There are multiple reasons a wound may not show pathogens by PCR including prior antibiotic use, sampling error and no pathogen present, i.e., no actual infection. A delay in wound healing may be caused by local factors such as tension, trauma, impaired circulation (e.g. lower leg) as well as the severity and/or cause of the wound. Systemic factors include advanced age, smoking, diabetes, poor nutrition and immunosuppression.
There’s always a chance that a particular reaction did not amplify a present target to the limit of detection. However, having a positive result of the positive-control confirms that the negative result is due to the absence of a target and the sample is a true negative.