Analysis of the bacterial communities present in lungs of patients with cystic fibrosis from American and British centers

Abstract

The aim of this study was to determine whether geographical differences impact the composition of bacterial communities present in the airways of cystic fibrosis (CF) patients attending CF centers in the United States or United Kingdom. Thirty-eight patients were matched on the basis of clinical parameters into 19 pairs comprised of one U.S. and one United Kingdom patient. Analysis was performed to determine what, if any, bacterial correlates could be identified. Two culture-independent strategies were used: terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA clone sequencing. Overall, 73 different terminal restriction fragment lengths were detected, ranging from 2 to 10 for U.S. and 2 to 15 for United Kingdom patients. The statistical analysis of T-RFLP data indicated that patient pairing was successful and revealed substantial transatlantic similarities in the bacterial communities. A small number of bands was present in the vast majority of patients in both locations, indicating that these are species common to the CF lung. Clone sequence analysis also revealed that a number of species not traditionally associated with the CF lung were present in both sample groups. The species number per sample was similar, but differences in species presence were observed between sample groups. Cluster analysis revealed geographical differences in bacterial presence and relative species abundance. Overall, the U.S. samples showed tighter clustering with each other compared to that of United Kingdom samples, which may reflect the lower diversity detected in the U.S. sample group. The impact of cross-infection and biogeography is considered, and the implications for treating CF lung infections also are discussed.

FIG. 1.

Phylogenetic tree of clones from United Kingdom and U.S. patients. Clone sequences are clustered with the bacterial type strains to which they showed highest sequence similarity (minimum of 98% similarity for cluster membership). Clones were grouped into unique sequences; each labeled sequence indicates the patient it was isolated from and the number of redundant clone sequences it comprises. Clones isolated from United Kingdom patients are shown in green, clones isolated from U.S. patients are shown in blue.

FIG. 2.

Venn diagram grouping patients according to the presence of one or more of the four most commonly occurring T-RF band lengths in the sample set. Circles correspond to T-RF band lengths; patients within one or more circles shared these particular T-RF band lengths. T-RF band lengths corresponded to the following organisms: 103 bases, Prevotella spp.; 155 bases, P. aeruginosa; 565 bases, Pseudomonas/Bordetella/Achromobacter spp.; 580 bases, not assigned.

FIG. 3.

Cluster diagram of the Raup and Crick similarity coefficient assessment of United Kingdom and U.S. patient T-RFLP data.

FIG. 4.

Cluster diagram for the Morisita similarity coefficient assessment of United Kingdom and U.S. patient T-RFLP data.