Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
Several hotspots of elevated LD risk have emerged across Canada as I. scapularis expands its range. Focusing on a hotspot in southeastern Ontario, we used high-throughput sequencing on whole ticks and dissected salivary glands and midguts. Compared to whole ticks, analysis of salivary glands and midguts revealed greater β-diversity among microbiomes that are less dominated by Rickettsia endosymbiont bacteria and enriched for pathogenic bacteria including a Bbsl- associated Borrelia, Borrelia miyamotoi, and Anaplasma phagocytophilum. We also find evidence of co-infection of I. scapularis in this region by multiple microbes. Overall, our study highlights the challenges and opportunities associated with the surveillance of the microbiome of I. scapularis for pathogen detection using metabarcoding and metatranscriptome approaches.