Evidence for natural selection on the <i>Staphylococcus aureus</i> genome during asymptomatic carriage.

<p>A) The relative number of synonymous versus non-synonymous SNPs on all branches of the within-host genealogies relating colonies sampled from hosts A-M. Each pie represents a branch in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061319#pone-0061319-g001" target="_blank">Figure 1</a>, divided into segments according to the proportion of synonymous (green) and non-synonymous (orange) mutations on that branch. The area of the pie is proportional to the number of synonymous and non-synonymous mutations on that branch. The solid line is the uncorrected <i>dN</i>/<i>dS</i> ratio estimated from SNPs within hosts, which was significantly greater than the uncorrected <i>dN</i>/<i>dS</i> ratio estimated from SNPs between hosts (dashed line, McDonald-Kreitman test <i>p</i><0.001). B) The sample frequency of SNPs, represented by the minor (less frequent) allele. Bars are color-coded according to SNP type: synonymous (green), non-synonymous (orange), nonsense (red) and intergenic (grey). C) The expected and observed number of within-host mutations per gene (solid and hatched bars respectively), combined across participants A–M, Q and R.</p

Examples of large insertion-deletion polymorphisms within single hosts.

<p>A) 23.9 kb deletion of a Panton-Valentine leukocidin-encoding prophage in four colonies isolated from participant J (contig C618:c65). B) 3.5 kb indel knocking out <i>adhE</i> in three colonies isolated from participant F (contig C608:c44). In both panels, the deleted region is indicated in red. The presence of coding sequences (CDS, dark blue), tRNA (dark red), rRNA (purple) and other features (gray) are indicated by filled rectangles. Sliding windows are shown indicating GC content (black), and positive (green) or negative (purple) GC skew. Positions are indicated relative to the concatenated Velvet assemblies of the host-specific reference genomes. Figures extracted from circular chromosome plot generated using CGView <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061319#pone.0061319-Stothard1" target="_blank">[81]</a>.</p

Genomic diversity in asymptomatically carried nasal populations of <i>Staphylococcus aureus</i>.

a<p>Recent antibiotic use: ★ amoxicillin, ★★ antibiotic with expected anti-staphylococcal activity (trimethoprim or ciprofloxacin). ^bAverage SNP divergence between colonies. ^cSingle-locus variant of ST22.</p><p>MLST: multilocus sequence type, MRSA: methicillin resistant <i>Staphylococcus aureus</i>, syn: synonymous, stop: premature stop codon, CDS: coding sequence, SNP: single nucleotide polymorphism, indel: insertion/deletion, ST: sequence type, CC: clonal complex.</p

Genomic diversity of <i>Staphylococcus aureus</i> in 13 singly-colonized nasal carriers.

<p>For each carriage study participant (A–M) a representation of the maximum likelihood tree is shown relating all colonies isolated and sequenced from that host. Gray circles represent observed genotypes, where area is proportional to sample frequency, and small black circles represent hypothetical intermediate genotypes. Edges (branches) represent mutations, color-coded as follows: synonymous (green), non-synonymous (orange), premature stop (red), non-coding (grey), structural variant (black). Solid edges represent SNPs and dashed edges represent indels. The ordering of mutations along a branch is arbitrary.</p

Estimating the number of transmission events from genomic divergence.

<p>We used a simple population genetics model to calculate the probability of the number of mutational differences between two bacterial genomes, conditional on the number of transmission events that have occurred since their most recent common ancestor, under A) slow transmission (0.3 transmissions per year) and B) rapid transmission (1.2 transmissions per year). We employed the model to estimate the Bayesian posterior probability of the number of transmission events conditional on the observed number of mutational differences, under C) slow and D) rapid transmission. E) When we applied the model to CC22 genomes under the slow transmission model, we detected evidence for very recent transmission between some pairs of hosts, including the possibility of direct transmission. In A) and B), the lines are color-coded according to the number of transmission events, indicated by the key. In C) and D), the magnitude of the posterior probability is indicated by the intensity of the shading, as shown by the key. In E), the ten pairs of hosts with most evidence for recent transmission are shown. The colors distinguish transmission pairs.</p

Genes affected by multiple mutations among hosts A–M, Q and R.

<p>Genes affected by multiple mutations among hosts A–M, Q and R.</p

Large structural variation within hosts.

a<p>Underscoring indicates contigs that were present in the host-specific reference.</p