Loads of different ways.
You can identify their genetic material through PCR. You can grow them under culture conditions that some survive and others don’t. You can look at them under a microscope. Etc etc.
Not everything is viable for every pathogen, and many techniques require that you know what you’re looking for to some degree. Signs/symptoms in the patient as well as their history (clinical but also certain risk behaviours) can point you in the right direction.
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