Claudia Antonella Colque

Antibiotic resistance is a major global health threat. While its role in reducing drug susceptibility is well established, the broader consequences of resistance mutations on bacterial physiology and phenotype during infection remain poorly understood. Carbapenem-resistant Pseudomonas aeruginosa is considered among the highest-priority bacterial threats, with resistance commonly driven by loss-of-function mutations in the carbapenem uptake porin OprD. Here we show that such mutations can arise in clinical isolates even without prior carbapenem treatment, suggesting that their biological impact during infection is not limited to antibiotic resistance. Consistent with this, we found that oprD mutants exhibit enhanced early attachment to and translocation across airway epithelial barriers in an in vitro human infection model, an effect observed across strains with distinct clinical genomic backgrounds and infection dynamics. Our findings indicate that loss of OprD alters the bacterial outer membrane charge and reduces mucus entrapment, thereby facilitating epithelial barrier colonization. Overall, these results illustrate how antibiotic resistance mutations can directly shape infection dynamics, extending their impact well beyond antimicrobial susceptibility.

Background: Air-liquid interface (ALI) cell culture systems have improved the study of host-microbe interactions in respiratory infections. However, most ALI models lack immune components, limiting their ability to capture epithelial-immune crosstalk. To address this, we developed a dual-cell ALI model incorporating human peripheral blood monocyte-derived macrophages beneath differentiated airway epithelial cells. Methodology: Macrophages were seeded on the basolateral side of transwell inserts using fibronectin coating. Model characterization included transepithelial electrical resistance (TEER) to assess epithelial barrier integrity, IL-8 secretion as a marker of epithelial inflammatory signaling, and confocal microscopy to evaluate cellular architecture before and after infection. Mono-and dual-cell cultures were infected with the laboratory strain Pseudomonas aeruginosa PAO1. Results: Macrophages adhered stably to the basolateral surface without compromising epithelial barrier integrity. Following infection, IL-8 secretion was elevated in epithelial monocultures compared to dual-cell cultures, suggesting early immune modulation in the presence of macrophages. While overall bacterial burden was comparable, confocal imaging revealed clustered bacterial growth in monocultures and a more dispersed spatial distribution in dual-cell cultures. Conclusions: This dual-cell ALI model enables investigation of early epithelial-immune interactions, inflammatory modulation, and bacterial colonization dynamics during airway infection. The system provides a versatile and human-relevant platform for studying respiratory host-pathogen interactions.

Pseudomonas aeruginosa is the leading cause of death in cystic fibrosis (CF) patients, yet the genetic mechanisms driving its fitness in the host remain poorly defined. Previously collected transcriptomic data of clinical samples showed that expression of the gene PA14_RS04555 (sirB2) is stimulated in the CF lung environment. In this work, we show that sirB2 is regulated by the global transcriptional regulators Vfr and AmrZ. Loss of sirB2 markedly enhanced P. aeruginosa pathogenicity, increasing virulence in Galleria mellonella, and promoting bacterial translocation and biofilm formation in a differentiated airway epithelial infection model. Deletion of sirB2 triggered the emergence of biofilm-proficient rugose small colony variants (RSCVs), driven by elevated c-di-GMP and increased Pel polysaccharide production when cultures were grown in static conditions. The RSCV phenotype depends on suppressor mutations in the wsp operon, possibly as a response to redox imbalance caused by the lack of sirB2 under oxygen-limited conditions. Indeed, the sirB2 mutant exhibited impaired fitness during anaerobic respiration when nitrate was the sole electron acceptor, in a manner independent of the ubiquinone pool. Our findings show that sirB2 inactivation promotes RSCV emergence and identify sirB2 as a novel genetic determinant of metabolic fitness under host-relevant conditions, thereby underscoring the role of redox balance in chronic CF infections.

