Brain Infection and Neuroinflammation in ME/CFS and Post-COVID Encephalitis: A Case-Based Perspective

[SWAlexander]

It ultimately comes down to the brain—what it was, and what it is now.​

excerpt:
Several months ago, I conducted a non-standard sputum culture using a direct Petri dish inoculation method on samples from seven individuals presenting with persistent headache or cognitive dysfunction consistent with Long-COVID-related brain fog. Preliminary microbiological analysis yielded the following isolates: three colonies of Candida species, two isolates comprising Enterococcus and Streptococcus species, and two isolates of Penicillium. These findings suggest the presence of opportunistic or commensal organisms that may warrant further investigation in the context of post-viral neuroinflammatory conditions.
more at: https://swaresearch.blogspot.com/2025/08/brain-infection-and-neuroinflammation.html

 

[Rufous McKinney]

Preliminary microbiological analysis yielded the following isolates: three colonies of Candida species, two isolates comprising Enterococcus and Streptococcus species, and two isolates of Penicillium.

testing that on some health controls would be interesting

Do we know if these types of organisms can be generally present in the mouth? The mouth is not a sterile place.

 

[SWAlexander]

Do we know if these types of organisms can be generally present in the mouth

Yes, oral mucus can serve as an early clinical indicator of Candida species or other fungal pathogens.

Conventional laboratories often avoid culturing samples on agar plates due to the prolonged incubation period—typically 2 to 3 weeks at 25–30°C—required for reliable fungal growth and identification.

Instead, laboratories often prefer faster diagnostic methods, such as specific IgE testing (via blood tests or skin prick tests), to detect mold-related sensitivities or allergic responses.

Here are two examples I have done with Petri-agar plates:
https://swaresearch.blogspot.com/2025/08/why-im-focusing-on-fungi.html
and
https://swaresearch.blogspot.com/2025/06/aspergillus-trichoderma-and-penicillium.html

 

[Wishful]

I would guess that those organisms are floating around in the air everywhere, so you'd find them all over the human body (maybe even right after a shower) and certainly in all mucus membranes. Depending on how sensitive the testing technique is, you should find at least traces of most common microbes. So, without proper context (as Rufous pointed out, proper controls), the findings are meaningless.

 

[SWAlexander]

I would guess that those organisms are floating around

You say: "the findings are meaningless."
I say: maybe for you, since you don't have (allergic) symptoms.

Aspergillosis is a lung infection caused by the fungus Aspergillus, which is commonly found in the environment. It can cause various lung conditions, ranging from mild allergic reactions to severe, life-threatening invasive infections. The infection can spread beyond the lungs in severe cases, potentially affecting other organs like the liver and kidneys:
https://www.mayoclinic.org/diseases-conditions/aspergillosis/symptoms-causes/syc-20369619

People with symptoms, I recommend being tested:

If a mold allergy is suspected, skin tests (prick tests) or blood tests (IgE antibody tests) are performed. If invasive aspergillosis, a severe mold infection, is suspected, blood tests such as the galactomannan test can be performed. Other methods such as contact lenses, sedimentation plates, or culture medium tests are generally used to determine mold contamination in indoor air.
A specific ISAC® IgE biochip is also used for allergy diagnostics, such as mold allergy (rAsp f 6).

Allergy to mold: Skin tests (prick tests):
An allergist can test for mold allergens using a prick test by applying small amounts of the allergen to the skin and assessing the reaction.

Blood tests (IgE antibody tests):
These tests measure the concentration of allergen-specific IgE antibodies in the blood, which indicates sensitization to mold.

Multiparametric testing methods (e.g., ISAC® IgE biochip):
These tests enable a comprehensive analysis of sensitization to various allergens, including mold.

Mold infections: Aspergillosis.
If invasive aspergillosis, a severe infection with the mold Aspergillus, is suspected, blood cultures or the galactomannan test can be performed to detect the fungus or its metabolites in the blood.

Other infections: For other mold infections, further specific tests may be required depending on the suspected diagnosis, such as the detection of fungi in tissue samples.

I have a diagnosis and was tested later because I am immunodeficient. Lab test confirmed Aspergillus.

 

[Dysfunkion]

I actually had the idea lately based on everything I experienced so far with so much multi-systemic dysfunction starting from small cognitive cascades and immune responses. What the article outlines here may be key.

"A consistent pattern emerged: when the brain is affected by infection or inflammation, symptom severity escalates and cognitive decision-making deteriorates. The Default Mode Network (DMN) is a central player in how the human brain processes internal thoughts, memories, emotions, and self-referential thinking and vulnerable to infection. In this state, individuals become more vulnerable and may desperately pursue unproven or misguided therapeutic interventions.

