It sounds as though your vet is treating for a (presumed) herpes virus infection with the L-lysine.
Herpes viruses need an amino acid called arginine to replicate and survive. If you give lysine, it substitutes in for arginine but does NOT allow the virus to replicate! Thus, it can stop the virus from multliplying and really help the cat's immune system to win. It does NOT kill the virus just stops it from mutiplying... so it can take several weeks to see improvement. Don't give up yet!
With L-Lysine I usually suggest that cats be given 250mg twice daily for 3 weeks. The capsules with powder in them are easiest to give, as you can simply open it, and mix the powder in with some canned food.
You can read more about it here: http://www.thensome.com/herpes.htm
What you are describing in your cat sounds like Rhinitis and sinusitis. There are a number of things that could cause this.
This could be due to allergies, bacterial and viral infections, and fungal infections. There could also be a physical irritant in the back of her throat or oro-pharyngeal area. Things that can do this are polyps or even blades of grass.
Let me explain a bit more about all of these things:
1. Allergies - cats do have allergies, though inhalant allergies (what we would call hayfever) is not the most common form. With inhalant allergies, I would expect clear, watery nasal discharge, but no lethargy.
2. Bacterial infections - your cat could have a tooth root abscess. In older cats, they can quite often have infection in the gums that can get into the root of the tooth. The roots are long and extend up into the nasal sinuses. So, the infection can get into the nasal area and cause sneezing and nasal discharge. Dental x-rays would help to identify this problem.
Cats can also have Bartonella infections which commonly causes "chronic snuffles" as you are describing. It is a difficult bacteria to kill, and the best antibiotic for the job is Azithromycin (Zithromax) which your cat has not been on. Here is more about it: . http://www.petplace.com/cats/bartonellosis-cat-scratch-disease/page1.aspx and http://www.petplace.com/drug-library/azithromycin-zithromax/page1.aspx )
Bartonella IS WHAT I FEEL IS MOST LIKELY FROM YOUR DESCRIPTION!
7. Mites (Pneumonyssoides caninum )can be found in the nasal passageways. They are rare, but possible.
8. And, finally, we do have to consider that a tumour could be growing in her nasal passageways and leading to this chronic sneezing.That seems very unlikely!
So, in terms of treatment, it is going to be most successful if first we have a diagnosis. If your cat were on her way in to see me, and we did not have to consider expense, I would do bloodwork and x-rays of her chest and skull. I would do dental x-rays and take a culture sample from her nose. I would give a light anesthetic and do a thorough retro-pharyngeal exam, looking for masses or abnormalities. I would remove any abscessed tooth roots. I would biopsy any tissue that appeared abnormal.
Other things that you could do for Nikki that would do no harm are the following:
1. Start her on a pro-biotic as this seems to normalize immune function in many cats. This is a natural way of treating and seems to really help a lot of cats, and certainly does do no harm! The 2 products that I have had the most luck with are Culturelle, at 1/4-1/2 capsule twice daily, and Forti-Flora (through a vet) at 1 sachet per day. Here is more about them: http://www.culturelle.com/ and http://www.healthypets.com/fortiflora30.html
2. Steam her. Take your cat into the bathroom while you run a hot shower for 15 minutes. The hot, steamy air will help to loosen any nasal secretions so she can sneeze the mucus out and clear the airways. Doing this twice a day would be great! You could offer her some canned food while the shower is on so she didn't get too frightened. Alternatively, you could use a humidifier in the room that she is in.
3. Put drops in her nose. Just go to the pharmacy and ask for ophthalmic saline, or have a look in the contact lens section. What you want it just sterile saline drops to relieve dry eyes - NO medication in it. The pharmacist should be able to point it out to you. Put one drop in each nostril twice daily. The idea is that you are helping to moisten the area so your cat can sneeze out any congestion in there. Continue for a week.
4. Lysine capsules. This is a great idea!
Without knowing what is causing your cat's symptoms, it is hard to know what treatment is going to be effective. Given that she has greenish and sometimes bloody discharge, I would certainly recommend further diagnostic tests with your vet. I would start with blood tests if she were my patient.
Here is more information about sneezing and rhinitis in cats:
I hope that this helps. If you have questions, just let me know!
Good luck with your cat! She is lucky to have someone looking out for her!
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The above is given for information only. Although I am a licensed veterinarian, I cannot legally prescribe medicines or diagnose your pet's condition without performing a physical exam. If you have concerns about your pet I would strongly advise contacting your regular veterinarian.