Comparative genomics of clinical isolates of Pseudomonas aeruginosa from cystic fibrosis patients in Mexico

Pseudomonas aeruginosa ( P. aeruginosa ) is the primary pathogen responsible for morbidity and mortality in patients with cystic fibrosis (CF). Its genomic plasticity and constant selective pressure from antimicrobial treatments have favored the emergence of multidrug-resistant clones. This study conducted a comparative genomic analysis of 41 P. aeruginosa isolated from pediatric patients with CF in Mexico from 2015 to 2024, with the aim of characterizing their evolutionary dynamics, resistome, and virulome.

Whole-genome sequencing (MGI, Illumina, and PacBio platforms) was used, with de novo assemblies performed using Unicycler v0.4.8 on the BV-BRC platform. The databases used for the resistome were CARD and NDARO, and for the virulome, VFDB. Phylogenetic reconstruction was based on core-genome alignments generated with Roary v3.13.0, with maximum likelihood reconstruction performed in IQ-TREE v2.1.2. The statistical significance of the segregation of resistance and virulence patterns was evaluated using PERMANOVA analysis.

The results revealed a significant clonal prevalence of sequence types (ST) 307 and ST 167. Phylogenomic analysis grouped the isolates into three main clades; Clade 1 stood out for having the highest resistance gene load (mean of 75 genes/genome), establishing itself as the main reservoir of multidrug-resistant profiles. Genotype-phenotype concordance reached 65.5% overall, with high accuracy for aminoglycosides (87.8%) and fluoroquinolones (82.9%). Furthermore, virulome analysis identified 67 distinct patterns that were significantly segregated among the clades (PERMANOVA: R ² =0.31, p =0.001). These findings demonstrate that the evolution of P. aeruginosa lineages in the pediatric clinical setting involves parallel and coordinated adaptations in both their resistance potential and their virulence arsenal.

This study underscores the need to adopt a multidisciplinary approach to the clinical management of chronic P. aeruginosa infections in pediatric patients. The persistence of extensively drug-resistant (XDR) strains calls for the integration of genomic surveillance and functional diagnostics, as well as the search for therapeutic alternatives for the clinical management of patients with cystic fibrosis.

Impact statement

This study identifies high-risk, circulating P. aeruginosa lineages in pediatric patients with cystic fibrosis in Mexico. By demonstrating the parallel evolution of the resistome and virulome, we provide a genomic framework that enhances our understanding of chronic infection persistence. These findings offer a critical foundation for optimizing the surveillance of circulating strains and advancing therapeutic strategies to improve patient outcomes.

Data summary

All genomic data generated in this study have been deposited in the National Center for Biotechnology Information (NCBI) database under the BioProject accession number PRJNA1439432. Specific accession numbers for each isolate are listed in Table S1 (Supplementary Data). The authors confirm that all supporting data, code, and protocols have been provided within the article or through supplementary data files.

Repositories

All genome assemblies and raw sequencing data have been deposited in the NCBI BioProject database under accession number PRJNA1439432. Individual isolate accession numbers are listed in Table S1.