Dr Markov CBIS Theory of ME/CFS - General Discussion

Cipher

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for example live blood taken from a vein is simply re-injected under the skin in sheep autovaccination and was proven effective in the studies discussed earlier in this thread. That would also have had v low counts of bacteria in it - or the animal would have been dead already from acute bacteraemia.
I don't remember seeing that study, could you link it? Autovaccines used in veterinary medicine are normally produced in a lab in a similar fashion to human autovaccines.

also, since the patients with CFS/ME are already exposed to antigens at some level from the biofilm colonies inside them ( if Markov is correct ) - adding more antigens - no matter if its a small amount more - is unlikely to cause immunotolerance as it will be moving in the other direction.
The bacteria may not even exist at the oral tolerance induction sites in the GI-tract (e.g. Peyer's patches), so I still think that ingesting antigens in small amounts that aren't immunostimulatory seems risky in theory. I can't see how it could be effective anyway.

Re oral tolerance:
Oral tolerance is described as a physiological phenomenon that contributes to prevent pathological conditions to food protein and commensal microbiota, inhibiting responses that could cause damage such as hypersensitivity reactions, lymphocyte proliferation, and antibody formation [1]. Most of all, tolerance induced to these natural antigens that reach the intestinal lumen seems to be an analog of tolerance to self-components. Since microbiota and dietary antigens are part of our physiological interface with the external environment, tolerogenic mechanisms in the mucosal surfaces must have evolved to treat these antigens as complementary or quasi-self.
 

Garz

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OK Good!

The bacteria may not even exist at the oral tolerance induction sites in the GI-tract (e.g. Peyer's patches), so I still think that ingesting antigens in small amounts that aren't immunostimulatory seems risky in theory. I can't see how it could be effective anyway.
so - if i am understanding your reasoning correctly - you are considering the body to be virgin to antigens of the offending organisms - and so by adding a small amount of antigens of them - you concern is that this small level of antigens might promote immune tolerance to the very bacteria we are hoping to treat. NOT GOOD!

i am not sure if immunotolerance is based only on levels of antigens - i suspect the immune system has other criteria by which it senses foes vs friends - but lets assume it is quantity-dependent for the purposes of this discussion

Then, if Markov is correct and bacterial biofilm colonies are located inside the kidney and making people ill (or there are biofilm infections located anywhere inside the body for that matter) - then the immune system is already exposed to these antigens at some level.
The level cannot be zero as white blood cells or their equivalents go everywhere in the body to some extent - including the kidney.
indeed the theory is that it is these very chemicals that are circuiting in the blood stream and causing illness symptoms.

as such it wouldn't actually matter if the start point was below the threshold of immune activation or above it - more antigen exposure is always moving the host away from immune tolerance and towards more activation



also - if what you are proposing were a real issue - wouldn't people be becoming immunotolerant to the low levels of pathogens all around us - in the air we breath, the food we eat, the water we drink, the surfaces we touch and then touch our eyes, nose mouth etc

I think it much more likely that biofilm colonies - if present - are not sealed in some kind of 100% impervious barrier inside the body making them invisible to the immune system - but instead exist in a state exposed to the immune system - but in a kind of stalemate with the it.

we know the biofilm colony has lots of tools to wage the war against the host defences,
as described in the paper you posted above :
-redundancy of adhesins and structural elements - so even if the immune system makes antibodies to some, it always has others
-ability to kill macrophages with pore forming toxins - preventing them from chewing it up
-ability to disrupt host immune signalling pathways - dysregulating them
-etc

this is exactly what happens in other well studied biofilm infections - like diabetic wound infections, surgical implant infections etc.

I think this is the sheep auto-inoculation paper -
https://vetjournal.it/images/archive/pdf_riviste/4672.pdf
 

Hip

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I think it much more likely that biofilm colonies - if present - are not sealed in some kind of 100% impervious barrier inside the body making them invisible to the immune system - but instead exist in a state exposed to the immune system - but in a kind of stalemate with the it.
That stalemate situation could be the case.

