2.3 Pseudomonas aeruginosa WGS and analysis
Whole genome sequencing (WGS) of the PCR confirmed P. aeruginosastudy isolates was performed using the Illumina NextSeq 2000 (Illumina
Inc., USA) instrument. Multiplexed, paired-end libraries (2 x 150bp)
were prepared using the Illumina DNA Prep kit (Illumina, San Diego,
USA), followed by sequencing at 100x coverage, according to the
manufacturer’s instructions. The raw paired-end P. aeruginosasequencing reads were processed using the Jekesa pipeline v1.0 and using
tools and methodology that included species identification and
multilocus sequence typing (MLST) as previously
outlined20,21. Genomic antibiotic resistance
(resistome) determinants in the study strains were characterised using a
combination of tools including the
Comprehensive Antibiotic
Resistance Database (CARD) v3.2.222 and
ResFinder23.