Morgellons short history
A biologist named Mary Leitao in 2001 began trying to find treatment for her two year old son Drew who was experiencing symptoms similar to a disease named Morgellons discussed in medical literature in the 1600s. Drew's skin was forming lesions and he would complain of being in pain. When Mary would rub cream to help with the lesions, something fiber-like would come out of the wounds. After going from doctor to doctor and not recieving any answers, Mary decided to create the Morgellons Research Foundation (MRF) to help figure out what was happening to her son. Soon after, thousands of Americans began contacting her explaining that they also had similar symptoms. In 2006 the Oklahoma State Neuroscientist Randy Wymore stumbled upon the MRF and contacted Leitao for samples of the fibers, which his request was granted. He examined the fibers, but he could not identify what the fibers were made out of so he asked for help from the Tulsa Police Department's forensics which they compared the fibers to over 800 different types of fibers and again could not identify it. They then used gas chromatography and compared the fibers to over 90,000 different organic compounds, and again no matches. The reason why they could not identify what these fibers were may be because these fibers from Morgellons patients may be a newly discovered fiber. 
The MRF closed down in 2012 and Leitao directed people to the Oklahoma State University for further information on Morgellons.
|Morgellon Lesions early in infection|
Symptoms of Morgellons: (From Oklahoma State University) Spontanteously Erupting Skin lesions
Sensation of crawling, biting on and under the skin
Appearance of blue, black or red fibers and granules beneath and/or extruding from the skin
Short-term memory loss
Obsessive-Compulsive disordersImpaired thought processing (brain fog)
Feeling of isolation
CDC study of Morgellons 2006 - 2008
A study done by the CDC  indicated that the skin lesions were most consistent with arthropod bites or chronic excoriations. 68% of patients had lesions on their back which would be harder to reach areas for patients. The test included surveys, clinical evaluations, and geospatial analyses and analyzed materials from patients skin.The tests used in this study do not detect all antigens in patients and there can also be false negatives in the tests which made the CDC researchers doubt that they could figure out what Morgellons is. There were major limitations to the study as well especially since they only studied patients who recently developed Morgellons (<3 months) and some antigens require a longer duration of time in order to be spotted on the tests they used.
Interestingly, the study found Staphylococcus aureus (cause of skin infections) and Streptococcus bacteria strains (pyogenes and sp.) among some patients which some strains among Streptococcus are known to cause necrotizing fasciitis. This condition is what we would wrongly refer to as flesh eating bacterias. They do not eat flesh, they rather infect areas near the skin and release toxins that damage soft tissue, muscles and fat. Other bacterias and multiple bacteria infections are also known to cause necrotizing fasciitis. The CDC released their study in 2012 and stated that they were unable to conclude whether this unexplained dermopathy represents a new condition, or a wider recognition of an existing condition such as delusional infestation
Possible causes of Morgellons:
Genetically Modified Organisms: Agrobacterium
Vitaly Citovsky, Professor of Biochemistry and Cell Biology at Stone Brook University in New York found that all the Morgellons patients he tested were positive for Agrobacterium. He also tested people who did not have Morgellons disease and they all tested negative. Agrobacterium is a bacteria created by H. J. Conn which is used in Genetically Modified Organisms to transfer DNA through Horizontal Gene Transfer from one species to another allowing for the transfer of bacteria DNA or animal DNA to be put inside plant DNA. Although biotech giants like Monsanto claims this newly created bacteria is harmless and only works in their GMO's, the Proceedings of the National Academy of Sciences  reported that agrobacterium is active in human cells and it keeps transforming human DNA. Another study confirmed this and further explained that Agrobacterium affects all life from fungi to human cells and interferes with "cell-cell surface receptor arrays, cellular motors, nuclear import, chromatin targeting, targeted proteolysis, DNA repair, and plant immunity" 
Dr. Omar Amin believes that Morgellons is caused by toxins that the body cannot remove such as Mercury. If necrotizing fasciitis bacterias work by producing toxins that destroys skin, muscles, and fats, toxins from other sources can also cause something similar. His treatment is based on removing toxins from the body which he claims 100% of his patients see remission of Morgellons. In his belief, the reason why researchers find Fungus on the lesions of Morgellons patients is not because Fungus causes Morgellons, but rather Fungus is drawn to the lesions and feeds on toxins like Mercury. Although it is possible that patients have necrotizing fasciitis by unknown antigens, detoxing toxins from patients may strengthen the immune system of the host which allows the hosts immune system to kill their active infection that is causing their symptoms.  
New Spirochete similar to Syphilis or Lyme
Ginger Savely a Nurse Practitioner that treats Lyme patients has been testing Morgellons patients for Lyme disease. 90% of patients test positive. She believes that either there may be a co-infection of Lyme disease we have not discovered yet, or whatever causes Morgellons is something that we all are exposed to, but it only develops in people with weakened immune systems like those who have Lyme disease. 
Bovine Digital Dermatitis (BDD)
Veterinary microbiologist Marianne J. Middelveen and Raphael Stricker, MD published a study linking Morgellons with bovine digital dermatitis which is a disease in cows that causes lameness, decreased milk production, weight loss, and skin lesions with unusual fibers coming out of the lesions. Their study found keratin from Morgellons fibers which proves that the fibers had to be developed from a living organism and are not synthetic.   BDD may be caused by spirochetes similar to Syphilis and Lyme.
New York Entomological Association researchers found collembolan which is a microscopic critter in 18 of the 20 patients they tested. 
Since the fibers from the lesions are made from keratin, Morgellons has been proven to be a real disease. William Harvey, MD, MS, MPH stated that 90% of Morgellons patients get 90% better when they stay on antibiotics for about 8 months which suggests that Morgellons patients may see results by being treated with antibiotics.  Morgellons patients can try contacting ILADS and find a Lyme Literate Medical Doctor to see if they will treat Morgellons like they would treat Lyme disease patients. Patients should also find a doctor experienced in detoxing which would help treat the symptoms of toxins as long as Morgellons works the same way as necrotizing fasciitis.