The collective noun for cultures from different sites (blood, urine etc.)

You are most likely talking of specimens.

"Data on specimens was collected from the department of clinical microbiology."

M-W:

specimen noun
1 b : a portion or quantity of material for use in testing, examination, or study : a urine specimen

ODO:

specimen NOUN
1.2 A sample for medical testing, especially of urine.

‘Specimens of blood or urine are the alternatives…’

‘Panel’ is the collective noun that physicians themselves often use. (You seem to be asking for the term of venery rather than a generic collective noun.) A panel of specimens from a single patient, might include different fluids and tissue types.