Fast and efficient Borrelia chromosome recovery from tick samples using whole-genome amplification

Genomic studies of Borrelia are essential for understanding Lyme borreliosis epidemiology and biology but are limited by slow, labor-intensive culture methods. Here, we introduce an approach that overcomes the need for extended culture by combining a short-term culture step with whole-genome amplification (WGA) of samples derived from field-collected ticks, which can be performed in parallel with classical culturing. The protocol is paired with a tailored bioinformatic pipeline to ensure accurate assembly and robust downstream analyses. Benchmarking on multiple control isolates shows that the method produces high-quality chromosomal assemblies. We further demonstrate applicability by generating five high-quality Borrelia chromosomes from freshly collected ticks (two B. lusitaniae, two B. afzelii, and one B. garinii). By producing sequencing-ready DNA in 5 days rather than months, this workflow streamlines genome generation and reduces reliance on culture-based isolation, facilitating broader genomic representation of understudied Borrelia species and enabling future epidemiological, ecological, and evolutionary studies.