Systems and methods for determining bacterial load in targets and tracking changes in bacterial load of targets over time are disclosed. An autofluorescence detection and collection device includes a light source configured to directly illuminate at least a portion of a target and an area around the target with excitation light causing at least one biomarker in the illuminated target to fluoresce. Bacterial autofluorescence data regarding the illuminated portion of the target and the area around the target is collected and analyzed to determine bacterial load of the illuminated portion of the target and area around the target. The autofluorescence data may be analyzed using pixel intensity. Changes in bacterial load of the target over time may be tracked. The target may be a wound in tissue.