The doxycycline treatments discussed in the NEJM article address 2 
situations.

1. A recent tick bite. Recommended treatment, a single 200-mg dose of 
doxycycline
    IF the tick "can reliably be identifed" as a deer tick
    IF it was attached for at least 36 hours
    IF treatment can be started within 72 hours of tick removal
    IF you are in an area where at least 20 percent of the ticks are 
infected with the spirochete
    IF there are no contraindications to doxycycline for this patient
In a randomized trial, this treatment reduced the risk of symptoms 
(erythema migrans) from 3.2 to 0.4 percent.

2. Erythema migrans, the characteristic rash (and it is usually 
accompanied by assorted symptoms)
    A 10- to 14-day course of treatment with doxycycline (or one of the 
other antibiotics).
    NEJM:
    *About 15 percent of patients experience a reaction "characterized 
by an increase in systemic symptoms and in the size or intensity of the 
erythema of the skin lesion" within 24 hours of beginning treatment.
     *"The majority of patients with erythema migrans who are treated 
with an appropriate antibiotic regimen have an excellent outcome. 
Nevertheless, when evaluated 6 to 12 months after treatment, 
approximately 5 to 15 percent of patients report subjective symptoms 
such as fatigue or musculoskeletal pains."

Lydia Schindler
Darnestown