Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America

Abstract

Background: The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is attributed to the spread of the USA300 clone. An epidemic of CA-MRSA closely related to USA300 has occurred in northern South America (USA300 Latin-American variant, USA300-LV). Using phylogenomic analysis, we aimed to understand the relationships between these 2 epidemics.

Methods: We sequenced the genomes of 51 MRSA clinical isolates collected between 1999 and 2012 from the United States, Colombia, Venezuela, and Ecuador. Phylogenetic analysis was used to infer the relationships and times since the divergence of the major clades.

Results: Phylogenetic analyses revealed 2 dominant clades that segregated by geographical region, had a putative common ancestor in 1975, and originated in 1989, in North America, and in 1985, in South America. Emergence of these parallel epidemics coincides with the independent acquisition of the arginine catabolic mobile element (ACME) in North American isolates and a novel copper and mercury resistance (COMER) mobile element in South American isolates.

Conclusions: Our results reveal the existence of 2 parallel USA300 epidemics that shared a recent common ancestor. The simultaneous rapid dissemination of these 2 epidemic clades suggests the presence of shared, potentially convergent adaptations that enhance fitness and ability to spread.

Keywords: MRSA; USA300; USA300-LV; epidemics.

Figure 1.

Phylogenetic analysis shows relationships between whole-genome Staphylococcus aureus isolates. A, Phylogenetic network is based on 1000 maximum likelihood nonparametric bootstrap iterations for 88 Staphylococcus aureus genomes. Only sequence type 8 (ST8) strains are shown (8 genomes used as outgroups have been excluded for clarity). Areas of low support show higher amounts of reticulation. Note that the 2 epidemic lineages in the North American epidemic (NAE) and the South American epidemic (SAE) can be robustly distinguished from each other but exhibit high levels of reticulation internally. Whole genomes of BR-VRSA, COL, FPR3757, Newman, RN4220, TCH1516, USA500, and VC40 are shown for comparative purposes. B, Chronogram was constructed using core genome single-nucleotide polymorphisms from the 48 sequenced strains in a Bayesian phylogenetic analysis that coestimated the phylogenetic relationships among isolates, the times since the divergence of the major clades, and the rate of evolutionary change. We used a relaxed-clock model and a constant-size coalescent tree prior probability. Calendar dates of isolation were used to calibrate the clock. Branches are colored based on parsimony reconstruction of geographical location in North America (blue) or South America (red). Numbers on or near branches are Bayesian posterior probability support values. Ancestral branches with uncertain geographical reconstructions are black. Pie charts show proportional likelihood reconstructed for each of the key branches based on the mkt1 model (see “Methods” section). Early branching (EB) strains are also indicated. Key evolutionary acquisition events (eg, arginine catabolic mobile element [ACME] and copper and mercury resistance [COMER] element acquisition events) are indicated with arrows. The binary matrix shows presence (green; 1) and absence (white; 0) of selected genes associated with each lineage. Abbreviations: abi α, abortive phage infection; arcA, arginine deiminase; copB, putative ATPase copper exporter; lipo, putative lipoprotein; lukSF-PVL, Panton-Valentine leukocidin; mecA, PBP2a; mco, multicopper oxidase; merA, mercuric reductase; sek, enterotoxin K; seq, enterotoxin Q; speG, spermidine N(1)-acetyltransferase.

Figure 2.

Circular whole-genome alignment of closed circular Staphylococcus aureus USA300 lineage genomes. Width of each circular track is relative to nucleotide identity as calculated by whole genome alignment based on mummer (available at: http://mummer.sourceforge.net). From inside out, the tracks are TCH1516 (gray), CA12 (yellow), M121 (green), CA15 (blue), HUV05 (red), and V2200 (orange). Areas of difference corresponding to mobile elements are noted. Abbreviation: ACME, arginine catabolic mobile element.

Figure 3.

Comparison of locus adjacent to SCCmec element in North American epidemic (NAE) and the South American epidemic (SAE) Staphylococcus aureus strains. A, The arginine catabolic mobile element (ACME) is characteristic of NAE strains, and the copper and mercury resistance (COMER) element is characteristic of SAE strains. Only the copB gene (corresponding to ABD21730.1 in FPR3757) and an adjacent putative lipoprotein (corresponding to ABD21221.1) are found in both elements. B, Unrooted maximum likelihood gene genealogy of copB genes from USA300 genomes and publicly available staphylococcal genome sequences. Clades for copB genes from North American USA300 (blue) and USA300 Latin American variant (USA300-LV; red) are distinct and appear to have been acquired in independent horizontal gene transfer events from other staphylococcal species. Black circles on branches represent nonparametric bootstrap values of 80%–100%; gray circles indicate bootstrap values of 50%–79%. The length of branches is proportional to the number of substitutions per site. Abbreviations: SA, S. aureus; SC, Staphylococcus capitis; SE, Staphylococcus epidermidis; SH, Staphylococcus haemolyticus; SP, Staphylococcus pettenkoferi; SS, Staphylococcus saprophyticus; SW, Staphylococcus warneri; SX, Staphylococcus xylosus; S_sp, Staphylococcus species.