Antibiotic resistance is a major global health threat. While its role in reducing drug susceptibility is well established, the broader consequences of resistance mutations on bacterial physiology and behavior during infection remain poorly understood. Carbapenem-resistant Pseudomonas aeruginosa is considered among the highest- priority bacterial threats, with resistance commonly driven by loss-of-function mutations in the carbapenem uptake porin OprD. Here we show that such mutations can arise in clinical isolates even without prior carbapenem treatment, indicating that their effects during infection extend beyond antibiotic resistance. Consistent with this, we found that oprD mutants exhibit enhanced early attachment to and translocation across airway epithelial barriers in infection models, an effect maintained across strains with distinct clinical genomic backgrounds and infection dynamics. Our findings indicate that loss of OprD alters the bacterial outer membrane charge and reduces mucus entrapment, thereby facilitating epithelial barrier colonization. Overall, these results illustrate how antibiotic resistance mutations can directly shape infection dynamics, extending their impact well beyond antimicrobial susceptibility.

Persistent bacterial infections constitute an increasing health problem, often associated with antibiotic resistance. However, despite extensive antibiotic treatment, Pseudomonas aeruginosa persists for decades in people with cystic fibrosis (pwCF), remaining susceptible. Host-pathogen interactions during infection may, therefore, be a major contributing factor to treatment failure. Using an infection model based on human airway epithelial cells, cultured at the air-liquid interface (ALI), we simulated the infection process of P. aeruginosa to investigate the colonization dynamics and virulence potential during infection in ALI models from non-CF and CF donors, and the BCi-NS1.1 cell line. Infections by reference strains and clinical isolates from pwCF revealed four infection clusters based on virulence, epithelial damage, and localization within the epithelium, in a strain-specific manner regardless of the type of ALI model or clonal lineage. Modulator treatment to restore CFTR channel function did not change infection patterns in CF ALI models. Dual RNA-seq revealed that bacterial colonization of ALI models significantly upregulated host inflammatory pathways, dependent on the strain’s virulence. Simultaneously, while bacterial gene expression was similar in non-CF and BCi-NS1.1 ALI models, CF models promoted differential regulation in a type III secretion mutant. Altogether, our results profile key infection dynamics occurring in pwCF and provide ground knowledge on the interplay between the airway epithelium and P. aeruginosa .

Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic and changing environments, the evolutionary processes controlling bacterial adaptation are difficult to monitor. Here, we follow 9 people with cystic fibrosis chronically infected with Pseudomonas aeruginosa, as a proxy for bacterial adaptation. We identify and describe the bacterial changes and evolution occurring between 15 and 35 yr of within-host evolution. We combine whole-genome sequencing, RNA sequencing, and metabolomics and compare the evolutionary trajectories directed by the adaptation of 4 different P. aeruginosa lineages to the lung. Our data suggest divergent evolution at the genomic level for most of the genes, with signs of convergent evolution with respect to the acquisition of mutations in regulatory genes, which drive the transcriptional and metabolomic program at late time of evolution. Metabolomics further confirmed convergent adaptive phenotypic evolution as documented by the reduction of the quorum-sensing molecules acyl-homoserine lactone, phenazines, and rhamnolipids (except for quinolones). The modulation of the quorum-sensing repertoire suggests that similar selective forces characterize at late times of evolution independent of the patient. Collectively, our data suggest that similar environments and similar P. aeruginosa populations in the patients at prolonged time of infection are associated with an overall reduction of virulence-associated features and phenotypic convergence.

Polymicrobial airway infections and detrimental inflammation characterize patients with cystic fibrosis (CF), a disease with heterogeneous clinical outcomes. How the overall immune response is affected in CF, its relationships with the lung microbiome, and the source of clinical heterogeneity are unclear. Our work identifies a specific CF immune profile characterized by widespread hyperactivation, enrichment of CD35 ⁺ /CD49d ⁺ neutrophils, and reduction in dendritic cells. Further, our data indicate signs of immune dysregulation due to alterations in Tregs homeostasis, which, together with an impaired B-cell immune function, are linked with patients’ lung function and are potentially the source of clinical heterogeneity. Indeed, clinical heterogeneity does not stem from a specific lung microbiome; yet, commensal bacteria correlate with higher concentrations of circulating immune cells and lower expression of leukocyte activation markers, a condition reversed by pathogenic microorganisms. Overall, our findings provide unique markers and immunomodulatory targets for improving the treatment of CF.

Antibiotics are becoming increasingly ineffective to treat bacterial infections. It has been consequently predicted that infectious diseases will become the biggest challenge to human health in the near future. Pseudomonas aeruginosa is considered a paradigm in antimicrobial resistance as it exploits intrinsic and acquired resistance mechanisms to resist virtually all antibiotics known.