A method and system for the detection and identification of a target pathogen in a sample is disclosed. The method and system involve the use of a capture matrix throughout resuscitation, growth, and detection. The method includes the steps of: placing the sample in a sampling container containing a medium (preferably a growth/resuscitation medium); optionally homogenizing the sample; placing a capture matrix in the sampling container with the sample; incubating the sample in the medium for a pre-determined amount of time at an appropriate temperature; optionally removing the capture matrix from the sampling container; and detecting the presence of the target pathogen in the sample.