While organ-specific pathology clearly contributes to disease burden, my observations suggest that insulin-related neuroinflammation and microglial abnormalities—particularly within the bilateral precuneus, regardless of etiology—can profoundly impair executive function, distort judgment, and sustain cycles of dysfunction and physical pain. This raises the question of whether certain presentations of brain inflammation could, in fact, meet the Sequential Organ Failure Assessment (SOFA) criteria currently applied in the diagnosis of sepsis."

I mean granted most experienced sufferers have heard and read it all at this point so the general message here is like saying "the sky is blue" but this may be how the gut or organs in general form these feedback loops in both directions. When one is bad the other gets even worse and unless you just stop doing almost everything this cycle will eventually cripple you with a worse baseline. But things that don't contribute to PEM still don't do anything.

In my case the worst beginnings of the worst symptom pattern cycles which I have found states my nervous system and immune system is prone to getting stuck in always start with 2 things. A cognitive load threshold that follows a specific pattern of cognitive exertion and a related immune response (usually a spicy feeling face and sinus issues flaring which can hit my ears like my most recent lovely inner ear flare I'm in now) and then trickle down digestive problems. Recently what did this is a bad series of crying spells which move around a lot of muscles in the head, move lots of fluids, and cause erratic connectivity in the brain. This if there is a dormant bacterial/viral load can be a death sentence. What has helped me the most in general? Bombarding myself with probably way too many herbal antibiotics a day, red/near infrared light, and protein degraders (which may be targeting byproducts of the infections)! I can have bad times like right now but as long as I keep that supplement stack in place I at least make it. This is just holding back the ocean though, if I stop I' know I will just get crippled again completely especially as I get older with this.

I can move my arms around, walk and run, work with my fingers, and lift things all day though and nothing happens but total exhaustion because my general state and way I need to live renders me the weakest person with the most pain tolerance induced physical endurance ever as I for some reason do not get physical PEM outside of eye movement.

I think, talk too much, feel emotions too strong, move my eyes too much, make my immune system the slightest bit angry, eat just the wrong thing, or get exposed to EMF's out of my tolerance and I'm rendered brain dead with physical fatigue and immune dysregulation that has me feeling like iron man in the worst way possible. This is of course complete with sensory states and states of mind that put psychedelic trips to shame.

Then this all starts feeding itself in a series of loops until I simply do nothing for long enough with some micromanagement to get back to mild. Over the years all of the worst I ever experienced can be traced back to a series of loops that I'm vulnerable to that I got stuck in involving the unholy trinity of my immune system, nervous system, and guts. In over the past few years through everything I've tried I found myself eventually in every single one of them again just in varying states of PEM. I fall out of one I'm just in another but overall improved in a stable baseline way on the things mentioned above with lifestyle control.

 

[SWAlexander]

just in varying states of PEM

Very clear and to the point.
Often, we don’t know exactly how or when a system malfunction begins—but medical professionals, if willing, may be able to identify the root cause.
In the absence of a clear diagnosis, our priority should be to reach for tools that help stabilize the system, relieve immediate symptoms, and prevent further issues like PEM.

 

[SWAlexander]

The mouth is not a sterile place.

That's absolutely true—nothing in or on the human body is truly sterile.
Viruses, bacteria, and fungi are everywhere; they’re part of our environment and even coexist with us as part of our natural microbiome. The real issue isn't their mere presence—it's which microbes become harmful and under what conditions they disrupt normal biological function.

In my case, this became critically clear. I developed sepsis, which could have been fatal. It originated from a lumbar spinal hardware infection in 2016. Fluid collected from my lower back revealed several organisms:

• Staphylococcus epidermidis
• Peptostreptococcus
• A single colony of Staphylococcus caprae
• Corynebacterium species

These bacteria, often considered part of the normal skin and mucosal flora, became pathogenic when introduced into a compromised site. This underscores how even typically "low-virulence" microbes can pose serious threats under the right (or wrong) conditions.

Infections like this can trigger immune dysfunction. An overwhelmed or dysregulated immune system can lead to gene methylation changes, disrupting normal gene expression and contributing to systemic malfunction. This cascade of events shows how microbial imbalance, immune deficiency, and genetic regulation can all intersect in serious disease.
This is fundamental knowledge in biology, immunology, and virology: the balance between host defenses and microbial presence is delicate. When that balance is disrupted, even common microorganisms can become life-threatening.

Another serious bacterial infection is tularemia, which is considered endemic in New Mexico—meaning it occurs regularly in the Torrance County region. (PDF file)

Latest case reported:
2019: Two human cases were reported in Santa Fe County.
https://www.nmhealth.org/news/disease/2019/5/?view=768#:~:text=In 2018 there was one human tularemia,visit the CDC 's Tularemia web page.

 

[Wishful]

You say: "the findings are meaningless."
I say: maybe for you, since you don't have (allergic) symptoms.

