When should infected kidney stones be removed?

Infected kidney stones should be removed shortly after detection or diagnosis. The infected stones generally grow rapidly and serve as a nidus (or center) for further stone formation. This stone matrix is believed to protect the bacteria from antibiotics. In essence, antibiotics cannot clear the associated infection unless the stone material is completely removed.
Johns Hopkins Medicine
In many cases when a kidney stone is infected, the infection cannot be cleared from the stone despite proper antibiotic treatment. This typically causes recurring urinary tract infections. In such cases, the only way to eradicate the infection is to remove the stone completely

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