Ah yes a .0000000001% chance that the patient develops super-MRSA, the disease that gets its characteristic deadliness from Multiple Resistances to antibiotics, which bacteria develop when antibiotics are overused. Sounds like a great reason to over prescribe antibiotics.
He's saying that they weigh some chance of increasing antibiotic resistance against the expected value of giving the antibiotic. Depending on your decision theory and utility that may be the right move.