Small mammals are important hosts for Borrelia. Their local presence plays a decisive epidemiological role, as it enables the monitoring of the diversity of Borrelia genotypes and the distribution of ticks. Lyme borreliosis is the most common tick-borne disease in Slovenia, with Borrelia sp. transmitted by Ixodes ricinus ticks. This study focuses on determining the prevalence of the Borrelia burgdorferi sensu lato complex and Borrelia miyamotoi in rodents captured in the Gorizia and Central Slovenia regions. Molecular methods were used to detect the presence of Borrelia in various organs of small mammals. Real-time polymerase chain reaction confirmed the presence of Borrelia in all organs examined – heart, liver, lungs and ears. The highest number of positive results among the samples was obtained from ear tissue. Borrelia from the B. burgdorferi sl complex was detected in 71,43 % of the ear samples and B. miyamotoi in 42,86 % of the ear samples.
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