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Subacute ruminal acidosis (SARA) is a common digestive disorder in dairy cows characterized by prolonged periods of undesirably low rumen pH (5.8) and is caused by the accumulation of volatile fatty acids in rumen. This disorder damages the ruminal mucosa, causes diarrhea, reduces dry matter intake (DMI), and can result in anorexia and death. In this study, nonlactating dairy cows were fed diets predisposing them to a high risk (HR; n = 6) or a low risk (LR; n = 6) for experiencing SARA. The goal was to investigate differences in antimicrobial resistance selection, proliferation, and characterization of Escherichia coli strain types among the two treatment groups. Fecal samples were used to isolate total, tetracycline-resistant (Tet(r)), and ampicillin-resistant E. coli, and selected isolates were examined. We found reduced total (1.2-fold) and Tet(r) (1.4-fold) E. coli in HR cows. Low ampicillin-resistant E. coli shedding was detected from both HR (0.22 colony forming unit/g) and LR (0.46 colony forming unit/g) cows. Overall, 39 pulsed-field gel electrophoresis (PFGE) profiles and 13 antibiotic resistance profiles (phenotypes) were identified from the total isolates examined (n = 144). The LR cows exhibited diverse genotypes (22 PFGE profiles) clustering into seven restriction endonuclease digestion pattern clusters (REPCs) within total and Tet(r) E. coli. In comparison, isolates from HR animals showed increased genotypic relatedness (16 PFGE profiles and 13 REPC with comparable phenotypes). From both HR and LR cows, no significant differences in the detection of a particular phenotype were observed (p0.05), and tet(A) allele was frequently detected among isolates from HR (45.2%) and tet(B) from LR (36.6%) cows. Changes in fecal E. coli genotypes should be explored further for its usefulness as an indicator for SARA since dairy cows are a reservoir of diverse E. coli strain types. Our results elucidate phenotypic and genotypic differences in fecal E. coli shed between HR and LR cows.