When Shell Rot Is More Than "Shell Rot": Understanding Fungal Dermatomycoses in Chelonians

Chelonians have survived for hundreds of millions of years, adapting to both terrestrial and aquatic ecosystems through remarkable evolutionary mechanisms such as their protective shell and prolonged lifespan. Yet today, more than 50% of the 360 recognized species are classified as vulnerable, endangered, or critically endangered^1,2. Alongside habitat loss, climate change, and illegal trade, infectious diseases, including fungal infections, are emerging as clinically significant threats¹. 

For practicing veterinarians, fungal dermatomycoses in turtles and tortoises are often underestimated or misdiagnosed as routine shell rot or secondary bacterial infections. However, these infections can progress aggressively, especially because reptiles lack substantial subcutaneous fat, allowing deeper invasion into muscles and bone¹. 

Clinical Presentation: Beyond Surface Lesions 

Dermatomycoses may involve: 

• Carapace and plastron  

• Keratinized scales  

• Soft tissues surrounding shell margins  

• Underlying bone in severe cases  

Typical lesions include inflammation, ulceration, necrosis, granuloma formation, shell pitting, softening of scutes, and erosive plaques. In tortoises, weakened lamellae and shell depressions may eventually lead to fractures¹. 

Trauma remains one of the most important initiating factors. Clinically, veterinarians should actively investigate: 

• Vehicle-related injuries  

• Predator attacks  

• Bite wounds from cage mates  

• Fishing net or fishing line injuries in aquatic turtles  

• Poor enclosure hygiene  

• Chronic moisture imbalance  

• Nutritional deficiencies  

• Overcrowding¹  

Many fungal infections begin as opportunistic colonization of damaged tissue. 

Which Fungi Are Commonly Involved? 

Chelonian shell lesions can harbor a surprisingly broad fungal spectrum. Reported organisms include yeasts such as Candida spp., Cryptococcus spp., Geotrichum candidum, and Rhodotorula spp., along with molds including Aspergillus, Fusarium, Cladosporium, Alternaria, Mucor, Penicillium, and Absidia¹. 

One extensive French study investigating shell lesions in Testudo spp. demonstrated fungal hyphae in 73% of specimens and cultured 34 fungal genera. Dematiaceous fungi dominated the isolates, particularly Alternaria, Cladosporium, and Aureobasidium¹. 

Among clinically important pathogens, Fusarium species deserve special attention. Fusarium semitectum was associated with necrotizing scute disease in Gopherus berlandieri and shell mycosis outbreaks in Testudo hermanni populations. Interestingly, the organism was cultured directly from the soil, and affected tortoises improved only after both antifungal treatment and environmental relocation¹. 

This highlights a practical clinical message: treating the patient without correcting the habitat often results in recurrence. 

Emerging Diagnostic Challenges 

Modern molecular diagnostics have significantly changed the understanding of chelonian mycoses. What was previously classified simply as Fusarium solani is now recognized as part of the Fusarium solani species complex (FSSC), comprising more than 60 phylogenetic species^1,3. 

In sea turtles, isolates have included: 

• Fusarium falciforme  

• Fusarium keratoplasticum  

• Haplotypes 9, 12, and 27^1,4 

Interestingly, some Fusarium haplotypes were isolated even from clinically healthy turtles, suggesting environmental colonization may precede disease development¹. 

Melanin-pigmented fungi causing phaeohyphomycosis are also increasingly recognized. Exophiala oligosperma was identified in a Geochelone gigantea case involving deep bone infection¹. 

Practical Veterinary Approach¹ 

For clinicians managing suspected fungal shell disease: 

Consider fungal culture and cytology when: 

• Lesions fail empirical antibacterial therapy  

• Necrosis progresses despite wound care  

• Shell softening becomes multifocal  

• Pigmented lesions or granulomas appear  

• Environmental contamination is suspected  

Management should include: 

• Aggressive environmental correction  

• Humidity and temperature optimization  

• Debridement of necrotic scutes  

• Targeted antifungal therapy where feasible  

• Isolation of affected animals in group settings  

Veterinarians working with rehabilitation centers should also recognize that water quality and substrate contamination may act as persistent reservoirs. 

The Bigger Conservation Picture 

Fungal shell disease is no longer just an individual animal problem. Increasing evidence suggests that environmental fungi are becoming important drivers of morbidity in wild and captive chelonian populations. For endangered species already stressed by habitat destruction and climate change, even opportunistic fungal pathogens may become population-level threats. 

Early recognition, environmental management, and targeted diagnostics are therefore becoming essential tools not only in reptile medicine but also in wildlife conservation practice. 

References 

1. Nardoni S, Mancianti F. Mycotic diseases in chelonians. Journal of Fungi. 2023 Apr 27;9(5):518. https://www.mdpi.com/2309-608X/9/5/518 

2. Stanford CB, Iverson JB, Rhodin AG, van Dijk PP, Mittermeier RA, Kuchling G, Berry KH, Bertolero A, Bjorndal KA, Blanck TE, Buhlmann KA. Turtles and tortoises are in trouble. Current biology. 2020 Jun 22;30(12):R721-35. https://www.cell.com/current-biology/pdf/S0960-9822(20)30636-9.pdf 

3. Sarmiento-Ramirez JM, Abella-Perez E, Phillott AD, Sim J, Van West P, Martín MP, Marco A, Dieguez-Uribeondo J. Global distribution of two fungal pathogens threatening endangered sea turtles. PloS one. 2014 Jan 21;9(1):e85853. https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0085853&type=printable 

4. O'Donnell K, Sutton DA, Wiederhold N, Robert VA, Crous PW, Geiser DM. Veterinary fusarioses within the United States. Journal of Clinical Microbiology. 2016 Nov;54(11):2813-9. https://journals.asm.org/doi/pdf/10.1128/jcm.01607-16