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It should not be a problem. Infection is infection. Organisms are not selective for which they infect.
Bacteria gets a foothold in traumatic wounds and stressful conditions just like people.
Cipro is better then E-mycin because it has a broader spectrum of coverage.
You could also use Bactrim (would need ot treat in the nighttime cycle due ot light degradation)
In a perfect world, dripping vancomycin would be THE definitive drug of choice for any anemone/invert but its not available outside of the hospital and requires dripping and maintenance of peaks and troughs.
Cipro is really the easist to use.
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