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