From Quora: How do doctors determine if a patient has a viral or bacterial infection when the symptoms look like a common cold?

Unfortunately, they don’t.  The vast majority of these infections are viral, yet some 60% of patients walk away with a prescription for antibiotics that will do them no good whatsoever.

The chart below gives you some idea of the number of visits to primary care physicians for respiratory infections (a lot), the frequency of these that are bacterial infections (few) and the rate of antibiotic prescriptions for these infections (way too many).

Gonzales et al (2001)

There are no good rapid diagnostics that will distinguish bacterial from viral infections.  There are rapid Strep tests for pharyngitis, but their sensitivities are only about 80%, meaning that a negative result does not rule out the possibility of Strep throat.  There are the Centor criteria and other signs algorithms, but their accuracy is also around 80% at best.  White blood cell counts are of no value in differentiating viral from bacterial pneumonia, and it is unlikely that they are any more accurate in differentiating other respiratory infections.

Doctors know that they are overprescribing antibiotics, but they do it anyway.  The principal reasons they cite are patient expectations, time pressures and diagnostic uncertainty.  There is a perception that there is some prophylactic value in prescribing antibiotics to patients who have viral infections; that this will reduce the risk of a complicating bacterial infection.  However there is no evidence for this view.

Instead, there is a significant risk of adverse events from needless prescription of antibiotics.  There are some 140,000 visits to Emergency Departments each year due to antibiotic use, mostly for allergic reactions and diarrhea.  C. difficile infections kill some 14,000 Americans each year, and are almost always associated with prior use of antibiotics.  Our increasing understanding of the gut microbiome suggests that antibiotics may increase the risk of asthma, obesity and diabetes, especially when given early in life.  And of course, antibiotic overuse is undoubtedly a contributing factor to antibiotic resistant infections, which kill some 23,000 Americans each year.

So, back to your question: Doctors use a variety of methods to distinguish bacterial from viral infections; none of these is very good; consequently, they overprescribe antibiotics; public health is damaged.