Molecular detection and phylogenetic characterization of pathogenic and endosymbiont microorganisms in Hyalomma ticks collected from livestock

Background: Hyalomma ticks serve as vectors for a range of pathogens and harbor endosymbiotic bacteria that influence tick biology and the dynamics of pathogen transmission. In the United Arab Emirates, Hyalomma dromedarii and H. anatolicum are prevalent on livestock; yet, limited data exist on their microbial communities. This study aimed to determine the prevalence and phylogenetic relationships of key bacterial endosymbionts and tick-borne pathogens in Hyalomma ticks collected from livestock across all seven Emirates. Methods: A total of 671 ticks (532 H. dromedarii and 139 H. anatolicum) were collected from camels, cattle, sheep, and goats between October 2022 and October 2023. DNA was extracted and screened using specific polymerase chain reaction (PCR) assays targeting Francisella-like endosymbionts, ‘Candidatus Midichloria mitochondrii,’ Anaplasmataceae (‘Candidatus Neoehrlichia sp.’, uncultured Ehrlichia sp.), Theileria/Babesia, and Trypanosoma brucei. Representative amplicons were sequenced and phylogenetically analyzed. Results: In H. anatolicum collected from cattle, the following microorganisms were detected: ‘Ca. M. mitochondrii’ (54.2%; 95% confidence interval [CI] 45.2–63.0), Francisella-like endosymbionts (1.7%; 95% CI 0.2–5.9), uncultured Ehrlichia sp. (6.7%; CI 3.0–12.8), and Theileria annulata (5.0%; CI 1.8–10.6). In contrast, H. dromedarii collected from camels harbored only ‘Ca. M. mitochondrii’ (0.6%; 95% CI 0.1–1.8), and Francisella-like endosymbionts (7.1%; 95% CI 5.1–9.7). ‘Candidatus Neoehrlichia sp.’ (9.1%; CI 0.3–41.3) was detected exclusively in H. anatolicum ticks collected from sheep. In addition, H. anatolicum ticks collected from goats were positive for endosymbionts, with a high prevalence of ‘Ca. M. mitochondrii’ and Francisella-like endosymbionts (50.0%; 95% CI 15.7–84.3). Trypanosoma brucei was not detected. Co-infections occurred in 2.1% of ticks, predominantly involving both endosymbionts. Phylogenetic analyses revealed host-specific clustering patterns, with camel-derived sequences forming distinct clades from the cattle/sheep/goat-derived isolates for most taxa. Conclusions: This study provides the first comprehensive molecular survey of Hyalomma-associated microorganisms in the UAE, revealing high endosymbiont prevalence and significant host specificity in microbial communities. The detection of T. annulata exclusively in ticks collected from cattle, along with the absence of T. brucei, provides important insights into regional surveillance and control strategies. These findings enhance our understanding of tick–microbe interactions in an arid environment and support targeted vector control approaches.