In various embodiments, the present disclosure describes methods and systems for detecting microbes in a sample. The methods are generally applicable to quantifying the number of target bacteria in a sample counted from a detection region of a flow cytometer histogram. The detection methods can be employed in the presence of other microorganisms and other non-target microbe components to selectively quantify the amount of a target microbe. The methods are advantageous over those presently existing for testing of foodstuffs and diagnostic evaluation in their speed, accuracy and ease of use. Various swab collection devices and kits useful for practicing the present disclosure are also described herein.