TL;DR: 3 years of sulfur-tasting post-nasal drip, brain fog, low-grade fever, fatigue, exercise intolerance, and tonsil stones after a viral illness. Multiple ENTs in Tokyo found nothing. Standard cultures, CT scans, allergy panels and blood work all came back normal. I tried 3 different antibiotics and all failed. I sent a nasopharyngeal swab to a US molecular diagnostics lab (MicroGenDX) for 16S rRNA sequencing and discovered my nasopharynx was 86% Citrobacter koseri and 12% E. coli, both gut bacteria that don't belong there. A Japanese culture confirmed E. coli at heavy growth with virtually no normal flora. Ten days of the right antibiotic (TMP-SMX/Baktar) and the sulfur taste that haunted me for 3 years disappeared. Brain fog lifted. Energy returned. I could run again.

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So I'm 37, living in Tokyo. About 3 years ago, I got hit with this flu-like illness. Nothing unusual, just a standard upper respiratory infection. But after it resolved, certain symptoms never went away.

See my previous posts: 1 2 3 4

The most distinctive was a persistent foul taste in the back of my throat. Sulfurous, like rotten eggs. It was there every day, all day. Alongside it came a low-grade fever, tonsil stones, brain fog, and fatigue that was different from standard tiredness. It felt like being sick rather than being tired. I also had exercise intolerance that took me from running 5km three times a week to barely managing 10-20 minutes once a week before feeling wiped out.

The ENT runaround

I saw multiple ENTs in Tokyo over the course of these 3 years. The workup was always the same: nasal endoscopy (looks normal), CT scan (looks normal), allergy testing (negative), fungal/bacterial testing also negative (!), blood work (normal). The conclusion was always some variation of "we can't find anything wrong".

Along the way, different ENTs prescribed empiric antibiotics like amoxicillin, clarithromycin, and fosfomycin. None of them worked. Each course came and went with zero change in symptoms.

(!) Despite 4 or 5 attempts, one ENT did independently culture E. coli from my nasopharynx on standard culture, and at the time prescribed Levofloxacin. However, after researching about the drug I didn't take it because I was worried about severe side effects after seeing many advise against Fluoroquinolone antibiotics. In addition (I didn't know it at the time) the bacteria in my throat were carrying the qnr gene, which dramatically increases the risk of the bacteria growing resistant. I was also sceptical since previous cultures had found nothing, so why would they suddenly discover e. coli. ? With that said, in hindsight, levofloxacin likely would have worked (at least initially).

The diagnostic breakthrough: molecular sequencing

After exhausting conventional options, I started researching on my own. I learned about 16S rRNA gene sequencing, a molecular technique that identifies bacteria by their genetic signatures rather than trying to grow them on culture plates. It can detect organisms that standard cultures miss, particularly biofilm-embedded bacteria and anaerobes.

I found MicroGenDX, a CLIA/CAP-accredited lab in the US that offers this testing for sinus and ear infections. I ordered their SinusKEY test kit, collected a nasopharyngeal swab, and shipped it from Tokyo to the US (which was its own adventure involving UN3373 biological specimen shipping regulations, FedEx International Priority, and a CDC Importer Certification Statement that nearly got my package stuck at customs).

The results came back and the picture was immediately clear:

• Bacterial load: HIGH
• Citrobacter koseri: 86% relative abundance
• Escherichia coli: 12% relative abundance
• Quinolone resistance gene (qnr): detected
• Fungal: Negative

Neither C. koseri nor E. coli belongs in the nasopharynx. These are gut bacteria. The healthy nasopharynx should be dominated by Corynebacterium, Dolosigranulum, Streptococcus, Haemophilus, and Moraxella, with no single species exceeding 20-30% relative abundance. Having enteric bacteria at 98% combined dominance with high bacterial load is profound dysbiosis.

The E. Coli. finding earlier from that one culture suddenly started to make sense.

What these bacteria were doing to me

Once I understood what was growing there, the symptoms made perfect sense.

The sulfur/rotten egg taste was produced by bacterial metabolism. E. coli and other gram-negative bacteria break down sulfur-containing amino acids (cysteine, methionine) in mucus and produce volatile sulfur compounds, primarily hydrogen sulfide. These compounds are detectable by humans at incredibly low concentrations.

The brain fog and fatigue were caused by chronic low-grade inflammation. Research has shown (Jafari et al., JAMA Otolaryngology, 2021) that sinus inflammation causes measurable changes in brain connectivity, specifically decreased frontoparietal network function affecting attention and problem-solving. The bacteria were producing a constant inflammatory stimulus, releasing cytokines (TNF-α, IL-1β, IL-6) that cross the blood-brain barrier and cause what's called "sickness behavior," which includes fatigue, cognitive impairment, and reduced motivation.

The exercise intolerance was the systemic inflammatory burden manifesting as reduced physical capacity. A body constantly fighting an infection diverts resources from exercise tolerance.

Getting the Japanese healthcare system to act

Having a molecular diagnosis from a US lab is one thing. Getting a Japanese ENT to prescribe based on it is another challenge entirely.

Japanese medical consultations average about 8 minutes. A MicroGenDX report from a foreign lab using technology not standard in Japanese practice could easily be dismissed. I needed to get a confirmatory culture from a Japanese lab in a format that any ENT would trust and act on.

