In an interview with the San Francisco Chronicle, veterinary dermatologist Dr. George Doering makes a pretty obvious but very important comment that is worth repeating:

"The biggest problem we have in almost all the fields of veterinary medicine is compliance. You say to a client, "This dog needs to take this antibiotic twice a day." Well, the reality is we might be lucky if they get it once a day. …They don’t want to accept the seriousness of the problem."

This very true and very important. Compliance with recommended antibiotic therapy is probably a major factor in treatment failure, recurrent infection and antibiotic resistance. Antibiotic dosing regimens are specifically designed to ensure that the right concentration of drug is present in the body for the appropriate time. Missing doses, skipping days, not making sure the animal actually ingests the drug, and other problems that result in the pet not getting what is was supposed to get are very important.

It’s easy to understand why this happens, because administering antibiotics (particularly to some difficult-to-pill dogs and cats who can smell the medication when it comes in the house!) can be a hassle. Because of this (and the very natural human tendency to take the easy way out), it’s really important for people to understand the concerns about inadequate antibiotic administration and what they need to do.

• Follow the entire treatment course. You should have no antibiotic left at the end of the recommended treatment time.
• Make sure your pet actually swallows the antibiotic. If you add pills to food, make sure you check to see that the pill isn’t left behind. It’s amazing how animals can eat a big bowl of food and leave behind a little pill. The picture shows how my dog Meg can, in the process of inhaling her food at an incredible rate, leave behind a tiny ephedrine pill.
• If your pet will not eat the drug voluntarily, talk to your vet about other ways to administer it, such as compounded in chewable treats. Depending on you and your pet, opening your pet’s mouth and placing the pill at the back of the tongue may be an option. Talk to your vet about this first and make sure you wash your hands after. If you think there is a risk you might be bitten, if you are at high-risk for infection because you are immunocompromised, elderly or pregnant, don’t try to "pill" an animal in this manner.
• If you still can’t get the drug into your pet, talk to your vet right away.  If you wait a couple of days or a week or more to tell your vet, your pet may be even sicker by then. There may be other options to oral drugs such as injectable antibiotics. This might end up being more expensive or difficult (e.g. you may have to take your pet to the vet every day for its medication), but it will be better for your pet and may even save you money in the long run by ensuring the infection is properly and completely treated the first time.
• Never stop treatment because your pet looks better. Often, signs of infection get better before the bacterium is completely eliminated. Stopping too soon allows the bacterium to regrow, potentially as a more resistant form.
• If you are supposed to take your pet to the vet for a recheck at the end of treatment, then do so. Sometimes longer courses of antibiotics may be needed, and it’s much better to continue the current treatment course than to have to start again a couple weeks down the road when the infection has returned (sometimes with a vengeance).
• If in doubt about anything, call your veterinarian.  He or she is there to help, and wants your pet to get the best treatment possible.