Micropathogen community identification in ticks (Acari: Ixodidae) using third-generation sequencing

Ticks are important vectors that facilitate the transmission of a broad range of micropathogens to vertebrates, including humans. Because of their role in disease transmission, it has become increasingly important to identify and characterize the micropathogen profiles of tick populations. The objective of the present study was to survey the micropathogens of ticks by third-generation metagenomic sequencing using the PacBio Sequel platform. Approximately 46.481 Gbp of raw micropathogen sequence data were obtained from samples from four different regions of Heilongjiang Province, China. The clean consensus sequences were compared with host sequences and filtered at 90% similarity. Most of the identified genomes represent previously unsequenced strains. The draft genomes contain an average of 397,746 proteins predicted to be associated with micropathogens, over 30% of which do not have an adequate match in public databases. In these data, Anaplasma phagocytophilum and Coxiella burnetii were detected in all samples, while Borrelia burgdorferi was detected only in Ixodes persulcatus ticks from G1 samples. Viruses are a key component of micropathogen populations. In the present study, Simian foamy virus, Pustyn virus and Crimean-Congo haemorrhagic fever orthonairovirus were detected in different samples, and more than 10–30% of the viral community in all samples comprised unknown viruses. Deep metagenomic shotgun sequencing has emerged as a powerful tool to investigate the composition and function of complex microbial communities. Thus, our dataset substantially improves the coverage of tick micropathogen genomes in public databases and represents a valuable resource for micropathogen discovery and for studies of tick-borne diseases.