Negative pressure wound therapy (NPWT) is gaining acceptance as a physical therapy for a wide variety of infected wounds. To gain insight into the response of bacteria to NPWT in vivo, the adaptive expression of biofilm regulators and adhesion factors of Staphylococcus aureus (S. aureus), the most frequently isolated pathogen in the clinic, during acute wound infection was investigated. A 3 cm full-thickness dermal wound was created on each side of a rabbit back and inoculated with green fluorescent protein-labeled S. aureus. NPWT was initiated at 6 h post inoculation, with the wound on the contralateral side as the untreated self-control. The wounds were subjected to a 28 day observation period. Histological analysis, laser scanning confocal microscopy and scanning electron microscopy revealed a transition of S. aureus to a free-living phenotype in tissues treated with NPWT, compared with microcolonies in untreated wounds. Viable bacteria counts showed a modest reduction in the bioburden of NPWT group on day 8 (P<0.001), with ~1x10⁶ colony-forming units/g tissue. Transcript analysis of biofilm- and colonization-related genes were investigated using reverse transcription-quantitative PCR on postoperative days 1, 2, 4 and 8. The poly-beta-1,6-N-acetyl-D-glucosamine synthase locus and holin-like protein CidA/antiholin-like protein LrgA network were less active in the NPWT group compared with the untreated control group. Accordingly, the expression profile switched to an elevated expression of the adhesive factors UDP-phosphate N-acetylglucosaminyl 1-phosphate transferase (at days 0-4) and fibronectin-binding protein A and iron-regulated surface determinant protein A at >4 days during both stages of colonization. Meanwhile, low expression levels of the effector molecule (RNAIII) of the accessory gene regulator type I (agr) system was detected in NPWT group, suggesting that the bacterial density in NPWT-treated wounds was under the threshold for agr activation, thus not leading to an active and invasive infection. The wounds treated by NPWT healed completely on day 28, compared with an average of an 8.11% defect area in the control group (P<0.001). The results of the current study indicated that S. aureus responds to NPWT by regulating gene expression, manifesting a decrease in biofilm formation and an increase in bacterial colonization in vivo, which potentially benefits the wound repair and healing process.