Yes, meaningless because it depends on the particular situation. As you pointed out, even normally safe bacteria can cause serious problems if they're in the wrong place, or if a person's immune system has unusual problems in dealing with them. People having common strains in their mouth is meaningless without data showing that it is actually causing problems. Showing a correlation needs more data, such as comparisons to controls. People with brainfog also--approaching 100%--also have toenails, but that doesn't mean that toenails cause brainfog.

 

[SWAlexander]

A very extensive paper.​

Antimicrobial resistance burden landscape in Germany in 2019: a comparative country-level estimation​

Published: 14 August 2025

Excerpt:
Antimicrobial resistance (AMR) remains a critical public health challenge, contributing to increased morbidity, mortality and healthcare costs worldwide. The global burden of AMR was extensively documented by Murray and colleagues,1 who estimated 4.95 million deaths associated with bacterial AMR and 1.27 million deaths attributable to bacterial AMR in 2019.
Bloodstream, respiratory and intra-abdominal infections were the major contributors to the fatal AMR burden. The leading pathogens responsible for AMR-associated deaths were Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae and Pseudomonas aeruginosa. E. coli resistant to β-lactam/β-lactamase inhibitors and aminopenicillin were top pathogen-drug combinations causing deaths attributable to and associated with AMR, respectively.

Part of a large list.
Results:

AMR, antimicrobial resistance; BSI, bloodstream infections; CNS, infections of the central nervous system (include meningitis); DALY, disability-adjusted life year; LRI, lower respiratory infections; iNTS, intestinal non-typhoidal salmonellae; UTI, urinary tract infections.
https://academic.oup.com/jacamr/article/7/4/dlaf142/8234293

 

[Dysfunkion]

Very clear and to the point.
Often, we don’t know exactly how or when a system malfunction begins—but medical professionals, if willing, may be able to identify the root cause.
In the absence of a clear diagnosis, our priority should be to reach for tools that help stabilize the system, relieve immediate symptoms, and prevent further issues like PEM.

I tend to just go for what keeps things the most stable, when I first started getting sick way back my worst downwards spiral in 2013 into 14 (but I was was having growing issues before that with fatigue, slow gut motility, and the first signs of neuropathy a couple years before that). To this day almost all tests are normal besides somewhat elevated liver enzymes and protein in urine occasionally which I've had since being a small child (I also frequently got sick with all sorts of things and much harder than others despite a diet no different than most other kids). Only a couple years back now I believe I got my diagnosis for lyme but not other coinfections. No parasites or stool abnormalities either. I know from very obvious symptoms upon exposure in my old home things really went south from mold toxicity as that situation got much worse before moving leading to my most extreme hyper sensitivities and neuro-psychiatric issues. It's hard to find what was the chicken or the egg, and when something started so early without proper care I suppose what matters most is managing the immediate issues and just identifying what prevents the most of happening later. Did I contract some infections born in a weaker state early on from something undiagnosed that became dormant and prone to reactivations slowly doing more damage? Or did my weakened state just allow a lot more in much easier leading to more problems much easier?

 

[SWAlexander]

Or did my weakened state just allow a lot more in much easier leading to more problems much easier?

I believe that a weakened immune system, partly due to impaired interferon function, leaves the body more susceptible to additional infections.

Just because we believe we've recovered from an infection doesn't necessarily mean our immune system—specifically our IgG antibodies—is fully functioning.

In a recent video presentation (translated from German to English), Prof. Dr. Dunja Bruder shared this insight:

“…My suspicion is that viral infections can leave long-lasting effects on the body.”
“Shockingly, traces of these infections can still be detected in the cerebrospinal fluid (CSF) up to eight months after the initial illness.”

Her example: Viral Infections: A Serious Concern for Physical Exercise

How can damaged lungs—particularly malfunctioning alveoli—adequately supply the oxygen needed for exercise, if oxygen cannot efficiently reach the muscles?

Excerpt:

Why certain pneumococcal serotypes can be particularly dangerous after a bout of influenza. While over 90 serotypes are known, only a few cause invasive, life-threatening infections. Prof. Dunja Bruder's team was able to demonstrate for the first time in a preclinical mouse model how a recovered influenza infection influences the response of alveolar type II epithelial cells to various pneumococcal serotypes. "In contrast to previous studies, which mostly examined secondary infections during the acute phase of influenza, our work shows that susceptibility to pneumococci persists during the recovery phase – but primarily to invasive serotypes," summarizes Bruder. The new findings on epigenetic and immunological changes in AECII provide valuable mechanistic clues as to how previous viral infections can sustainably impair the antibacterial defense capacity of the lungs – an aspect that could be important in the long term for the development of improved therapeutic and diagnostic approaches for bacterial superinfections.

