Thank you for the additional information about Mr. Watson.
Now as I am sure you can appreciate, respiratory signs can arise with a range of conditions. If his signs are non-responsive to antibiotics, then we do have consider that either this is a non-bacterial issue (ie fungal, foreign bodies causing chronic inflammation in the nasal passageways, growth/neoplasia/polyps, allergic, etc) or that the bacteria present are resistant to the drugs that have been used.
Now if he doesn't have nasal discharge and just sounds congested, then I would initially put infectious causes of upper respiratory disease (this are since you have noted that the increased noise is within the upper part of the tract and not appreciated in the lungs when auscultated by the vet) lower on my list of concerns for him. That said, the majority of upper respiratory diseases we'd be thinking about wouldn't usually cause this degree of stunting of his growth. This is especially suspicious because you noted that he eats normally (so nutritional intake is normal) but the protein isn't being used for growth (and you didn't note any diarrhea or profuse urination that could explain protein losses). This means we do have to also consider that the respiratory signs could be a secondary issue if there is something else underlying (ie birth defect, chronic systemic disease, etc) that is greatly weakening his immune system.
In Mr. Watson's case, especially as hehas had multiple courses of antibiotics with no allaying of his symptoms, further diagnostics really would be indicated to let you 'see' what is going on inside. To start, xrays could be very helpful here. While he has had his lungs and heart listened to by multiple vets, we do have to appreciate that we can only hear so much. And it is possible that mild to moderate lung or heart disease might be missed on auscultation alone. Therefore, xrays aid us in allowing us to see the lungs and the heart and make sure that they are truly normal (ie no fluid build up in the lungs from heart disease or signs of lingering pneumonia, that the heart is the right shape and size and that there is no fluid within the pericardium compressing it, etc). As well, the skull can be xrayed and if there is a mass (be it a benign polyp, tumor, or fungal granuloma) in one of the nasal passages then this can be identified. Depending on the findings, the vets will be able to start to narrow the cause of his respiratory signs and hopefully pinpoint a diagnosis to then treat.
If the xrays are found to be normal or if the vet thinks this is purely upper respiratory disease, then you might want to consider checking to see if the cavy specialist is equipped with scoping equipment for this size of pet (since most of the standard scopes are likely to be geared more for dog and cat sized critters). If they do, then a bronchoscope could be used to explore the nasal passages, nasopharynx (the are behind the nasal passages where they connect), and the lungs. As I am sure you will appreciate, the scope's wee camera will let them actually see into these areas in real time where they will be able to appreciate if there is a mass or fungal plaques inside the airway. Furthermore, they will be able to take biopsies of the tissue in the airway for evaluation under the microscope to see what is actually going on in this tissue.
Finally, in regards XXXXX XXXXX testing, this is not an airway specific diagnostic tool. Still it would have value here since bloods would allow you to appreciate if there is an ongoing immune issue (based on white cell levels) and get a baseline for his organ function (in case he has dysfunction due to disease or birth defects). It can help you rule out some of those systemic/body causes that could be weakening the immune system to just cause chronic airway infections.
Now you haven't noted any home support treatments for his congestion, therefore I will just touch briefly on a few to try if you haven't already. First, if he is congested you can take him in the bathroom while you run a hot shower. The steam will help loosen and clear some of the snot congesting him and can help him breathe easier. Furthermore, you can also use a baby nebulizer/humidifier, but often animals don’t like things held up to their faces. That said, you can alternatively make little ‘steam tents’ with Mr. Watson in his carrier and the nebulizer under a thin bed sheet.
As well, if he is building up mucus that the steam isn't shifting, use a cotton ball moistened with warm water to wipe away crust and mucus. Use saline nasal drops (like Ocean Mist) but not anything medicated. Tilt the head back and drop two to three drops in one nostril. They don't like this, but it helps. After the drops go down, you can let the head up and wipe away any discharge that gets loosened. Then repeat with the other nostril If the vet feels that the congestion is due to nasal passage inflammation, steroid drops may be indicated or even anti-inflammatory treatment.
Overall, there are a number of agents that could induce these chronic signs of Mr. Watson's. That said, I am a little worried that there may be something more sinister here since he really shown a failure to grow normally like his brother. Therefore, it is worth a chat with his vets about taking the next step with advanced diagnostics to see what is going on inside. Because at the end of the day, once you can see what is in his chest and upper airway you will be in a better position to address it properly and treat it as effectively as possible for him.
I hope this information is helpful.
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