I came across this study of the genome of Borrelia burgdorferi and Treponema pallidum
https://www.ncbi.nlm.nih.gov/pmc/articles/pmc97324/Subramanian et al said...
...the proofreading 3′-5′ exonuclease—the ɛ subunit of DNA polymerase III (e.g., the E. coli DnaQ protein)—whose role in DNA replication seems to be conserved in all other bacteria, is missing in B. burgdorferi.
This would seem to explain why b. burgdorferi is unusually vulnerable to nucleotide analogues.
This paper also notes that b. burgdorferi produces proteins similar to von Willebrand factor, which may help to explain how it triggers autoimmune disorders.