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There is concern that a relationship exists between antibiotic use in livestock production and the emergence, spread, and persistence of antibiotic resistance. It is important to understand the impact that therapeutic doses of antibiotics for treatment of disease have on resistance because disease treatment typically involves higher doses of antibiotic over short time spans. Absolute quantities of the antibiotic resistance gene bla(CMY-2) were measured by real-time quantitative polymerase chain reaction (qPCR) in the bacterial community DNA of fecal samples from dairy cattle that were given a 5-day course of ceftiofur and untreated cattle during a longitudinal, observational study. A hierarchical linear model that accounts for left-censored data and repeated measures was used to estimate group means of bla(CMY-2) from the qPCR data. Ceftiofur-treated animals had significantly higher mean quantities of bla(CMY-2) than untreated animals during treatment. On the first day post-treatment, mean quantities of bla(CMY-2) returned to pre-treatment levels and remained low in both groups for the remainder of the study. The use of qPCR to measure bla(CMY-2) quantities provided evidence that the burden of resistance in treated animals may have increased temporarily, a result that was not evident when using only cultivation-based methods of testing for resistance.