Ms. Weintraub hit on an emerging theme that is actually part of the picture for all of microbiology - that scientist's know very little about which pathogens cause disease, not just mortality, and that new forces are being discovered all the time. It is unfortunate that these promising areas are often severely underfunded.

Questions of latency, reactivation, and new tests designed to ferret these culprits out and elicit evidence of the damage they wreak are all part of the picture.

As far as as 19th century bacteriologist Robert Koch's findings go, scientists are now finding that one pathogen may cause many different diseases OR many different pathogens may cause the same or overlapping diseases.
Read more about Koch here: http://ocp.hul.harvard.edu/contagion/koch.html

Also part of the picture is evidence that many microbes and toxins may actually be the sustaining forces of chronic disease as well as possible lifestyle factors.

Although he doesn't work specifically with Lyme Disease, readers may find Vincent Racaniello Ph.D., Professor of Microbiology at Columbia University Medical Center, blog of interest as he explores many different, but essentially relevant areas in virology. He also twitters and does podcasts.
http://www.virology.ws/