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PLoS One. 2016 Oct 12;11(10):e0164397. doi: 10.1371/journal.pone.0164397. eCollection 2016.

Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit.

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College of Public Health and Health Professions and College of Medicine, Department of Epidemiology, University of Florida, Gainesville, FL, United States of America.
Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America.
Infectious Diseases and Immunology, Wolfson Children's Hospital, Jacksonville, FL, United States of America.
University of Florida Center for HIV/AIDS Research, Education and Service, University of Florida, College of Medicine, Jacksonville, FL, United States of America.
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States of America.
Division of Infectious Diseases, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, United States of America.


Despite infection prevention efforts, neonatal intensive care unit (NICU) patients remain at risk of Methicillin-resistant Staphylococcus aureus (MRSA) infection. Modes of transmission for healthcare-associated (HA) and community-associated (CA) MRSA remain poorly understood and may vary by genotype, hindering the development of effective prevention and control strategies. From 2008-2010, all patients admitted to a level III NICU were screened for MRSA colonization, and all available isolates were spa-typed. Spa-type t008, the most prevalent CA- genotype in the United States, spa-type t045, a HA- related genotype, and a convenience sample of strains isolated from 2003-2011, underwent whole-genome sequencing and phylodynamic analysis. Patient risk factors were compared between colonized and noncolonized infants, and virulence and resistance genes compared between spa-type t008 and non-t008 strains. Epidemiological and genomic data were used to estimate MRSA importations and acquisitions through transmission reconstruction. MRSA colonization was identified in 9.1% (177/1940) of hospitalized infants and associated with low gestational age and birth weight. Among colonized infants, low gestational age was more common among those colonized with t008 strains. Our data suggest that approximately 70% of colonizations were the result of transmission events within the NICU, with the remainder likely to reflect importations of "outside" strains. While risk of transmission within the NICU was not affected by spa-type, patterns of acquisition and importation differed between t008 and t045 strains. Phylodynamic analysis showed the effective population size of spa-type t008 has been exponentially increasing in both community and hospital, with spa-type t008 strains possessed virulence genes not found among t045 strains; t045 strains, in contrast, appeared to be of more recent origin, with a possible hospital source. Our data highlight the importance of both intra-NICU transmission and recurrent introductions in maintenance of MRSA colonization within the NICU environment, as well as spa-type-specific differences in epidemiology.

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