A method for identifying and quantifying viable microbial cells in one or more samples containing a microorganism of interest, comprising: (a) amplification of species-specific DNA from pre-rRNA-containing samples using a reverse transcription-polymerase chain reaction, said amplification step comprising: using a first primer complementary to a pre-rRNA region of said microorganism of interest; using a second primer complementary to a mature rRNA region of said microorganism of interest; and performing multiple cycles of amplification using said first primer and said second primer to yield detectable levels of amplified species-specific DNA; and (b) quantitation of said amplified species-specific DNA, said quantitation step comprising: using a fluorescently labeled hybridizing probe complementary to said mature rRNA region of said microorganism of interest; using said first primer complementary to said pre-rRNA region of said microorganism of interest; using said second primer complementary to said mature rRNA region of said microorganism of interest; and performing multiple cycles of amplification using said fluorescently labeled hybridizing probe and said first primer and said second primer to yield increasing levels of fluorescence signal above fluorescence background; wherein said amplification of said species-specific DNA indicates the presence of said viable microbial cells in said one or more samples, and wherein said quantitation of said amplified species-specific DNA provides a relative measurement of the amount of said viable microbial cells in said one or more samples. (a) amplification of species-specific DNA from pre-rRNA-containing samples using a reverse transcription-polymerase chain reaction, said amplification step comprising: using a first primer complementary to a pre-rRNA region of said microorganism of interest; using a second primer complementary to a mature rRNA region of said microorganism of interest; and performing multiple cycles of amplification using said first primer and said second primer to yield detectable levels of amplified species-specific DNA; and using a first primer complementary to a pre-rRNA region of said microorganism of interest; using a second primer complementary to a mature rRNA region of said microorganism of interest; and performing multiple cycles of amplification using said first primer and said second primer to yield detectable levels of amplified species-specific DNA; and (b) quantitation of said amplified species-specific DNA, said quantitation step comprising: using a fluorescently labeled hybridizing probe complementary to said mature rRNA region of said microorganism of interest; using said first primer complementary to said pre-rRNA region of said microorganism of interest; using said second primer complementary to said mature rRNA region of said microorganism of interest; and performing multiple cycles of amplification using said fluorescently labeled hybridizing probe and said first primer and said second primer to yield increasing levels of fluorescence signal above fluorescence background; wherein said amplification of said species-specific DNA indicates the presence of said viable microbial cells in said one or more samples, and wherein said quantitation of said amplified species-specific DNA provides a relative measurement of the amount of said viable microbial cells in said one or more samples. using a fluorescently labeled hybridizing probe complementary to said mature rRNA region of said microorganism of interest; using said first primer complementary to said pre-rRNA region of said microorganism of interest; using said second primer complementary to said mature rRNA region of said microorganism of interest; and performing multiple cycles of amplification using said fluorescently labeled hybridizing probe and said first primer and said second primer to yield increasing levels of fluorescence signal above fluorescence background; wherein said amplification of said species-specific DNA indicates the presence of said viable microbial cells in said one or more samples, and wherein said quantitation of said amplified species-specific DNA provides a relative measurement of the amount of said viable microbial cells in said one or more samples.