Nanopore Sequencing Enables Broad Detection and Surveillance of Tick-Borne Pathogens in Ixodes scapularis

Surveillance of tick-borne diseases in the United States largely relies on PCR-based detectionof predefined targets, limiting the ability to identify emerging pathogens or characterize tick-associated microbiomes. The blacklegged tick (Ixodes scapularis), the primary vector ofseveral medically important pathogens including Borrelia burgdorferi, Babesia microti, andAnaplasma phagocytophilum, is of particular relevance in the eastern United States. Toaddress limitations of conventional testing, we developed an Oxford Nanopore Technologies(ONT) metagenomic sequencing workflow incorporating adaptive sampling for real-time, field-deployable detection. We sequenced genomic DNA from I. scapularis ticks provided by theConnecticut Agricultural Experiment Station Tick Testing Laboratory (CAES-TTL) andperformed taxonomic classification using Kraken2, enabling simultaneous detection ofbacterial, protozoal, and viral taxa.