Tick-Borne Pathogen Surveillance at the Human-Livestock Interface in Benue State: A Metagenomics Approach

Tick-borne pathogens represent an undercharacterised zoonotic disease risk in sub-Saharan Africa, and unbiased metagenomic sequencing offers a discovery-oriented approach to pathogen surveillance that transcends traditional single-pathogen diagnostic limitations. This doctoral study conducted metagenomic surveillance of tick-borne pathogens in ticks collected from livestock and humans in Benue State, North Central Nigeria. A total of 840 ticks representing seven Ixodid species were collected from cattle, goats, sheep, and human skin attachments across 12 communities over 18 months. Ticks were pooled by species, host, and site and subjected to total DNA extraction. Metagenomic library preparation and next-generation sequencing were performed on the Illumina NovaSeq platform. Bioinformatic analysis used a validated pathogen-discovery pipeline including Kraken2, MetaPhlAn3, and de novo assembly. Known and novel Theileria, Babesia, Rickettsia, Anaplasma, and Borrelia sequences were detected. Three novel Theileria-like genotypes with no reference genome match were assembled. Rickettsia africae and R. conorii were confirmed in 14.3 percent of Amblyomma variegatum pools. Anaplasma marginale and A. phagocytophilum were detected in human-attached tick pools from two communities. The study provides the first metagenomic tick-borne pathogen atlas for Benue State and establishes a surveillance baseline for emerging tick-borne diseases at the human-livestock interface. Keywords: tick-borne pathogens, metagenomics, Ixodid ticks, surveillance, Benue State.