25Purpose: Little is known about the molecular epidemiology of Staphylococcus aureus in 26 Chinese neonatal intensive care units (NICUs). We describe the molecular epidemiology of S. 27 aureus isolated from neonates on admission to Beijing Children's Hospital. 28 29 Methods: From May 2015-March 2016, nasal swabs were obtained on admission from 536 30 neonates. Cultures were also obtained from body sites with suspected infections. S. aureus 31 isolates were characterized by staphylococcal chromosomal cassette (SCCmec) type, 32 staphylococcal protein A (spa) type, multilocus sequence type (MLST), sasX gene, antimicrobial 33 susceptibility and cytotoxicity. Logistic regression assessed risk factors for colonization. 34 35Results: Overall, 92 (18%) infants were colonized with S. aureus and 23 (4%) were diagnosed 36 with culture-positive S. aureus infection. Of the colonized infants, 72% harbored MSSA, while 37 74% of infected infants were culture-positive for MRSA. Risk factors for colonization included 38 female sex, age 7-28 days, birthweight and vaginal delivery. The most common MRSA and 39 MSSA clones were community-associated ST59-SCCmecIVa-t437 (60%) and ST188-t189 40 (15%), respectively. The sasX gene was not detected. Some MSSA isolates (16%) were 41 penicillin-susceptible and some MRSA isolates (18%) were oxacillin-susceptible. MRSA and 42 MSSA had similar cytotoxicity, but colonizing strains were less cytotoxic than strains associated 43 with infections. 44 45 Conclusions: S. aureus colonization was common in infants admitted to our NICU and two 46 community-associated clones predominated. Several non-modifiable risk factors for S. aureus 50 51 Key words: Staphylococcus aureus, neonatal intensive care unit, colonization, MRSA, MSSA 52 4 53 54 Staphylococcus aureus infections represent a significant clinical burden for infants worldwide 55 and were recently found to be the second most common cause of late-onset sepsis in very-low 56 birth weight (VLBW) infants admitted to neonatal intensive care units (NICU) in the United 57 States and United Kingdom.[1, 2] Preterm infants are also at high risk for S. aureus 58 colonization[3], a potential risk factor for subsequent infection. In a recent meta-analysis 59 involving patients admitted to NICUs and ICUs, methicillin-resistant S. aureus (MRSA) 60 colonization was associated with a 24.2 times increased MRSA infection risk.[4] Endemic 61 transmission and outbreaks due to MRSA and methicillin-susceptible S. aureus (MSSA) occur 62 frequently in NICUs.[5] Studying the molecular epidemiology and virulence factors of S. aureus 63 in the NICU population can promote an increased understanding of pathogenesis and ultimately 64 guide preventive strategies. 65 66 While the molecular characteristics of and risk factors for S. aureus colonization and infection 67 have been described for NICU populations across the globe and have increased our knowledge of 68 the global burden,[3, 6] no previous reports have described the molecular characteristics of S. 69 aureus strains...