DNA-Seq of P. aeruginosa from human sample
Total DNA was extracted from all isolates using a QIAamp UCP Pathogen mini kit (Qiagen, Dsseldorf, Germany) according to the manufacturer's protocol. Briefly, from each isolates genomic DNA was purified, and later quantified using a Qubit dsDNA high sensitivity assay (ThermoFisher, Waltham, USA). Libraries were prepared using Nextera XT and sequenced via (2x 250 bp) v2 500 cycle, MiSeq (Illumina Inc., USA). The raw sequences were subjected to a quality check and analysis using our in-house pipeline, BacPipe (Xavier et al., 2020). Briefly, the reads were quality assessed, trimmed, followed by de novo assembly (SPAdes), typing (MLST), annotation (Prokka), and resistance gene prediction (ResFinder and CARD). In order to determine the incompatibility type of the plasmids present in our isolates, the isolates were run through Plasmid Finder (Carattoli et al., 2014). Insertion element (IS) families were analyzed through IS Finder  (Siguier, 2006). Genetic characterization and chromosomal modifications were assessed using CLC Genomics workbench v9.5.3 (CLCbio, Denmark).