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Background The molecular characteristics and antimicrobial susceptibility of Staphylococcus aureus (S.aureus) in general pediatric wards and county-level hospitals were rarely reported in China.Methods Staphylococcus aureus was isolated from children hospitalized with respiratory tract infection (RTI) in Zhongjiang and Youyang counties in 2015.All isolates were typed by multilocus sequence,staphylococcal protein A,accessory gene regulator (agr),and staphylococcal cassette chromosome mec [SCCmec,for methicillin-resistant S.aureus (MRSA) only].Polymerase chain reaction was used to screen 21 super-antigen (SAg) genes and panton-valentine leukocidin (pvl).Antimicrobial susceptibility testing was performed by E test.Results A total of 2136 children were enrolled.Overall,125 (5.9％) children carried S.aureus,among which MRSA accounted for 42.4％.ST59-SCCmec type Ⅳ-t437-agr group Ⅰ (58.5％) was the most prevalent genotype in MRSA,and ST188-t189-agr group Ⅰ (22.2％) was the top genotype in methicillin-sensitive S.aureus (MSSA).The pvl carriage rate in MRSA and MSSA was 15.1％ and 9.7％,respectively (P =0.4112).About 96.8％ of S.aureus isolates were positive for at least one SAg gene.The most common SAg gene profile in the dominant ST59 clone was seb-sek-seq (42.8％).All S.aureus isolates were resistant to penicillin and erythromycin (minimum inhibitory concentration 90 was ＞ 32 and 256 mg/L to penicillin and erythromycin,respectively),but usually susceptible to other tested non-β-lactam antimicrobials.Conclusions Staphylococcus aureus and MRSA were detected with a high frequency in children with RTI in county-level hospitals of China.ST59-SCCmec type Ⅳ-t437-agr group Ⅰ was the dominant MRSA clone.The S.aureus isolates exhibited high resistance to penicillin and erythromycin.