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

Abstract

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.

Fig 1. Maximum likelihood (ML) phylogenetic relationship among spa-type t045 and t008 MRSA isolates and patient length of stay with date of positive culture.

The left side of the figure displays the ML phylogeny scaled in SNPs per site and ordered by decreasing genetic distance (i.e., closer phylogenetic relationships appear on top). Asterisks represent clades with bootstrap support values above 80% (i.e., well supported). The right side of the figure displays the corresponding clinical data for each patient. Bars associated with each tip (patient) of the phylogeny span the day of admission to day of discharge, and black point represents the collection date of positive surveillance culture. Shading and numbering of the epidemiological data corresponds to transmission clusters displayed is S7 Fig. A.) 40 spa-type t008 isolates obtained from infants hospitalized from 2008–2010 and corresponding length of stays. B.) 16 spa-type t045 isolates obtained from infants hospitalized from 2008–2010 and corresponding length of stays.

Fig 2. Bayesian maximum clade credibility (MCC) phylogeny of 97 spa-type t008 from multiple healthcare facilities including 46 from colonized patients hospitalized in Hospital-A’s NICU (blue branches and diamond tips).

The phylogeny is scaled in time with tip dates corresponding to collection dates of positive MRSA cultures. The shaded area represents a monophyletic clade comprised of 31/48 (64.6%) of Hospital-A NICU isolates.

Fig 3. Comparison of effective population sizes (Ne) of t045 (green) and t008 (orange) lineages estimated from Bayesian phylogenetic analysis of 46 spa-type t008 isolates and 40 spa-type t045 isolates from colonized patients hospitalized in Hospital-A’s NICU from 2003–2010 as well as 97 spa-type t008 (purple) from multiple healthcare facilities in northeast Florida.