Hospital Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

Figure 2

(a) Maximum likelihood SNP phylogenetic tree of forty ST-8 S. aureus genomes. Raw reads from genomes were mapped to a reference genome of Staphylococcus aureus USA300_FPR3757 (accession number CP000255, chromosome length 2,917,469 bp) to generate 3511 qualified SNPs. SNPs generated from each genome were concatenated to single alignment corresponding to position of the reference genome. The concatenated sequences were used for constructing a maximum likelihood tree using FastTree. The tree was visualized by using FigTree version 1.4.0. Of the forty genomes, 6 were from Tanzania (TZ) presented in red; 23 from United States (USA) presented in blue; 6 from Switzerland (CH) presented in pink; one from Japan (JP), Denmark (DK), and Australia (AU) presented in magenta, green, and orange, respectively. USA500_2395 strain genome was included and presented in aqua blue. (b) Bayesian temporal phylogenetic tree of the 40 MRSA genomes from Tanzania (TZ), United States (USA), Switzerland (CH), Japan (JP), Australia (AU), and Denmark (DK). A total of 3148 (90%) SNP sequences were used for reconstructing Bayesian temporal phylogenetic tree using Bayesian Evolutionary Analysis Sampling Trees (BEAST) version 1.8.3. USA300_FPR3757 (accession number CP000255, chromosome length 2,917,469 bp) was used as reference during SNP generation. The mutation rate estimated by BEAST was SNPs/site/year.

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