some clinical samples are labour to process and also some bacterial agents are fastidious or slow growing. on the other hand, there is a need for detection with high specificity.
Hi, ddPCR is quite sensitive, but in majoroty of cases TaqMan real time PCR is sensitive enough and cheep, more over it is very important how many samples do you have to estimate per day, per mounth etc.
If you have big amount of samples, for example 100-1000 in a week even in the case of perfecr GMP in clinical applications you able (of course it depends on you) to touch with contamination.
Better way in this case nanosensors - it is PCR free approaches that desreases contamination probability.
Regarding nested, yes it is e very sensitiive, but we cant even compare this approach with ddPCR because ddPCR more sensitive and less contamination-dangerous.