Though Dr Markov believes there may be some dysfunction in mucosal immunity in ME/CFS patients, which makes it hard for them to clear a mucosal dysbiosis.

In fact, when I was Googling for things that might improve mucosal immunity, I discovered that progesterone boosts mucosal immunity. That's interesting, because during pregnancy, progesterone levels increase 4 to 10-fold, and it's often been noted that ME/CFS patients substantially improve during pregnancy.

What the mucosal dysfunction Dr Markov refers to might be is difficult to guess though.


Prof Michael Maes published a paper exploring whether endotoxin tolerance might be the cause of ME/CFS. Endotoxin tolerance is where the body's inflammatory immune response to LPS becomes diminished with repeated exposure to LPS.

The paper says:
Endotoxin tolerance which involves profound systemic immune and metabolic downregulation, with the latter phenomenon involving sequential shifts in energy production via glycolysis and oxidation of fatty acids, following prolonged TLR upregulation in macrophages and monocytes
The paper then goes on to describe the complex way in which endotoxin tolerance induces a down-regulation of energy production.

So maybe the mucosal immunity dysfunction Dr Markov talks about might involve endotoxin tolerance, which then down-regulates the powder of the immune response.



With vaccines, from what I have read, the risk of creating immune tolerance is a possibility in inactivated vaccines which require an adjuvant.

Live vaccines do not need an adjuvant, as the live infection itself is sufficient for stimulating the immune system. But vaccination with dead inactivated pathogens may not on its own stimulate a strong immune response, so immune stimulation from an adjuvant is required to get the vaccine to work. If however you administer dead pathogens without any adjuvant, that can be a recipe for immune tolerance.

With autovaccines, which use inactivated bacteria, adjuvants are not added, as the bacteria themselves contain factors which stimulate the immune response, so are their own adjuvants. Whether there might be some circumstances (eg low levels of inactivated bacteria) in which inactivated bacterial vaccines lead to immune tolerance, I don't know.
 
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Cipher

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as such it wouldn't actually matter if the start point was below the threshold of immune activation or above it - more antigen exposure is always moving the host away from immune tolerance and towards more activation
I think it much more likely that biofilm colonies - if present - are not sealed in some kind of 100% impervious barrier inside the body making them invisible to the immune system - but instead exist in a state exposed to the immune system - but in a kind of stalemate with the it.
The immune system isn't fully acting as one entity, it's compartmentalized & decentralized. My point was that in theory, if the oral tolerance inductions sites in the GI-tract gets exposed to low levels of antigens which they locally aren't being exposed to regularly, they might start to sway the rest of the immune system to be more tolerant against those antigens. That's perhaps not true in practice, but it's something to consider.

so - if i am understanding your reasoning correctly - you are considering the body to be virgin to antigens of the offending organisms - and so by adding a small amount of antigens of them - you concern is that this small level of antigens might promote immune tolerance to the very bacteria we are hoping to treat. NOT GOOD!
Just to clarify, I meant that the oral tolerance induction sites might be virgin to the antigens, not the immune system as a whole.
 
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I found a fascinating article which describes some of the ways biofilms can skew the immune system. I've only skimmed it but found some highlights:

Biofilms evade the immune response by various mechanisms including (i) acting as physical barriers, helping bacteria to avoid detection and phagocytosis (ii) genetically by activating response regulators, genetic switches or suppressors that affect immune cell activity (Leid 2009). One of the key characteristics that allow biofilms to persist is that they can keep the bacteria ‘under the radar’ of the immune system. This is usually attributed to the action of the extracellular polymeric substance (EPS). Perhaps the best-studied EPS is Pseudomonas aeruginosa alginate, which has been shown to reduce chemotaxis, inhibit activation of complement, scavenge hypochlorite and inhibit phagocytosis by macrophages and neutrophils (Jensen et al.2010; Moser et al.2017). The opportunistic pathogens belonging to the Burkholderia cenocepacia complex (BCC) have an EPS with a different chemical composition from alginate but can also inhibit important components of the II response by inhibiting neutrophil chemotactic migration and scavenging of reactive oxygen species (Bylund et al.2006).
So, seeing that biofilm communities can inhibit neutrophil chemotactic migration, this sounds like exactly what the team of Ron Davis has found in their preliminary findings studying neutrophils in ME/CFS. That is, the neutrophils in ME/CFS move slower when presented with a stimulus.


