Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA (CA-MRSA) strains have now invaded healthcare settings. A convenience sample of 97 clinical MRSA isolates was obtained from seven hospitals during a one-week period in 2010. We employed a framework integrating Staphylococcus protein A typing and full-genome next-generation sequencing. Single nucleotide polymorphisms were analyzed using phylodynamics. Twenty-six t002, 48 t008, and 23 other strains were identified. Phylodynamic analysis of 30 t008 strains showed ongoing exponential growth of the effective population size the basic reproductive number (R0) ranging from 1.24 to 1.34. No evidence of hospital clusters was identified. The lack of phylogeographic clustering suggests that community introduction is a major contributor to emergence of CA-MRSA strains within hospitals. Phylodynamic analysis provides a powerful framework to investigate MRSA transmission between the community and hospitals, an understanding of which is essential for control.

Figure 1. Distribution of MRSA spa types across six different hospitals in Jacksonville (J) and one in Gainesville (G), both in northeast Florida, USA, collected during 2010 (n = 97).

Figure 2. ML phylogenetic analyses of MRSA t008 in northeast Florida by HCF.

Colored tip branches correspond to healthcare facility from which the isolate was obtained. The numbers along the monophyletic branches correspond to bootstrap values (500 replicates). Branch lengths in nucleotide substitutions per site were scaled according to the bar at the bottom of the tree.

Figure 3. Bayesian skyline plots of MRSA t008 in Jacksonville.

Non-parametric curves of MRSA effective population size (Ne) over time were estimated by employing a Bayesian framework. Genetic distances were transformed into a timescale of years by enforcing a relaxed molecular clock model. Solid lines indicate median (blue), and 95% upper and lower high posterior density (HPD) estimates of Ne (black).

Figure 4. MRSA t008 phylogeographic patterns in Jacksonville.

Phylogeographic analysis using a rooted ML genealogy inferred for 26* sequences from Hospitals J.a, J.c, J.d, J.e, and J.f. A. The most parsimonious reconstruction (MPR) of the state of origin for each internal node (ancestral sequence) in the tree is indicated by the color of the subtending branch according to the legend in the figure. Equivocal branches indicate multiple MPRs. *Note: The four G.a sequences were omitted from the ML genealogy. B. Tree length distribution of 10,000 trees obtained by random joining-splitting. The arrow points to the number of observed migrations in the ML tree.