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.