Agree with many of the previous posters...
....gut bacteria is always affected. I would add that often in my experience the insult to the digestive system is more the cause for fatigue than any residuals from the illness. If anything I think the effect of ATB is underestimated. One note, if you're trying to supplement with probiotics there are 5 main bacteria to include....most good yogurt has only 2 or 3. There are some good supplements out there which is key because you have to eat a TON of yogurt to make a dent.
.....fluoroquinolones have been thought to be linked tendon injury for 30 years. Achilles tendon is the main site -- 90-95% of the time with ruptures and tendinopathy. I've had client that it affected fascia in the back, biceps tendon...almost anywhere. I caution my athletes (because of the forces they put on their body compared to the general population) and anyone with diabetes or renal insufficiency to take it easy for 4 to 6 weeks after they finish their course. Overly cautious? Maybe but nothing slows you down quite as much as a tendinopathy (or worse).
Endurance Nerd