The emergence of virulent Pseudomonas aeruginosa clones is a threat to cystic fibrosis (CF) patients globally. Characterization of clonal P. aeruginosa strains is critical for an understanding of its clinical impact and developing strategies to meet this problem. Two clonal strains (AES-1 and AES-2) are circulating within CF centers in eastern Australia. In this study, phenotypic characteristics of 43 (14 AES-1, 5 AES-2, and 24 nonclonal) P. aeruginosa isolates were compared to gain insight into the properties of clonal strains. All 43 isolates produced bands of the predicted size in PCRs for vfr, rhlI, rhlR, lasA, lasB, aprA, rhlAB, and exoS genes; 42 were positive for lasI and lasR, and none had exoU. Thirty-seven (86%) isolates were positive in total protease assays; on zymography, 24 (56%) produced elastase/staphylolysin and 22 (51%) produced alkaline protease. Clonal isolates were more likely than nonclonal isolates to be positive for total proteases (P ؍ 0.02), to show elastase and alkaline protease activity by zymography (P ؍ 0.04 and P ؍ 0.01, respectively), and to show elastase activity by the elastin-Congo red assay (P ؍ 0.04). There were no other associations with genotype. Overall, increasing patient age was associated with decreasing elastase activity (P ؍ 0.03). Thirty-two (74%) isolates had at least one N-acylhomoserine lactone (AHL) by thin-layer chromatography. rhl-associated AHL detection was associated with the production and level of total protease and elastase activity (all P < 0.01). Thirty-three (77%) isolates were positive for ExoS by Western blot analysis, 35 (81%) produced rhamnolipids, and 34 (79%) showed chitinase activity. Findings suggest that protease activity during chronic infection may contribute to the transmissibility or virulence of these clonal strains.Pseudomonas aeruginosa lung infection is a major determinant of morbidity and mortality in cystic fibrosis (CF) patients (16). The pathogenesis of P. aeruginosa infection depends on multiple cell-associated and extracellular virulence factors including proteases (elastase [LasB], alkaline protease [AprA], and staphylolysin [LasA]), hemolysins (rhamnolipids), and toxins such as exoenzyme S (ExoS) and exotoxin A (13). Proteases contribute to pathogenesis in the lung through the induction of tissue necrosis and inflammation, destruction of surface receptors on neutrophils resulting in the inhibition of chemotaxis, phagocytosis, and the oxidative burst and degradation of surfactant proteins (27, 32).Many P. aeruginosa virulence factors, including the proteases, are regulated by cell-to-cell communication systems that rely on diffusible N-acylhomoserine lactones (AHLs) to monitor population size in a process known as "quorum sensing" (QS) (7, 31). P. aeruginosa has two AHL-regulated circuits: las, consisting of the transcriptional activator LasR and the AHL synthase LasI, which directs the synthesis of N-(3-oxododecanoyl)-L-homoserine lactone (OdDHL), and rhl, consisting of RhlR and RhlI, which directs the synthesis of N-...