This invention is related to methods pertaining to the determination of bacteria and yeast wherein the methods comprise: a) filtering a sample containing bacteria and yeast through at least one filter; b) treating the filter or filters with a medium which facilitates the growth of the bacteria and yeast; c) growing the bacteria and yeast on the filter or filters to thereby produce colonies or microcolonies of the bacteria and yeast; d) fixing the colonies or microcolonies to the filter or filters; e) treating each filter under suitable hybridization conditions with one or more enzyme labeled PNA probes wherein, each PNA probe comprises a probing nucleobase sequence complementary to a target sequence in the nucleic acid of the bacteria and/or yeast; f) removing excess enzyme labeled PNA probe from each of the filters; and g) determining enzyme activity remaining on each filter to thereby identify or enumerate colonies or microcolonies on the filter or filters.