*3.3. Enrofloxacin MICs Distributions of the Commensal E. coli Isolates*

The percentage of frequency of MICs distribution of the 576 commensal *E. coli* isolates from cloacal swabs and manure samples to enrofloxacin during the AT and ET stages are shown in Figure 3a–d. For *E. coli* from chickens and turkeys, the Clinical Laboratory Standard Institute (CLSI [28]) determined a veterinary specific breakpoint of ≥2 μg/mL for enrofloxacin.

When comparing the three trials (Figure 3a–d), a large number of resistant *E. coli* isolates during the AT and ET stages were found in trial 2, 93% and 99% in cloacal swabs, respectively (Figure 3a,b) and in manure samples, 79% and 92% during the AT and ET stages, respectively (Figure 3c,d). On the other hand, all *E. coli* isolates from trial 3 during the AT stage were susceptible to enrofloxacin (≤0.25 μg/mL).

Regarding the MICs distribution for enrofloxacin, susceptible isolates from cloacal swabs in trial 1 decreased gradually from 52% during the AT stage to 42% at the end of the study (Figure 3a,b). In contrast, the percentage of resistant *E. coli* isolated in trial 2 slightly increased from 93% to 99% during the AT and ET stages, respectively (Figure 3a,b). On the other hand, nearly all of the *E. coli* isolates from the cloacal swabs and manure samples in trial 3 had enrofloxacin MIC-values below the clinical breakpoint (MIC ≤ 2 μg/mL).
