Objective:To investigate the multilocus sequence typing feature of the virulence-associated genes of Staphylococcus aureus(S. aureus) separated from the clinical specimens of a multi-center cohort children in Guangzhou area. Methods:A total number of 412 Staphylococcus aureus strains isolated from 2 059 non-repeated fecal specimens of children by three groups′ researchers in Guangzhou Women and Children′s Medical Center from August 2018 to November 2018. While collecting specimens, patient clinical information is also properly collected and preserved. After extracting the DNA of the strain, the virulence-associated genes were detected by polymerase chain reaction (PCR), including the staphylococcal enterotoxin (SE) genes ( sea, seb, sec, sed, see) and the Panton-Valentine leucocidin-encoding gene ( pvl).The multi-locus sequence typing (MLST) method was performed to reveal the MLST feature of these genes and the statistical difference were examined by the the χ 2 test. Results:Among the 412 isolates of S. aureus, 256 strains (256/412, 62.1%) contains at least one SE gene. Among the enterotoxin gens, the sec (125/412, 30.3%), seb(98/412, 23.8%)and sea (66/412, 16.0%)genes were the three most prevalent members of SEs. The frequency of pvl gene in Staphylococcus aureus was 18.7%(77/412).Among them, the frequency of Staphylococcus aureus sea gene isolated from patients with gastroenteritis (58/319, 18.2%) was significantly higher than that from the non-gastroenteritis group (8/93, 8.6%)(χ2=4.912, P=0.027). The frequency of Staphylococcus aureus pvl gene isolated from the patients with pneumonia (8/21, 38.1%) was greater than that from the non-pneumonia group (6/47, 12.8%)(χ2=4.252, P=0.039). In addition, the virulence-associated gene of S. aureus was closely related to the specific ST type, 82.4% (28/34) of ST6 carried sea gene, all ST338 and ST59 carried seb gene, 96% (48/50) ST45 carried sec gene, and the pvl gene carrying rate of ST338 was 5/5. Conclusions:The SEA toxin produced by ST6 Staphylococcus aureus may be closely related to the diagnosis of gastroenteritis in children. The frequency of pvl virulence gene in Staphylococcus aureus in children with community-acquired pneumonia was higher than that in the non-pneumonia group, and closely related to the CC59.