Computational protocol: MRSA Transmission on a Neonatal Intensive Care Unit: Epidemiological and Genome-Based Phylogenetic Analyses

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Protocol publication

[…] Staphylococcal colonies on agar plates were randomly selected for analysis. Following DNA extraction, multiplexed sequencing of genomic DNA from S. aureus isolates was performed on an Illumina GAIIx sequencer, providing 100-fold average coverage. Single-nucleotide polymorphisms (SNPs) were identified by mapping paired-end sequencing reads against the genome sequence from a related ST22 isolate and subsequently verified through dedicated PCRs and capillary sequencing. An alignment of SNPs in the non-repetitive core genome was used to reconstruct the isolates’ phylogeny by applying PhyML 3.0.1 and to calculate evolutionary rates and divergence times with the BEAST software (http://beast.bio.ed.ac.uk/) . Results were virtually independent from clock models (strict, relaxed) and tree priors (constant population size, exponential growth, Bayesian skyline). Phylogenetic affiliations of six additional isolates whose genomes had not been sequenced were determined by sequencing informative SNPs (). […]

Pipeline specifications

Software tools PhyML, BEAST
Application Phylogenetics
Organisms Staphylococcus aureus, Homo sapiens
Diseases Staphylococcal Infections