A new study of Rhesus Monkeys clearly shows that Borrelia burgdorferi persists following long term antibiotic treatment. There are three reasons this study stands out:

• Macaques were used, not mice. It's more expensize and kinda sad, but it's a better animal host.
• Treatment was longterm and multiple antibiotics were used, ceftriaxone (4 weeks) and doxycycline (8 weeks)
• Persistence was detected using xenodiagnosis using nimphal ticks and PCR/Fluorescence

This type of study is exactly the kind of research that needs to be done to bring more attention to the persistant nature of Borrelia burgdorferi. Followup research will need to show that the Bb is pathogenic. Signs of heart inflammation were found during the autopsies. 

The paper was published on PLoS One so it can be accessed by everyone at: Link to Paper