More at: https://www.helmholtz-hzi.de/en/research/research-groups/details/immune-regulation/

 

[Dysfunkion]

I believe that a weakened immune system, partly due to impaired interferon function, leaves the body more susceptible to additional infections.

Just because we believe we've recovered from an infection doesn't necessarily mean our immune system—specifically our IgG antibodies—is fully functioning.

In a recent video presentation (translated from German to English), Prof. Dr. Dunja Bruder shared this insight:

“…My suspicion is that viral infections can leave long-lasting effects on the body.”
“Shockingly, traces of these infections can still be detected in the cerebrospinal fluid (CSF) up to eight months after the initial illness.”

Her example: Viral Infections: A Serious Concern for Physical Exercise

How can damaged lungs—particularly malfunctioning alveoli—adequately supply the oxygen needed for exercise, if oxygen cannot efficiently reach the muscles?

Excerpt:

Why certain pneumococcal serotypes can be particularly dangerous after a bout of influenza. While over 90 serotypes are known, only a few cause invasive, life-threatening infections. Prof. Dunja Bruder's team was able to demonstrate for the first time in a preclinical mouse model how a recovered influenza infection influences the response of alveolar type II epithelial cells to various pneumococcal serotypes. "In contrast to previous studies, which mostly examined secondary infections during the acute phase of influenza, our work shows that susceptibility to pneumococci persists during the recovery phase – but primarily to invasive serotypes," summarizes Bruder. The new findings on epigenetic and immunological changes in AECII provide valuable mechanistic clues as to how previous viral infections can sustainably impair the antibacterial defense capacity of the lungs – an aspect that could be important in the long term for the development of improved therapeutic and diagnostic approaches for bacterial superinfections.

More at: https://www.helmholtz-hzi.de/en/research/research-groups/details/immune-regulation/

My lungs themselves feel alright, my air hunger I feel like comes from limited supply getting to the brain, when that happens all physical anything I;'m going will have a layer of fatigue over it like right now drinking coffee. I'll pick up the mug, drink a gulp, and my body processing this will be extremely taxing. Walking and everything is about the same but same pattern in not being able to physically induce PEM from these things and everything is just much slower and delayed. The usual PEM things will still do their thing.

My reactions are also spine centered too, I learned this from my RLT sessions where zapping anywhere on my spinal column will have the same benefits but if I just did some random spot on my hand for example nothing happens. I have a feeling traces of mine are floating around in there and the lymph, if they're largely being suppressed my quality of life is alright and I stay in mild. If not then I need to beat them back before the immune system gets too dysregulated, there's too many chain reactions all over, and my baseline lowers which of course leads to more problems in the spinal fluid and brain. Any kind of immune response to potentially start a disaster if uncontrolled.

The problem is to avoid all of it I need to live in a bubble with a plain diet so strict I mind as well not eat at all and that's not very workable. One of my main issues is living entirely healthily isn't possible because my system overall at a baseline has never functioned like it should to withstand the environment normally. I could eat the perfect diet, live the perfect lifestyle with the best resources, BUT it just takes one wrong exposure to cause my system to go haywire. I can't handle a lot of ordinary things including certain stressors. Most people around me live weekly in ways that would actually kill me. The micromanagement and lack of flexibility itself is suffocating with conditions like this.

A very extensive paper.​

Antimicrobial resistance burden landscape in Germany in 2019: a comparative country-level estimation​

Published: 14 August 2025

Excerpt:
Antimicrobial resistance (AMR) remains a critical public health challenge, contributing to increased morbidity, mortality and healthcare costs worldwide. The global burden of AMR was extensively documented by Murray and colleagues,1 who estimated 4.95 million deaths associated with bacterial AMR and 1.27 million deaths attributable to bacterial AMR in 2019.
Bloodstream, respiratory and intra-abdominal infections were the major contributors to the fatal AMR burden. The leading pathogens responsible for AMR-associated deaths were Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae and Pseudomonas aeruginosa. E. coli resistant to β-lactam/β-lactamase inhibitors and aminopenicillin were top pathogen-drug combinations causing deaths attributable to and associated with AMR, respectively.

Part of a large list.
Results:
View attachment 56112
AMR, antimicrobial resistance; BSI, bloodstream infections; CNS, infections of the central nervous system (include meningitis); DALY, disability-adjusted life year; LRI, lower respiratory infections; iNTS, intestinal non-typhoidal salmonellae; UTI, urinary tract infections.
https://academic.oup.com/jacamr/article/7/4/dlaf142/8234293

Does BSI here mean brain stem infection? What does that stand for?

 

[SWAlexander]

Does BSI here mean brain stem infection? What does that stand for?

BSI (Bloodstream Infections): BSIs are capable of crossing the blood-brain barrier (BBB), potentially leading to serious neurological complications, even in the mid-brain.