Methicillin-resistant Staphylococcus aureus (MRSA) is a recognized cause of community-associated (CA) skin and soft tissue infections in otherwise healthy individuals (1, 2). These infections have been especially frequent in certain high-risk groups such as military recruits, prison and jail inmates, athletes, and children in daycare (reviewed in reference 1). Common risk factors associated with CA-MRSA include sharing of personal items, superficial abrasions, crowding, limited access to showers, and exposure to others with MRSA infections (3-6).MRSA infections that occur in correctional facilities (both prisons and jails) are of special concern due to the high risk for outbreaks and the potential for more invasive infections, as well as the risk of recurrent infections among inmates (7,8). While a prison holds inmates with extended sentences following conviction, jails hold detainees awaiting trial, inmates awaiting sentencing, and inmates that have been given a sentence of Յ1 year. Newly released inmates may introduce epidemic strains of CA-MRSA into the community, while inmates awaiting transfer may transmit their strains to the prison population (8, 9). Thus, jails may serve as an important reservoir and amplification center of epidemic MRSA strains for both the community and prison populations (9).Outbreaks of CA-MRSA in jails have occurred in different geographic regions of the United States (6, 10). Notably, a MRSA outbreak in 2002 at the Los Angeles County Jail involved 928 inmates (6). We recently reported that the prevalence of MRSA colonization among inmates entering two New York State (NYS) prisons was 10.6% for females and 5.9% for males, far higher than the prevalence of 0.5% to 1.5% reported for the general population (5, 11).There have been few investigations that describe MRSA clinical isolates from inmates of large jails (12,13). No such studies have been performed at Rikers Island Correctional Facility (RICF), one of the largest jails in the country. Of note, 46% of inmates under custody in NYS prisons are committed from New York City (NYC), and most inmates committed from NYC are jailed at RICF (see http://www.doccs.ny.gov /Research/Reports/2013/UnderCustody_Report_2013.pdf). We therefore characterized a large collection of MRSA clinical isolates from RICF with the goal of better understanding the contribution of jail transfers to the introduction of MRSA into the prison system. This would be an initial step toward developing strategies to reduce the introduction and spread of MRSA.According to the NYC Department of Corrections report from October to December 2012 (14), RICF houses roughly 12,700 inmates, including detainees awaiting trial (76.0%), new convicts serving sentences (16.0%), and new convicts awaiting transfer to a state prison facility (8.0%). The average length of stay for an inmate is 54 days; Ͼ75.0% of inmates are discharged directly into the community after their release. In 2012, there were Ͼ87,000 admissions to and 88,000 discharges from RICF. Most inmates were male (93.0%)...