Mucoid Pseudomonas aeruginosa isolates maintain the biofilm formation capacity and the gene expression profiles during the chronic lung infection of CF patients BAOLERI LEE, 1,4 CHARLOTTE K. SCHJERLING, 2 NIKOLAI KIRKBY, 3 NADINE HOFFMANN, 1 REHANNAH BORUP, 2 SØREN MOLIN, 4 NIELS HØIBY 1,3 and OANA CIOFU 1 1 Department of International Health, Immunology and Microbiology, Panum Institute, University of Copenhagen; 2 Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen; 3 Department of Clinical Microbiology, Rigshospitalet, University of Copenhagen; and 4 Center for System Microbiology, Technical University of Denmark, Lyngby, Denmark Lee B, Schjerling CK, Kirkby N, Hoffmann N, Borup R, Molin S, Høiby N, Ciofu O. Mucoid Pseudo- monas aeruginosa isolates maintain the biofilm formation capacity and the gene expression profiles during the chronic lung infection of CF patients. APMIS 2011; 119: 263–74. Phenotypic and genotypic diversifications of Pseudomonas aeruginosa in the airways of patients with cystic fibrosis (CF) promote long-term survival of bacteria during chronic lung infection. Twelve clon- ally related, sequential mucoid and non-mucoid paired P. aeruginosa isolates obtained from three Danish CF patients were investigated. The in vitro biofilm formation capacity was studied under static and flow through conditions and the global gene expression profiles were investigated by Affymetrix GeneChip. Regulatory genes of alginate production and quorum sensing (QS) system were sequenced and measurements of the alginate production and the detection of the QS signal molecules were per- formed. Comparisons of mucoid and non-mucoid isolates from early and late stages of the infection showed that the mucoid phenotype maintained over a decade the capacity to form in vitro biofilm and showed an unaltered transcriptional profile, whereas substantial alterations in the transcriptional pro- files and loss of the capacity to form in vitro biofilms were observed in corresponding isolates of the non-mucoid phenotype. The conserved gene expression pattern in the mucoid isolates vs the diversity of changes in non-mucoid isolates observed in this particular P. aeruginosa clone reflects different adap- tation strategies used by these two phenotypes in the different niches of the CF lung environment. Key words: Cystic fibrosis; P. aeruginosa; mucoidy; gene expression; biofilm. Oana Ciofu, Department of International Health, Immunology and Microbiology, University of Copenhagen, Panum Institute, 24.1, Blegdamsvej 3, 2200N Copenhagen, Denmark. e-mail: ociofu@ sund.ku.dk Chronic infection with the opportunistic patho- gen Pseudomonas aeruginosa is the primary cause of morbidity and mortality in patients with cystic fibrosis (CF) (1, 2). Most patients acquire P. aeruginosa early in their lives and initial colonization is typically caused by environmental strains displaying the wild-type phenotypes associated with this species (3, 4). Genotyping of longitudinal P. aeruginosa iso- lates from CF patients revealed that individual patients often carry during the chronic infection a single bacterial clone (5, 6), which has to adapt to multiple selective pressures imposed by the prolonged antibiotic treatment, host immune Received 1 January 2011. Accepted 17 January 2011 APMIS 119: 263–274 Ó 2011 The Authors APMIS Ó 2011 APMIS DOI 10.1111/j.1600-0463.2011.02726.x 263