Introduction With their remarkable flight capabilities, wild and captive birds play a pivotal role in the global dissemination of zoonotic pathogens including Chlamydia psittaci, Avian Influenza viruses (AIV), Chikungunya virus (CHIKV), Usutu virus (USUV), and West Nile virus (WNV). They function both as hosts and reservoirs responsible for transporting the mentioned infectious agents across vast geographic regions. Additionally, captive birds and birds inhabiting urban environments, particularly in tourist destinations, present significant public health concerns due to facilitated close interactions with humans. Methods A total of 358 samples originating from fifteen bird species were collected across 21 locations in Sarajevo Canton, over three consecutive years (2022–2024). Upon collection, the samples were subjected to molecular analysis to detect the presence of zoonotic pathogens. For detection of Chlamydia spp., and C. psittaci, real-time PCRs (qPCR) were used following established protocols. Additionally, reverse transcriptase real-time PCR (RT-qPCR) were utilized for the detection of emergent viral pathogens including avian influenza viruses, Chikungunya, Usutu, and West Nile virus. Results Chlamydia spp. was detected in 29.9% (95% CI: 25.2–34.9) of samples. Further, C. psittaci was identified in 10.3% (95% CI: 5.2–17.7) of positive samples originating from captive birds and birds inhabiting urban environments. One sample (0.3%) originating from a wild bird was positive to West Nile Virus. None of the samples tested positive for Avian Influenza viruses, Chikungunya and Usutu virus. Discussion The identification of C. psittaci and West Nile virus highlights the increased likelihood of zoonotic transmission. This underscores the imperative for bolstered biosecurity measures and public health strategies aimed at mitigating the risk associated with both environmental exposure and direct contact, especially in areas characterized by substantial tourist activity.

Bats are a natural host for a number of viruses, many of which are zoonotic and thus present a threat to human health. RNA viruses of the family Filoviridae, many of which cause disease in humans, have been associated with specific bat hosts. Lloviu virus is a Filovirus which has been connected to mass mortality events in Miniopterus schreibersii colonies in Spain and Hungary, and some studies have indicated its immense zoonotic potential. A die-off has been recorded among Miniopterus schreibersii in eastern Bosnia and Herzegovina for the first time, prompting the investigation to determine the causative agent. Bat carcasses were collected and subjected to pathological examination, after which the lung samples with notable histopathological changes, lung samples with no changes and guano were analyzed using metagenomic sequencing and RT-PCR. A partial Lloviu virus genome was sequenced from lung samples with histopathological changes and found to be closely related to Hungarian and Italian virus sequences. Further accumulation of mutations on the GP gene, coding the glycoprotein responsible for cell tropism and host preference, enhances the need for further characterization and monitoring of this virus to prevent spillover events and protect human health.