I found a new ENT and took a strategic approach. I led with my symptoms, not the lab report. I let them examine me, do their endoscopy. Then I introduced the MicroGenDX results as supplementary reference and requested what I actually needed: a standard nasopharyngeal bacterial culture with antibiotic susceptibility testing.

The ENT was initially skeptical, again saying "those bacteria sometimes show up," but agreed to order the culture. The swab went to SRL, one of Japan's major reference laboratories.

Four days later, the results confirmed everything:

• Gram-negative rods: 4+ (maximum reading)
• E. coli: 3+ (heavy growth)
• Corynebacterium sp.: 2+ (only surviving normal flora)
• Normal flora: virtually absent
• TMP-SMX (co-trimoxazole): Susceptible
• Ampicillin: Resistant (explaining why amoxicillin had failed)
• Cefpodoxime: Intermediate
• Amoxicillin-clavulanate: Intermediate

The C. koseri that MicroGenDX had found at 86% didn't grow on the Japanese culture, likely because it was more deeply embedded in biofilm. But the E. coli confirmation at heavy growth with a full antibiogram was exactly what I needed.

Choosing the right antibiotic

Based on extensive research into the pharmacokinetics of available antibiotics, I identified TMP-SMX (known as Baktar/バクタ in Japan, Bactrim in the US) as the optimal choice:

• Near-perfect oral bioavailability (~100%)
• Sinus tissue concentrations exceeding serum levels (tissue:serum ratio of 1.33 for trimethoprim)
• ~99% susceptibility rate for C. koseri in published surveys
• Confirmed susceptible against my E. coli isolate
• Unaffected by the qnr quinolone resistance gene
• Available in Japan under NHI coverage

I got a 14-day prescription. I started taking it April 6.

Day 3-4: Brain fog began lifting. Post-meal drowsiness disappeared. Energy improved noticeably. The sulfur taste started to diminish. I went for a run and noticed something remarkable. I was tired afterward, but it was normal exercise tired, not the "something is wrong with me" tired I'd been experiencing for 3 years.

Day 4-5: Sulfur taste continuing to decrease. Vision felt sharper. I described it as "looking at life through HD." This is consistent with neuroinflammation resolving, since brain fog affects sensory processing, not just cognition.

Day 5-6: Sulfur taste essentially gone. Tonsils visibly less swollen. Tonsil stones smaller and less frequent. The ENT was genuinely surprised at the clinical improvement.

Day 7-8: Caught a coincidental cold (bad timing). Fever hit 38°C. But even through the cold, the chronic infection improvements held. The sulfur taste stayed gone and the brain fog didn't return.

Day 10: Sulfur taste completely absent for nearly a week. All systemic symptoms resolved. Developed a skin rash on hands and feet, which is a known side effect of TMP-SMX affecting 3-5% of patients. I ultimately stopped at day 10 due to the rash spreading.

What I learned

Standard ENT workups have a massive blind spot. Nasal endoscopy, CT scans, and allergy panels cannot detect nasopharyngeal dysbiosis. Standard cultures are rarely ordered from this site, and when they are, the significance of enteric bacteria is often not recognized. The diagnostic gap isn't in the technology. 16S sequencing has existed for years, Japanese labs do MIC testing by default, and the antibiotics are on pharmacy shelves. The gap is in the clinical workflow that connects symptoms to the right diagnostic test.

One ENT at some point did not know the bacteria on my test and was literally looking it up on Google while she was with me, while I had done tons of research already. I did not feel she was in the right position to suggest medication for me. For edge cases, I suggest that you use ENTs as tools, not as decision makers. Do the research yourself and suggest to your ENT an antibiotic, and get their approval.

Prior antibiotic failures were predictable, not evidence of untreatable disease. Amoxicillin failed because my E. coli was ampicillin-resistant. Clarithromycin has zero activity against gram-negative Enterobacteriaceae because the outer membrane is impermeable to macrolides. Fosfomycin only reaches therapeutic concentrations in the urinary tract. None of these failures indicated treatment-refractory disease. They indicated wrong drug selection.

At some point I hit rock-bottom and really thought I had some weird virus and I was just doomed forever. This is also why it took 3 years, I got stuck/depressed many times along the way. Imagine ENTs looking in your nose cavities and telling you everything looks fine, and dismissing your symptoms over and over again.

Post-viral dysbiosis is a real mechanism. The leading theory for how this started is that the viral illness damaged my nasopharyngeal epithelium, depleted normal flora, and upregulated bacterial adhesion receptors. Enteric bacteria, probably from reflux or oropharyngeal contamination, colonized the damaged, competition-free mucosal surface and established biofilm. Once entrenched, the infection was self-sustaining.

Where things stand now

I completed 10 days of a planned 14-day course before stopping due to a drug rash. The sulfur taste has been gone for about a week. All systemic symptoms including brain fog, fatigue, exercise intolerance have resolved. I'm げんき. I'm planning a repeat nasopharyngeal culture about 5 days after stopping to check whether the bacteria have been eradicated or whether survivors are repopulating. If the culture is clean, I wait and monitor. If it grows E. coli again, I'll do another course with a different antibiotic (several other options showed susceptibility on the antibiogram) and potentially pursue tonsillectomy to remove the likely reservoir.

Final note: I used Claude extensively to do deep research about my symptoms and possible medications. I kept a diary all this time and fed all information back into a project inside Claude so it was able to see the big picture. I also asked Claude to help me draft this post, since it knows everything that has happened.