I have seen very few fungal infections in my aviary, but have included the information here so that you
have an understanding of them and what the signs may be of infection.
ASPERGILLIOSIS

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Fungal Infections
CANDIDA (Yeast or Thrush)
RINGWORM
This is a mold commonly seen on decaying food like bread or cheese and is caused by the
fungus aflatoxin.  In the aviary, it may be found in seed that has been in an unsealed
container that has absorbed moisture, on soft or wet foods that have sat too long, or in
bedding used in cage trays or aviary floors.  It is spread through spores and infects the bird
when inhaled or ingested causing pneumonia-like symptoms.  This fungus can produce
poisonous toxins that can damage internal organs, much the way some of the bacterial
infections do.  Seed that has gotten wet and has become moldy, warm, humid conditions,
and poor hygiene can all contribute to this establishment of this disease.

Once the fungus takes hold, it multiplies by branching out and creating "mats" in the airways
including the nostrils, sinuses, eyes, and other cavities of the head, as well as the lungs.  
Symptoms include respiratory distress with the bird wheezing and gasping - generally,
"labored" breathing and tail bobbing, but may also include neurological symptoms such as
twirling and stargazing.  Clicking sounds may be heard.  In severe infections, the eyelids
may become filled with cheesy, yellow masses - as they are so close to the sinus cavities.

This disease is virtually impossible to diagnose while the bird is alive, and is only determined
upon necropsy of the infected bird.
However, you can test seed for aflatoxin by shining a
black light on it. If the fungus is present, the seed will fluoresce green.

The only known medication to have any effect is Amphotericin, however, it does not always
work and may not work at all - it is also very expensive.  Therefore, prevention is the best
course of action.  Keeping aviaries dry, clean, and free from dust and mold is the only way
to prevent this problem.  If this fungus does become a problem, the entire aviary must be
thoroughly cleaned with a bleach or Virkon S solution to kill the mold spores.  

Items with the potential for growing the mold must be disposed of.
BEAK, SCALE & OTHER FUNGUS
"Candida are colonies of single, oval cells which bud and in some circumstances develop into chains or hyphae.
 They most frequently attack the epithelium of the crop.  The infection can be induced by prolonged use of
antibiotics, such as the tetracyclines, in the drinking water.."  
Arnall and Keymer 1975
Candida, otherwise known as a yeast infection or thrush, is usually caused by
prolonged use of antibiotics, but may also be caused by poor hygiene,
overcrowding and poor animal husbandry management. Antibiotics kill good and
bad bacteria, and leave the immune system weak and unable to fend off other
problems - in this case, Candida.  In my aviary, I often give the birds Probiotics
after treating with antibiotics to help them regain a normal gut flora and rebuild
the "good bacteria" in their systems.

Signs of Candida may include regurgitation of food, loose dark green and tacky
droppings, a fluffy and messy look to the bird, and a "sleepy" look in the eyes.  
The bird may have patches of white, raised dead epithelial material in the mouth
and crop.  This will look "cheesy" and is easily scraped off.  On occasion, these
"lesions" may hinder breathing, causing the "tail bob" we commonly see with
respiratory distress.

Preventing Candida is easily achieved with proper hygiene, nutrition and the
use of Probiotics after prolonged antibiotic use.  It is thought that a vitamin B
complex (specifically - formic acid) deficiency may open up the bird to the
disease.

Most times, Nystatin (Medistatin for birds) is the medication of choice when the
infection cannot be controlled with probiotics.  Copper Sulfate is sometimes
given in the water.  Dimetridazole or Ronidazole have sometimes been effective
because it prevents a common secondary infection caused by Trichomonas
(most common protozoa in aviary birds).
While the name "ringworm" implies that this infection is a parasite, it is actually a fungal infection of the skin.  It is only included here for
reference as the probability of it entering your aviary is highly unlikely.

The ringworm fungus causes lesions that appear scaly and dusty, not unlike scaly face/leg mites.  It primarily affects the skin of the head, but
may affect any thin-skinned area on the bird.  It spreads slowly from bird to bird and can usually be stopped in it's tracks without spreading if
diagnosed early.

Treatment may be in the form of antifungal creams.  After diagnosing this issue, your Veterinarian may prescribe Griseofulvin, which is used
for all types of dermatomycosis (fungal infection of the skin).  If the infection has spread to other birds and cannot be controlled, your
Veterinarian may recommend euthanasia.
On rare occasion, we may find we have a bird with a beak or leg scale fungus.  This can only be diagnosed through scrapings, then viewed
under the microscope at high magnification.  These fungal infections are not unlike those found in humans affecting the finger and toenails, or
with athletes foot.  Well established fungal infections are difficult to eradicate, but with an over the counter fungal cream (Terbinafine
Hydrochloride, Butenafine Hydrochloride or Clotrimazole), can usually be controlled and eventually cured.

It is important to be consistent in the application of any cream or salve you use. It should never be applied directly to feathers, and should not
get in the nares (nostrils), or in the birds mouth.

Your Veterinarian may give you a prescription fungal medication that may be more effective than an over the counter type.
AVIAN GASTRIC YEAST (AGY)
Also known as Megabacteria, AGY is difficult to cure and the only medication known to be remotely effective - Amphotericin B - is very
expensive.  It is NOT highly contagious as long as the overall health of the flock is good, though it is advisable to add an acid based water
cleanser like Citric Acid to the water (1/4 tsp to 1 litre of water) for the rest of the flock.

It is easily diagnosable through fecal smears and viewing under the microscope.  Even at 100x, this mostly rod-shaped bacteria is easily
spotted and looks like fine hairs.

Word of caution - if you use diatomaceous earth (d-earth) on your birds food or in the cage/nest boxes, be sure to check several fecal
smears before panicking.  D-earth contains small particles in many shapes and forms.  It is not digested and absorbed, so it is passed in the
droppings whole.  Many of the shapes d-earth contains look very much like AGY, coccidia, worm eggs, etc.  Be sure to view all foods and
supplements under the microscope so you have an idea of what you are looking at before you panic!

Symptoms of AGY include vomiting, going light, general weakness and depression, failure to thrive, fluffing, increased appetite with no weight  
gain, trembling, hunched over, and/or metabolic disturbances.  In very ill birds, neurological problems or those affecting the central nervous
system like twirling and star gazing may be present.  Hens may go egg bound or become paralyzed after laying their eggs.
Avian Gastric Yeast - Megabacteria 400x
Avian Gastric Yeast - Megabacteria 400x + 5x zoom
Aspergillus from stock photo - Electron Microscope
Aspergillus from Gouldian Finch Necropsy - 800x magnification
Under Electron Microscope
800x magnification from Gouldian
Finch necropsy.
Foot fungus in Gouldian
Foot fungus in Gouldian
A client from Brazil sent these photos of her Gouldian
finch giving credence to the need for dry perches. Due to
a foot fungus caused by consistently high heat and
humidity situations, this bird lost several of it's toes, but
once the fungus was treated and eradicated, he went on
to live a healthy and fruitful life.   
***Photos courtesy E. Patton, Brazil
***Photo from
http://www.iclickfun.com/microcosmos-discovering-the-world-through-
microscopic-images-from-20-x-to-over-22-million-x-magnifications/