Following on from this, and related to earlier discussion:
The above-mentioned characteristics allow biofilm infections to become chronic; ... It has been demonstrated that the host and bacterial biofilm reach a stalemate in which the host physically contains the pathogen without complete elimination. The pathogen persists in a state of decreased activity and invasiveness, but survives within the host for a long period of time that has been hypothesized to be in the best interest of the bacteria (Parsek and Singh 2003).
So it is clear that in chronic biofilm infections the immune system has indeed reached a "stalemate" with the biofilm, and presumably autovaccination could be one way to end the stalemate, by training the adaptive immune system to encourage a stronger response — of macrophages, neutrophils, and any other methods at its disposal.

(From the Wikipedia article on autovaccines, "Mechanisms of action" section, I gather that the adaptive immune system can also influence responses of the innate immune system.)

One regulatory mechanism that the immune system uses to prevent good bacteria from being attacked is the dendritic cells. Presumably these or other regulating cells are hijacked (as in (ii) in first quote) by pathogenic biofilms to downregulate the immune response. But the dendritic cells (and perhaps other regulators?) also have an "emergency switch" which can be activated to ignore the immunosuppressing effect. I'm speculating that activating such "emergency switches" might be one of the ways a sufficiently prepared adaptive immune system can counter the immune inhibiting effects of the biofilms.
 
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Hip

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@Atlas, did the bacteria you sent to the Markov Clinic manage to get through alive, so that they can be cultured and potentially turned into an autovaccine (although I am not sure the lab is able to create autovaccines at present)?
 
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@Hip Yes! Even though they were delayed over a week in customs they apparently arrived in excellent condition, about 4 weeks after I sent them.

I did include a single RB1 foam refrigerant pack, which I did not freeze but refrigerated and then put in a polystyrene box with the dipslides, to prevent them overheating on the tarmac in NZ because it is summer here. It may not have been necessary, but I thought it also might have prevented the samples from freezing once the box was in eastern Europe.

I went possibly overboard in doing everything to ensure the Cat B guidelines were met, since it had to go through several borders. In addition to your instructions I cutout holes in a firm piece of cardboard and used it as a "tray" to separate the dipslides in case of drop test. Because there were some water droplets, I put absorbent paper towels within the ziplock bag (the secondary container), under the tray of dipslides. I also sealed the dipslide receptacle lids with parafilm tape before placing them in the tray. Then I put a wedge of polystyrene on top of them all so that they were all held in place when the lid was placed on the polystyrene box. In the outermost cardboard box, I left the packing slip and I put 3 extra copies of the packing slip in the outer pocket with the consignment note, because on the consignment note there was no space to write the full item description, I simply had to write "Uricult Plus Dipslide" on that.

Considering the box still got held up in customs all this perhaps still wasn't perfect.


The clinic was able to identify all the bacteria, and autovaccines are currently being made. They identified many strains, mostly strains of E Coli and Enterococcus faecalis, but due to my previous culturing photos we know we still did not capture all of them, so I'll be taking a polyvalent vaccine after the autovaccine to hopefully mop up extras.

Although Kyiv has been having many electricity outages, Dr. Oleg informed me that the clinic has purchased a generator, so they have a steady supply of electricity and are continuing to operate.
 

Hip

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Yes! Even though they were delayed over a week in customs they apparently arrived in excellent condition, about 4 weeks after I sent them.
That's great, amazing that they survived 4 weeks. I guess with sealed dipslide containers, this stops the bacteria from drying out. Drying I understand kills the bacteria.

How many separate dipslides did you sent the clinic? My assumption is that the more individual dipslide cultures you send them, the more likely you will capture all the species of bacteria present in the urine.
 
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I sent 6 dipslides, each dipslide had 3 agars.

