A surgical site infection (SSI) is an infection that occurs after surgery in the part of the body where the surgery took place. An SSI may range from a spontaneously limited wound discharge within 7-10 days of an operation to a life-threatening postoperative complication, such as a sternal infection after open heart surgery. Most SSIs are caused by contamination of an incision with microorganisms from the patient's own body during surgery. From the analytical point of view, the complex nature of these samples as well as the low concentrations of analytes require a system with high sensitivity and efficiency. Such situation requires a technique such as CE, which is a powerful and versatile separation technique that promises to rival HPLC when applied to the separation of both charged and neutral species. During the study, it has been demonstrated that CZE identifies characteristics of such groups of pathogens such as bacteria Gram (+) and different species of bacteria Gram (-), and also develops weekly individual profiles for patients after application of antibiotics. This was done in order to show the impact of antibiotic therapy in change numbers of bacteria present in the wound after surgery. The method proved to be the ideal straight specificity in the case of Escherichia coli (100%). Finally, analysis of the spectra and the second derivatives of the UV-Vis spectra confirmed the similarity in the profiles and showed that the CZE is a great method for fast screening test in bacterial infection.