Even if an organism can survive various transport conditions and will be recovered in available culture systems with reliability, identification protocols may not provide clear cut differentiation, based on phenotypic tests and characteristics. Sequencing techniques are increasingly utilized for certain classes of organisms. Good examples are the aerobic, non-spore forming gram positive rods, including Nocardia, Corynebacterium, and related genera, and mycology isolates.
A more routinely encountered application occurs in virology. Molecular methods allow for efficient typing of herpes simplex (type I versus type II) and subtyping of specimens positive for influenza A.