BackgroundAtopic dermatitis (AD) is an inflammatory skin condition distinguished by an activated Th2 immune response. The local skin microbial dysbiosis is a contributing factor to the development of AD. The pathogenic coagulase-positiveStaphylococcus aureusis the primary species responsible for the progression of AD. Even thoughStaphylococcus pseudintermediusis an animal-origin pathogen, it is increasingly becoming a source of concern in human diseases. As another coagulase-positiveStaphylococci, it is crucial to pay more attention toS. pseudintermediusisolated from the lesion site.ResultsIn our investigation, we presented a case of cheilitis in a patient with atopic dermatitis (AD). We utilized culture and next-generation genomic sequencing (NGS) to identify the bacteria present on the skin swabs taken from the lip sites both prior to and following treatment. Our findings indicated that the predominant bacteria colonizing the lesion site of AD wereS. pseudintermediusandS. aureus, both of which were eradicated after treatment. The Multi-locus sequence typing (MLST) ofS. pseudintermediusandS. aureusdemonstrated coordinated antibiotic susceptibility, with ST2384 and ST22 being the respective types. Although the skin abscess area resulting fromS. pseudintermedius infection was significantly smaller than that caused byS. aureusin mice, the expression of cytokines interleukin-4 (IL-4) and interleukin-5 (IL-5) were significantly higher in theS. pseudintermedius-infected mice.ConclusionsTheS. pseudintermediusstrain isolated from the lesion site of the AD patient exhibited a higher expression of IL-4 and IL-5 when colonized on mouse skin, as compared toS. aureus.This observation confirms thatS. pseudintermediuscan effectively induce the Th2 response in vivo. Our findings suggest that animal-originS. pseudintermediusmay play a role in the development of AD when colonized on the skin, emphasizing the importance of taking preventive measures when in contact with animals.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-023-02837-6.