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Dr. Lipkin and the search for microbes in CFS/ME

Prof Ian Lipkin (New York, USA) was the special guest speaker and his talk was entitled “Small Game Hunting”. He said they were still able to use the earlier XMRV samples. He explained how one started with a hunt for “possible” microbes and then moved onto the “probable” when one could consider treatment options, followed by the “confirmed” when one looked at drugs and vaccines.

He told us how emerging diseases usually came from animal sources. He explained how micro-array techniques moved onto unbiased sequencing. There are 24 million peptide micro-arrays needed to investigate the vertebrate organism. He discussed as an example Kawasaki Disease, an autoimmune condition in children. Often diseases are due to an immunological response to an environmental trigger.

He then went on to discuss the human microbiome—abnormalities of which can create gastrointestinal symptoms, which in children are sometimes predictors for autism. He is interested in this relation to autism. There maybe reduced enzyme and transporter RNA. The organism suterella is increased in autism and there may be an antibiotic cause, and a lack of the gene affecting gastrointestinal metabolism.

He then talked about his involvement with the Chronic Fatigue Initiative, who are doing multiplex assays. He is working closely with Montoya looking at viruses. HHV-6 has been found in the plasma of 4 out of 6 cases. Looking for HHV-6 in PBMCs, 13% were positive in patients and 11% positive in controls. Annellovirus was found in 75% of the samples—this may not be useful, but negative findings are as important as positive.

Looking immunologically at CFS/ME, IL-17 was elevated in the first 3 years and then decreased. Lower levels were found in the CFS/ME patients’ cerebrospinal fluid. They are doing RNA sequencing looking at biomarkers in 100 cases compared to 100 controls. This equates to 117million reads divided into 3 “libraries”. But there is a need to control for library effects, as the “library” construction reflected the results—i.e., processing may be different.

They are also looking for chemicals produced by bacteria which may have systemic effects. He confirmed that there was zero evidence now for XMRV. Contamination is always a problem and contaminants must be eliminated prior to any analysis.

Eight professional workshops were then held throughout the first day. I attended the immunology workshop outlined below.