For 5 months, I've had recurrent urethritis. It started with (apparent, but negative) Gono (mild pus and dysuria), and this went away after treatment.

I've been tested for, 3 times, on diff occasions

Chlam, Gono

Ureaplasma / Micoplasma (culture),

Fungus,Trich, Herpes

All negative.

Taken:

Azithro 2000mg + Shot
Azithro 2000mg again
Doxy 200mg x10
Cefixime x10
Metronidazole x10
Moxifloxacin 400mg x10

Symptoms:

Intermittent sharp sting on meatus when NOT peeing. Sometimes mild, rarely it is like a shock, travelling up urethra.

Have days where I don't feel it, or days I feel it 1-3x

Discomfort walking, due to friction.

Very rare mild burn after peeing. Generally no dysuria.

Occasional, scant clear discharge.

The symptoms can go on their own for a few weeks (with no meds), and then come back for a few weeks. Cycle.

Symptoms aren’t bad, but mentally I’m devastated. I’ve tested for everything so many times, but I feel like I’ve lost my sexual health, due to some undiagnosable/untreatable infection.

1.   Are there cases like this where they can’t detect any bacteria, yet problems persist after Gono?

2.  Can I in good conscience tell a potential partner that I am ‘clean’?(Main concern)

3.  Are there other possible pathogens? E.coli? What else can I ask the labs to test for?

4.  Whenever I've been swabbed, there’s  been no discharge. Can this affect accuracy? I've been treated for everything anyway.

a)    Masturbation irrelevant
b)    This is not in my head
c)    Not constantly ‘milking’

Welcome to our Forum.  I'll be happy to comment.  It certainly sounds as though at the beginning of things you had a urethritis which got better with treatment.   since then have you been examined by a health care provider (and if so, was it the same provider?). Were any of these episodes evaluated with measures of inflammation such as a urethral gram stain on a swab specimen or a urinalysis.  if so, please provide this information as well as I may have further comments. If not, your diagnosis of "urethritis" appears to be determined by your symptoms and the symptoms that you report are not suggestive of sexually transmitted urethritis.  I say this because sexually transmitted urethritis does not come and go, does not present with abrupt discomfort, and does not cause difficulty walking. 

Added to this is that you have been repeatedly treated with a variety of medications which would be effective for urethritis treatment, further making urethritis unlikely.  In answer to your specific questions:

1.   Are there cases like this where they can’t detect any bacteria, yet problems persist after Gono?

Yes they occur but they typically have objective evidence of inflammation which is the reason I asked.  Further, when such problems have been studied, they tend to go away over time and there is no evidence that the presence of urethral inflammation without detection of pathogens and which is unresponsive to antibiotics puts the person with the syndrome at risk for complications, nor is it associated with health problems for sexual partners. 

2.  Can I in good conscience tell a potential partner that I am ‘clean’?(Main concern)

Yes

3.  Are there other possible pathogens? E.coli? What else can I ask the labs to test for?

There is no need for further testing. This would be a waste of time and money.

4.  Whenever I've been swabbed, there’s  been no discharge. Can this affect accuracy? I've been treated for everything anyway.

Even without discharge, a swab can be quite informative.  If there was no sign of inflammation ( i.e. polymorphonuclear leukocytes (PMNs) being seen on the smear). 

I hope this information is helpful to you.  AT this time, my advice would be to assume that you are not a danger to partners, that you do not need for treatment or testing, and would seek to avoid hyper-vigilance for symptoms.  EWH

So no STI, I believe you, but questions:

1. What can be done for meatus irritation? I  walk around with cellophane on my glans to stop friction – not normal! Hard to ignore this and move on. What could cause this increased sensitivity? Tip is a little red today. Issue is more pronounced and daily than in previous recurrences. Ibuprofen useless.

2. Isn’t inflammation a response to an infection or injury?

3. Whatever this is, it’s a result of the initial infection, no doubt. 
a. How common is this issue I’m having? (STI opening door into recurrent issues)
b. What could cause periods of symptoms to come and go? When they come, it takes me by surprise –anxiety/hyper-vigilance is NOT the cause, but a symptom.

4. If I got WBC (a.k.a. PMNs?) swab: 
a. Does a negative guarantee 100% no infection (ST, or other)
b. What would positive indicate? i.e. could I take action based on this?.
c. You mentioned that with Gono, there are cases of recurrent issues, but if no WBC, what explains this? I never actually tested + for Gono, but doc thinks it is because I had Cipro (which I tried before gono treatment, from diff doc) in my system (forgot to mention). So initial infection could’ve been something else.
d. How long did symptoms take to stop in the cases you mentioned?

5. What could be the cause of the clear discharge, or occasional irritated feeling just inside urethra, if no infection?

6. E.coli thoughts?

Please answer in as much detail as possible, since I can’t ask more..

Final comments about this issue below.  typically, once folks can accept that they do not have an STI, symptoms resolve over time.  Further treatment and testing only prolongs and accentuates anxiety.  In some instances, clients have needed the help of a mental health specialist to address the anxieties which drive such problems.

1. What can be done for meatus irritation? I  walk around with cellophane on my glans to stop friction – not normal! Hard to ignore this and move on. What could cause this increased sensitivity? Tip is a little red today. Issue is more pronounced and daily than in previous recurrences. Ibuprofen useless.

Cellophane, if anything, would be occlusive and keep skin from healing.  I would try to keep your penis clean and dry and to keep you hands off it.  If this is a major problems you may wish to ask a dermatologist

2. Isn’t inflammation a response to an infection or injury?

Inflammation may have many causes including irritation from repeated examination or irritation or other process

3. Whatever this is, it’s a result of the initial infection, no doubt. I am not sure I agree with this.  You may be heightening your symptoms with your anxieties and concerns.  Alternatively, given the many antibiotics you have taken, you may have allowed a fungal skin infection to occur.
a. How common is this issue I’m having? (STI opening door into recurrent issues). 
b. What could cause periods of symptoms to come and go? When they come, it takes me by surprise –anxiety/hyper-vigilance is NOT the cause, but a symptom.

Problems of the sort you describe are uncommon but something we deal with rather regularly at this site and most often relate to excessive anxiety over possible STIs setting up a cascade of heightened awareness, unneeded therapy and complications of that therapy. 

4. If I got WBC (a.k.a. PMNs?) swab: 
a. Does a negative guarantee 100% no infection (ST, or other)
b. What would positive indicate? i.e. could I take action based on this?.
c. You mentioned that with Gono, there are cases of recurrent issues, but if no WBC, what explains this? I never actually tested + for Gono, but doc thinks it is because I had Cipro (which I tried before gono treatment, from diff doc) in my system (forgot to mention). So initial infection could’ve been something else.
d. How long did symptoms take to stop in the cases you mentioned?

You have already proven you do not have an STI, thus "what if" questions like a do not help.  If an increased number of PMNs are seen, this would indicate irritation/inflammation which has already been proven NOT to be an STI. 

5. What could be the cause of the clear discharge, or occasional irritated feeling just inside urethra, if no infection?

A Variable, usually relatively small amount of clear urethral secretions are normal and can be detected on examination.  Repeated examinations tend to increase and accentuate them

6. E.coli thoughts?

E. coli is a normal bacteria found n the urethra, I would not be chasing it if I were you.

In closing, I would repeat what I said to you in my earlier reply- "AT this time, my advice would be to assume that you are not a danger to partners, that you do not need for treatment or testing, and would seek to avoid hyper-vigilance for symptoms."  EWH