Stool routine - Varying results.

My daughter has severe diarrhoea. We met with the pediatrician who gave probiotics and some other medicines. He suggested to get a stool test done and give antibiotics (Taxim O) only if stool tests show signs of bacterial infection. Luckily I had taken a sample in the morning and given to the nearest diagnostic center who were going to send us the reports by 5 PM. However, the doctor suggested to give a sample at his clinic again as they would tell us the results within two hours so that we can start treatment in case of bacterial infection soon. Now, at the end of the day, we have both reports. The early morning sample says 10 to 12 pus cells. However, the latter one says 2 to 4 pus cells. Why do we see so much variation in the results? We have started with the antibiotics anyway but was wondering what would cause such varying results and what to do in such situations?