2.4 Phylogenetic comparison of global and study P. aeruginosa AUST-03 strains
A total of 61 P. aeruginosa ST242 genomes originating from human specimens were retrieved from the National Center for Biotechnology Information (NCBI) using the NCBI datasets tool v15.12.024 and were analysed together with genome assemblies from our study strains. Briefly, whole genome alignments were performed using scapper25 and P. aeruginosaZw92 strain was used as a reference. Recombinant regions were removed using Gubbins v3.2.126 and variable sites were obtained using snp-sites v2.5.127. Pairwise SNP distances were calculated using snp-dist v0.8.227 and a normalized pairwise SNP distance matrix was used as input for the cluster analysis using the R software environment v4.2.128. Assignment of core single nucleotide polymorphism (SNP) clusters was achieved by a combination of K-means clustering and custom functions written in R using a silhouette score and SNP cut-off of 0.5 and 20, respectively. Visualisation of cluster heat maps was performed using the ComplexHeatmap package v.14.0.29