PCR in diagnostics

[whusean]

Can someone explain exactly how PCR is used to diagnose the presence of a microbial infection. Are primers which are specific for certain microbial genes designed, and if that microbe is present, then that gene will be amplified??

[CharonY]

Basically yes. Most of the time it is a small part of a gene (though technically it can be any locus that is specific enough). Also, most of the time qPCR is done.

[whusean]

Ok i get that...so what happens when the infection could be caused by a number of possible pathogens. How can a specific gene specific to one pathogen be targeted?

[CharonY]

The purpose of PCR-based diagnostics is not necessarily to find out what infections you may have, but rather if you have the specific infections X, Y or Z. So even if you or some food stuff is infected by, say Salmonella, Bordetella, Campylobacter, using primers specific for Salmonella will only tell you whether that is present, but will not tell you anything about the other species.

If your question is how one can be sure, that those primers do not cross-react, then the answer is that they are only specific within the known genomic space (i.e. the complete known genome sequences of all species). While they are tested for cross-reactions, it is of course theoretically possible that there are some other not yet identified bacteria around that may also have that particular sequence.