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persistent cough after cardio surgery

Three or four days after open heart surgery (AVR) in March, I began what was initially a persistent, dry cough.  After a couple more days, I wondered if the inspirometer had become contaminated (it was about the right number of days to have symptoms after the first time I used it).  My capacity was fine, 2000 ml, so I gave it up. Somewhere in there, probably during the next week, I noticed difficulty getting my breath, and that is still the case after four months.  (During periods when it's worse, and I am struggling for breath, my O2 saturation is still okay, at least mid-90s; it is usually 98 or at least 97 when normally tested.)  

Two or three weeks after the cough started, I began to cough up a small amount of quite thick, slippery mucus, which was clear.  I thought maybe the coughing had irritated the bronchii or something, and the mucus was just in response to that.  There didn't seem to be a change in the character of the cough, and my cardiologist was not concerned.  (He did kind of assume allergies, but I'm fairly certain that is not the principal cause, for multiple reasons.)

The amount of mucus has increased slowly, until now the cough is pretty constant and there is substantial mucus most of the time.  It is very thick (not quite "globs" but almost sometimes) and has become yellow.  

This past week I had a viral cold with laryngitis.  Yesterday and the day before, I could tell the cold was just about over, I felt good, on the mend, like the last day before you're totally well?  Starting last night a little, and today a lot, however, I feel quite ill systemically, and have a low-grade fever (which had been gone).  I don't think it's the return of the viral thing, it is acting quite different, less acute for one thing.  What troubles me is that the coughing became much worse last evening, had a lot of thick mucus this morning, and it was a fairly dark yellow.  

The past four months, I have had no indication that the cough was in my lungs.  Today I am not so sure.  I don't have pain in my lungs or anything, but the cough is coming from lower and seems less localized.  Probably no connection, but two days ago I got out the inspirometer and used it a couple of dozen breaths--I'm sure it's coincidental that the cough started initially a couple of days after my first use and that the cough has had a step-up in seriousness and new symptoms of illness two days after using it again--but I wanted to tell you everything.

My concerns are:  (1) If this is bacterial, I was told to treat it as an emergency.  It acts more like it than in the past.
(2) I don't think this chronic cough, gradually becoming more symptomatic, should have been with me for four months unless something is wrong.  At first I thought maybe it was a "cardiac cough," having something to do with the heart's movement or blood flow, but as I said, it has gotten less mechanical and more disease-like.  (3) The BIG one--the difficulty breathing is very, very troubling.  Much of the time I have to make a point of breathing abdominally or else I feel I can’t inhale enough and I’m suffocating.  Many times when I go to bed, my chest hurts from the effort all day.  If it is permanent, it will have definite lifestyle impact.  My left ventricle wall was supposedly thickened but not impaired and is expected to return completely to normal, so my doctor and I haven't "borrowed trouble" until we could see how that came out, but now neither my cardiologist nor I have an opinion as to expected duration of the cough, and he has recently conceded that the shortness of breath may be permanent.  There have not been aggressive diagnostics to my knowledge (for example, diaphragm movement has not been observed; I don’t know when blood has been cultured for bacteria—they’ve had plenty and done plenty of tests, but I have no idea if that was one).

What I am asking from you is ideas regarding the breathing, the most important and most debilitating condition.  I would appreciate any ideas regarding the etiology of the cough, as well, and what role it may have in the breathing difficulty.

Thank you for any suggestions or hints you can provide.
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