I copied this from the tortoise trust website. It says everything you need to know about the desease. I would recommend a trip to the vet if you've never delt with tghis before. Also, a review of your husbandry procedures might be in order to prevent a recurrence of the desese once you get things under control. You don't mention what kind of filtration you have on your tank and how often you do water changes. That might be something to look at in the future.
"Shell-rot is a generic term which describes the visible effects of bacterial, fungal or even algal (in aquatic species) diseases of a tortoise's or turtle's shell. These diseases often follow damage or abrasions, even those that are seemingly minor in extent. In actuality, any penetrative damage to the shell may result in unwelcome bacteria, or other pathogens gaining access to the blood-rich living tissue present just below the outer, hard, layer of keratin.
Another common term heard in connection with shell-rot is SCUD; "Septicaemic Cutaneous Ulcerative Disease" a very serious condition involving septicaemia - or growth of bacteria in the blood stream. This condition can prove rapidly fatal as the pathogens begin to attack vital internal organs as they are distributed via the blood supply. Urgent systemic (injected) antibiotics are required in such cases if the tortoise or turtle is to be saved. The long-term prognosis is guarded.
Most cases of simple "shell-rot", however, respond well to debridement of loose or soft (affected) tissue and thorough cleansing, at least twice daily, with a povidone-iodine or chlorhexidine solution. This should be fairly vigorously applied using an old toothbrush or nail brush. Rinse off after each application. It is important that the affected area is kept dry and air is allowed to circulate freely - many of the organisms typically responsible for this condition are anaerobic, or do best when actually deprived of oxygen. If it should become necessary to cover the affected area (to prevent fly-strike, for example) then do so with a fine gauze which does not "seal" the area. All such cases require very careful follow-up and long term monitoring. The longer an infection of this type persists untreated, the greater the danger of it turning into a much more serious systemic infection or ulcerating abscess, deep in the bony tissue. Veterinary attention should be sought in all cases. Common symptoms may include:-
Unpleasant discharge or smell from the affected area;
Fluid, often reddish, visible under the plates of the shell;
Softening or lifting of the shell plates;
Soft areas or pitting appearing in or just under the surface of the shell;
Shell plates falling off, leaving live or necrotic bony tissue exposed.
Some common causes of shell-rot include:
Aggression by other tortoises: Some males are especially aggressive and will repeatedly "beat up" other males or females. At the typical main impact site, just above the tail, instances of shell rot are especially common. Mixing incompatible species is one sure way to initiate the problem - keeping aggressive T. ibera and T. marginata with T. hermanni, or North African T. graeca, for example.
Poor pen or vivarium hygiene: Dirty substrates will harbour innumerable pathogens. One small injury and serious consequences may well follow.
Incorrect substrate humidity: If turtles from humid environments are allowed to over-dry, shell and skin condition will rapidly deteriorate. If animals from arid environments are kept on damp substrates, the outer keratin may become soft and distorted and may permit pathogens to gain access. We have seen many cases of shell-rot in T. horsfieldii and Chersina angulata (South African Angulate tortoise) from precisely this cause. Keep all tortoises on an appropriate substrate - and keep it clean.
Ticks: Ticks can attach themselves to tortoises very easily, and will provide that essential penetrative injury shell-rot pathogens need to establish themselves..
In aquatic species, water hygiene: Good filtration is essential. If a turtle injures its shell in filthy water, shell disease often follows. Use of a UV-C steriliser in the filtration circuit can substantially reduce the danger of shell and skin infections. Soft-shell turtles are especially susceptible to problems of this nature.
Deep-seated shell abscesses are particularly serious. These invariably require surgical draining and removal, followed by selective treatment with systemic anti-microbials, based upon laboratory culture of the causal organisms. Shell abscesses can persist for many years if untreated, gradually becoming worse and worse, before finally turning into a generalised septicaemia. Substantial tissue damage can also result. X-rays and surgical investigation can help to establish the extent of such damage.
Shell rot can be highly contagious, and one infected animal can spread it rapidly to all others it comes into contact with. It is not a condition that should be ignored or underestimated. Seek professional advice at an early stage if you believe you have an affected tortoise or turtle. In the long term, untreated diseases of this nature are killers - but given appropriate treatment at an early stage, a complete recovery is usually assured."
