I think the whole infection/sputum sample/infection site issue makes the whole thing more complicated (according to my Respiratory Nurse, anyway). This is how I understand it.
When we cough up sputum, we don't know where it has come from in our lungs, left side or right side, or upper airways, or lower airways. Sputum samples may not contain, or be from, the same infection site. Which may go some way to explain why sometimes a specific sputum sample is clear, but we are still running a temperature, as we have not managed to cough up sputum from the infection site which is causing the lung inflammation. Clear as mud so far?
As well as the Sputum results, the Respiratory Nurse asks questions about how bad I feel, takes my temperature, listens to my chest for signs of infections such as crackles, asks me if I am managing to clear the mucus, drinking plenty of fluids to thin the mucus, and together we do everything in our power to clear the infected sputum, wherever it comes from. We also keep a note of the bacteria where identified, and which antibiotic was given, and which worked, if more than one antibiotic course necessary. (These details have only started coming to me in the last 4 years, and often have to ask for them, as it is not automatic).
In our lungs there are many many different types of bacteria, many of which don't bother us, our natural Immunity dealing with them. Some of them, once they get to a certain number really do cause us problems, and often take more than one course of antibiotic to get rid of, or if not possible, at least reduce the numbers down so that they are not causing any inflammation.
Does any of that make sense?