They identified 13 strains, 3 species.
E Coli
Enterococcus faecalis
Staphylococcus haemolyticus

I had cultured 2 or 3 per day for 3 days of which 3 had visible growth, plus I had already collected a few visible from previous days and included them.

Proteus had been identified via photo on a previous day but I think it was one of the ones I had already thrown out, which is how we know at least one species was missed.
 

Hip

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They identified 13 strains, 3 species.
E Coli
Enterococcus faecalis
Staphylococcus haemolyticus
I wonder how the clinic identifies the different strains.

Identifying species can be done via standard lab chemical tests, and by chromogenic agar. But I am not sure how strains are identified. You can of course identify strains by genetic sequencing, but I don't think the clinic employs that expensive technique.
 
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Yeah, I was about to ask them that actually.

I'm not sure if they actually mean strains guaranteed to be distinct or if something was lost in translation and what was meant by "strains" is "identifications", e.g. whether it is meant 2 distinct strains of E Coli, or E Coli identified separately on 2 different agars, but not guaranteed to be distinct strains. I will ask.

There is a table of antibiotics resistance which I assume is the antibiotics they tested on those strains, if the antibiotic resistance was different for the same species that would guarantee it's a different strain.
 

Garz

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interesting article - thanks for that

i read it in full and will read several of the referenced papers also - as these go into more depth on the specifics

the authors reference papers by Dr Bill Costerton in several places -

i believe something along these lines is going on in all chronic bacterial infections

its N=1 only stuff - but i have been using microscopy to track my own infections with a certain amount of success.

recently rather than venous blood, i tried sampling capillary blood to see if any differences were found (i have confirmed bartonellosis - and things like bartonella prefer to live in the capillaries)

i was surprised to find this very clear example of fungal hyphae in the capillary blood from my leg - along with free fungal cells in the blood stream.
this was a surprise - as there was no obvious lesion or fungal infection in the skin - and these fungal growths should not be tolerated in the bloodstream by the immune system.
but white blood cells in the same vicinity do not seem to be activated by the presence of these yeast cells and i found none that were phagotised by white blood cells as would be expected
hyphae.JPG



i mention it here as i think it shows that my immune response to this invasive pathogen has likely been suppressed - probably by the chronic bartonella infection - much along the lines the article describes

once this happens it seems other infectious organisms, that the body would normally deal with quite easily, have "the door held open for them" and they can take advantage.

i suspect this is one of the complicating factors of many chronic conditions such as ME/CFS with an infectious cause such as Markovs is proposing - as once the immune function is suppressed - a variety of other organisms can take advantage and complicate both the symptoms picture and treatment path.

i wonder if the autovaccine approach is somehow not only producing pathogen specific antibodies and t-cell activation - but also a generalised shift in the immune function that works to help re-centre the immune system.
 
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I wonder how the clinic identifies the different strains.
They have confirmed that my identified strains are in fact identical strains.

There is a table of antibiotics resistance which I assume is the antibiotics they tested on those strains, if the antibiotic resistance was different for the same species that would guarantee it's a different strain.
They confirmed that this antibiotic-testing is done on each identified strain, and is used as "passport data" to confirm identical strains. The fact that I had 13 identifications but all strains within a species had the same "passport data" is evidence that there was no contamination of my samples. E.g. E Coli was identified 7 times with matching passport data, which indicates they are identical strains and therefore all came from the same source.

If I understood correctly, the more antibiotic resistance a strain has, the longer that strain is likely to have been in the kidneys. They find that the more "freshly" infected bacteria tend to show up on dipslides first, and as these are killed off by the vaccines, more "ancient" and more resistant bacteria are likely to show up in urine cultures
 

Hip

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They have confirmed that my identified strains are in fact identical strains.
Perhaps what they are calling "strains" are simply separate colonies (spots of bacterial growth) on the agar. They may have tested multiple colonies isolated from the dipslide agar, and determined they are all the same species and strain.
 
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In my results, each PDF I was sent represents a single dipslide.

For each dipslide, one or more identified species are listed, but each identified species is only listed once.

Thus the numbered "strains" correspond to the same species identified separately on different dipslides.

