Development of a procedure for discriminating among Escherichia coli isolates from animal and human sources

Abstract

Counts of Escherichia coli cells in water indicate the potential presence of pathogenic microbes of intestinal origin but give no indication of the sources of the microbial pollution. The objective of this research was to evaluate methods for differentiating E. coli isolates of livestock, wildlife, or human origin that might be used to predict the sources of fecal pollution of water. A collection of 319 E. coli isolates from the feces of cattle, poultry, swine, deer, goose, and moose, as well as from human sewage, and clinical samples was used to evaluate three methods. One method was the multiple-antibiotic-resistance (MAR) profile using 14 antibiotics. Discriminant analysis revealed that 46% of the livestock isolates, 95% of the wildlife isolates, and 55% of the human isolates were assigned to the correct source groups by the MAR method. Amplified fragment length polymorphism (AFLP) analysis, the second test, was applied to 105 of the E. coli isolates. The AFLP results showed that 94% of the livestock isolates, 97% of the wildlife isolates, and 97% of the human isolates were correctly classified. The third method was analysis of the sequences of the 16S rRNA genes of the E. coli isolates. Discriminant analysis of 105 E. coli isolates indicated that 78% of the livestock isolates, 74% of the wildlife isolates, and 80% of the human isolates could be correctly classified into their host groups by this method. The results indicate that AFLP analysis was the most effective of the three methods that were evaluated.

FIG. 1.

CA of fluorescent AFLP results obtained by using primers EcoRI-A and MseI-G for 105 E. coli isolates from various host sources. Bacterial designation prefixes based on host origins are explained in Table 1. The tree was constructed with TREECON, version 1.3b.

FIG. 2.

Unrooted tree generated by a Perl program showing that most of the E. coli isolates were correctly classified into the host groups. The tree was visualized by using TreeView 1.6.5 software (26). Bacterial designation prefixes based on host origins are explained in Table 1. (a) AFLP results generated with primers EcoRI-A and MseI-G; (b) AFLP results generated with primers EcoRI-C and MseI-CA.