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I am new and came across this while looking for answers about my Yorkie (Timmy)'s cough.
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It doesn't sound like Timmy has a collapsed trachea. They usually would not appear at that young of age and collapsed tracheas (CT) produce a honking cough when excited. My 18 mth old yorkie has been diagnosed with CT. Did the xray show anything? I also think it may be an infection or a bad strain of Kennel Cough. Kennel cough can take several rounds of antibiotics before the puppy is able to shake it off. I adopted a little chihuahua who had to do 4 rounds of antibiotics before she got over her kennel cough that she picked up at the pound after they found her.
Good luck with Timmy. Please let us know how he is doing.