Pa REx: an open-source pipeline for the automated analysis of Pseudomonas aeruginosa resistomes from whole-genome sequences

ABSTRACT Whole-genome sequencing (WGS) has become a valuable tool for bacterial typing and resistome analysis. However, most existing antibiotic resistance databases and bioinformatics tools are not useful for P. aeruginosa resistome profiling as they fail to detect mutation-driven antibiotic resistance mechanisms. In addition, the increasing diversity of AmpC variants ( Pseudomonas- derived cephalosporinases [PDCs]) in recent years adds complexity to P. aeruginosa resistome profiling. To address these challenges, we have developed Pa REx, an open-source automated pipeline specifically designed for the analysis of P. aeruginosa mutation-driven (221 chromosomal genes) and horizontally acquired resistome from whole-genome sequences, along with the PDC analyzer web tool, a user-friendly platform that designates PDCs and detects resistance to novel antipseudomonal β-lactams. The utility of Pseudomonas aeruginosa Resistome Explorer ( Pa REx) was demonstrated through the analysis of 260 P. aeruginosa isolates, using its output to calculate five previously defined genotypic resistance scores, achieving results comparable to that of manual bioinformatic analysis. Likewise, the PDC analyzer web tool was validated with more than 30,000 global P. aeruginosa genomes, demonstrating its utility for PDC designation and detection of mutations conferring resistance to novel BL/BLI. Both Pa REx and the PDC analyzer web tool were shown to be user-friendly, accurate, and automated tools for resistome profiling in P. aeruginosa , enhancing current capabilities of existing tools. However, an ongoing refinement of these tools and its custom-built databases is needed to address remaining gaps and future challenges of whole-genome sequence-based resistance prediction.