(1) Background: Dogs are known as hosts of Leptospira interrogans and can spread this bacterium to the environment. Although Canicola is responsible for determining chronic disease in dogs, when affected by incidental serogroups such as Icterohaemorrhagiae, acute disease may occur with a predominance of clinical signs with hepatic and renal changes. In endemic areas, it is a serious public health problem. Thus, this study aims to estimate the incidence and duration of elimination of leptospires in the urine of dogs, taking another step from a previous study of our group, by a longitudinal, long-term and molecular approach. (2) Methods: A total of 125 dogs without apparent symptoms of leptospirosis were included in the study. The dogs were all PCR-negative and seronegative at the beginning of the study. Blood samples were collected for hematological examinations and urine for amplification of the lipL32 gene by PCR at five different time points during one year. (3) Results: Out of the 125 dogs, 62 became lipL32 PCR-positive (48.8% (95% CI, 47.9–49.7%)) at some point during the study, distributed as follows: at day 0, all negative; day 90, 18/125 (14.4% (95% CI, 13.5–15.3%)); day 180, 18/125 (14.4% (95% CI, 13.5–15.3%)); day 270, 12/125 (9.6% (95% CI, 8.7–10.5%)); and day 365, 14/125 (11.2% (95% CI, 10.3–12.1%)). Out of the 62 amplicons, 22 were sequenced, targeting a short region of secY gene. Of these, 20 (90.9%) were identical to the L. interrogans serovar Icterohaemorrhagiae, while two (9.1%) were Leptospira noguchii. (4) Conclusions: The fact that the leptospires of the Icterohaemorrhagiae serogroup were characterized was unexpected, since the animals remained clinically asymptomatic during the study. The fact that asymptomatic dogs shed leptospires is not new, but the extent of this fact and the characterized strain is impressive, with an impact on public health that cannot be overlooked.
