1, 2). The National Nosocomial Infections Surveillance System observed a Ͼ300% increase in the incidence of late-onset MRSA infections in NICUs, from 0.7 to 3.1 infections/10,000 patient days, between 1995 and 2004 (3). Unique host and environmental factors, including immature immune systems, high frequency of contact with health care providers (4), exposure to numerous invasive procedures, NICU overcrowding and understaffing (5, 6), and prolonged hospitalization (7), make NICU patients at especially high risk of becoming colonized and infected with MRSA. Since colonization with MRSA is a risk factor for development of MRSA infection, prevention of MRSA transmission within the NICU is critical (7,8). Many NICUs have implemented active detection and isolation (ADI) programs, which involve surveillance to rapidly identify affected patients, followed by cohorting and isolation with standard contact precautions, in attempts to prevent MRSA transmission and reduce infection rates.Several large NICUs have published reports regarding the clinical epidemiology of neonatal MRSA following implementation of surveillance, transmission prevention, and/or decolonization strategies (7,(9)(10)(11)(12). Some also incorporated molecular analyses in their studies, including antibiotic susceptibility testing (9, 10), strain typing (9, 11, 12), genotyping (9, 12), and/or Panton-Valentine leukocidin gene detection (9,12). No studies have comprehensively examined all of those molecular features of MRSA and additionally assessed the presence or absence of genes encoding proteins for a variety of staphylococcal toxins and potential virulence factors over an extensive time period following implementation of an ADI program in an NICU.In response to the appearance of MRSA in the NICU at YaleNew Haven Children's Hospital (YNHCH)