From Quora: Why is there no simple diagnostic test to determine if a URI is bacterial or viral?

You ask a great question.  The market for such a test is huge, and the clinical impact would be enormous.

The technical challenge in developing a bacterial/viral test is substantial.  Trying to detect the bacteria or the viruses directly is probably not a good approach - there are hundreds of them, and the presence of a certain bacterium or virus does not necessarily mean that it is the culprit causing the infection.

An alternative approach would be to detect not the bacteria or viruses, but the body's response to the infection.  Different parts of the immune system are activated for viral vs bacterial infections.  Unfortunately, there is no single biomarker that reliably distinguishes the two responses.  But there have been publications that report suites of genes that discriminate viral and bacterial infection responses.  Unfortunately, the technological platforms that can generate this information and return it in a reasonable amount of time - probably less than an hour - and for a reasonable cost (<$50) - don't yet exist.