Ciprofloxacin and tendon damage

Even if your doctor switches you to a diferent antibiotic it won't do any good, most if not all antibiotics cause tendon/ligaments damage.
If I were you I will wait until I am done with the antibiotics to introduce any physical activity.

You need to talk to your doctor about this drug and your barefoot running There are risks here. Call your doctor tomorrow and ask him about these warnings by the FDA

There have been a number of regulatory actions taken as a result of such adverse reactions, which included published warnings,[44][45]additional warnings and safety information added to the package inserts[46] together with the issuance of "Dear Doctor Letters"[47] concerning the recent addition of Black Box Warnings. In 2004, the U.S. FDA requested new warning labels to be added to all of the fluoroquinolones, including ciprofloxacin, regarding peripheral neuropathy (irreversible nerve damage), tendon damage, heart problems (prolonged QT Interval / torsades de pointes), pseudomembranous colitis, rhabdomyolysis(muscle breakdown), Stevens–Johnson syndrome, as well as concurrent usage of NSAIDs contributing to the severity of these reactions.[citation needed]
Subsequent to this, on 25 June 2007, the U.S. FDA required manufacturers to add an additional warning to the package inserts that stated "Other serious and sometimes fatal events, some due to hypersensitivity, and some due to uncertain etiology, have been reported in patients receiving therapy with quinolones, including ciprofloxacin."[48] It was not until 2008, (four years later) that the label revisions for ciprofloxacin included any warnings concerning heart problems (prolonged QT interval / torsade de pointes). Warnings concerning rhabdomyolysis and Stevens–Johnson syndrome were still absent from the package inserts as of September 2009.
The serious adverse effects that may occur as a result of ciprofloxacin therapy include irreversible peripheral neuropathy,[49][50] spontaneous tendon rupture andtendonitis,[51][52][53][54] acute liver failure or serious liver injury (hepatitis),[55][56] QTc prolongation/torsades de pointes,[20] toxic epidermal necrolysis(TEN),[57][58][58] and Stevens–Johnson syndrome, severe central nervous system disorders (CNS)[25] and Clostridium difficile associated disease (CDAD:pseudomembranous colitis),[59][60] as well as photosensitivity/phototoxicity reactions.

FWIW, I was on antibiotics a few weeks ago (cold turned into a bacterial infection). The Dr was going to put me on some antibiotic until I mentioned that I was going to be in a 10K and he switched me to Cefdinir, citing that the other antibiotic could lead to "tendon rupture" (ye gods).

wow. all those side effects and people don't even think twice about taking "drugs".