Except that they tested one of my dipslides twice for some reason, that's how I ended up with "7 strains" E Coli even though there were only 6 dipslides, because the results report is generated by a computer. (So I was told). So in that 7th case you are correct, they took multiple samples of the same species from the same dipslide/agar and it was counted as 2 strains, which turned out to be identical.

It was interesting to see that E Coli was found on every single dipslide that I sent.
 
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Garz

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so one thing that puzzles me with the Markov theory is the concept of a mixed biofilm colony in the kidney - but one that is not invasive and doesn't seem to cause obvious morphological changes - unlike most biofilm infections we could model it on.

for instance -
in diabetic wound biofilm infections - the biofilm infection just keeps growing - consuming healthy tissues - is very resistant to both the immune system and antibiotics both systemically - or topically - and surgical excision is usually needed to physically cut it out.

surgical wound infection, or surgical implant infections are essentially the same.

but then there are less obviously invasive bacterial biofilm infections - eg chronic prostatitis - to my knowledge - this goes on for years or decades but typically does not escape the prostate gland.
there are however distinct changes - eg in the size of the gland - often growing to 3-4x its original size - and the morphology / histology of the tissues - inflammation, white cell infiltration etc etc
surgery still often needed - but not so much because the bacteria are invading other tissues - more because the gland has grown so much its pressing on other structures and interfering with their function.

But then there is the example of the gut - lets take the the lining of the small intestine as an example - here the bacteria are not supposed to be in direct contact with the human cells lining the gut - but kept mostly at arms length by the production of mucous by the gut lining - and it is on this that most bacterial biofilms adhere and even consume the mucous as sustenance.
Again there is a kind of balance - where the gut lining makes mucous at a rate that governs the degree of contact between the bacteria ( and other organisms) and the immune system. the immune system also produces antimicrobial peptides to certain bacteria - and uses these and other mechanisms to essentially farm a desirable mix of bacteria for homeostasis.
so here - at least most of the time gut biofilms are not invasive at all - in fact the host tries to encourage biofilms of beneficial organisms to colonise the real estate of the gut so that there are less room for opportunistic pathogens of pathobionts to take hold.

i don't know enough about the structure or biology of the kidney - but the language used seems to imply that the kidney is more like the last example - like a mucous membrane in the gut - where there is a mucous membrane inside the kidney - and a mucous layer on that - and that it is on top of this layer that the bacterial colony is residing.

so presumably - as in the gut example - the bacteria are kept away from the tissues by mucous secretion - and this is why (again to my knowledge) we don't routinely see invasive kidney infections - or wild anatomical anomalies in the kidneys of ME/CFS patients.....

does anyone know if the kidney membrane is analogous to the gut in this way
 

Hip

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Has anyone been treated with autovaccines for a prolonged duration now? Experienced any positive effects?
Only three members of PR have tried these vaccines so far.

Myself, @Hipsman and @bensmith started the Markov protocol 12, 18 and 10 months ago respectively.

@Atlas is going to start the protocol shortly.

@Hipsman and @bensmith have both reported improvements in their ME/CFS after the 6 month point.

In my case, 4 months into the protocol, I caught COVID, and this noticeably and permanently worsened my ME/CFS (as COVID quite often does with existing ME/CFS patients). So I am unable to gauge whether any initial benefits of the vaccines may have manifested, because any mild improvements will have been masked by the worsening from COVID.

Dr Markov says improvements in ME/CFS symptoms are usually noticeable at around the 6 month point, and these improvements were observed by @Hipsman and @bensmith. But Dr Markov says that to reach the cured state, it takes 2 to 3 years (requiring one new set of vaccines every 6 months).

EDIT: time periods corrected for errors.
 
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Hip

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does anyone know if the kidney membrane is analogous to the gut in this way
The kidneys do contain an epithelium (epithelial cell layer), though I am not sure if these secrete mucous like other mucous membranes.

These epithelial cell are located in the Bowman's capsule, proximal tubules, distal tubules, and collecting ducts. Those components are shown in this kidney diagram:

nephron1_med.jpeg