. Two of the twenty resident ribotypes appeared at three sampling times, and the remaining eighteen appeared at two. The majority of the ribotypes, therefore, were transient and unique to each sampling time and steer. Both the apparent turnover of E. coli ribotypes and a clonal diversity index of 0.97 (indicative of extensive ribotype variability) suggest the necessity of ribotyping a large number E. coli isolates per host to establish a host origin database that is independent of temporal variability, or complete enough to be effective.