I don't know how common this phenomenon is but it is worth mentioning. A chronic Lyme patient was seen by another physician who changed the antibiotic regimen around.
He started him on Cipro. Some weeks later the patient developed severe lower abdominal pain, severe enough to send him to the emergency room. A workup including a CT of the abdomen and pelvis was negative. On questioning he denied urinary or bowel symptoms. He has had a recent colonoscopy which was negative. The exam showed marked tenderness of the suprapubic area (area over the bladder). A rectal exam revealed a tender prostate. Palpation of the prostate re-created his symptoms.
Many men suffer with chronic prostate symptoms. These include difficulty with urination, bladder- groin pain and even low grade fevers. These symptoms can be relapsing and remitting over a period of years and/or decades.(Symptoms related to benign enlargement of the prostate and prostate cancer typically do not have a pattern of spontaneous improvement and exacerbation). Urologists don't know what to do. It is the bane of their existence. Different terms have been used: non bacterial chronic prostatitis, prostatosis, prostadynia and others. An infectious cause is frequently suspected, but none can be found. Patients frequently get better with long term antibiotics and then relapse when the antibiotics are discontinued. Sometimes patients get worse with antibiotics.
Infections within the prostate are believed to be sequestered- hidden. There may be a prostate blood blood barrier. Bacteria may live in biofilm colonies. Bacteria may hide in deep parts of the tissue which have poor blood flow thus limiting access to the immune system cells. These infections seem to never go away. Although no microbe can be isolated by standard microbiology techniques, many believe that the condition is caused by persistent infection with cell wall deficient bacteria. These would include Chlamydia, Mycoplasma and Lyme species.
Antibiotics can cause a severe localized "Herx" as the bacteria are killed and the immune system reacts. This can go on almost indefinitely. The only way to stop it is to discontinue antibiotics; and then try later with lower doses. Drugs with less prostatic activity may need to be used.
The drugs which have perhaps the greatest effect in the prostate are the quinolones, like Cipro.
In this case the treatment was to stop the antibiotics and use anti-inflammatory medicines. Here is a case where I have found an herbal preparation to very beneficial. The herb Saw Palmetto can be very effective in relieving prostate inflammation.
Lyme has been implicated in other mysterious urinary syndromes including interstitial cystitis. I have seen this syndrome improve with Lyme therapy as well.