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.

True Microbiota Involved in Chronic Lung Infection of Cystic Fibrosis Patients Found by Culturing and 16S rRNA Gene Analysis

“…In the CF centers in Denmark, an intensive antibiotic treatment strategy has been shown to prolong the life expectancy of the CF patients (10). In recent studies, the chronically infected lungs of CF patients have been observed to harbor multiple species (19,21). However, the strict antibiotic strategy employed in Denmark has led to only a small variety of microorganisms being found in the lungs of CF patients, compared to what is found in other studies (8,18,23).…”

Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia

“…Prior approaches to bacterial identification by DNA sequencing have included fluorescent Sanger sequencing of hundreds of small variable regions of 16S ribosomal amplimer clones (19,20), length heterogeneity (LH) PCR for 16S ribosomal variable regions (21), restriction fragment polymorphisms in 16S (19,21), arrays with bacterium-specific probes, such as PhyloChip (22,23), and early applications of NGS (24,25). These methods have been applied to various clinical situations, such as the microbiome of suboptimally controlled asthma (22), cystic fibrosis (19,21), chronic obstructive pulmonary disease (COPD) (24,26,27), bronchiectasis (28), pleurisy (20), forensic assessment of drowning (25), and intubated patients (23). These studies have revealed unexpectedly large numbers of bacterial genera in patients with clinical illnesses and in healthy individuals (29,30).…”

Caracterización molecular de bacterias patógenas de las vías respiratorias de pacientes peruanos con fibrosis quística

“…En uno de los pocos estudios para evaluar las comparaciones geográficas, muestras de esputo de 19 pacientes con FQ en un centro en Reino Unido fueron comparados con las muestras obtenidas de 19 pacientes de un hospital de Estados Unidos (26) . Las diferencias en las especies entre los dos grupos mostraron diferencias significativas en la composición, abundancia y diversidad.…”

“…Por otro lado, la proteómica, basada en espectrometría de doble masa MALDI TOF/TOF (MS/MS), se está desarrollando rápidamente en investigaciones médicas, particularmente, comparando el proteoma de individuos sanos y enfermos (26) . En este estudio utilizamos esta técnica con el objetivo de obtener péptidos a partir de bacterias e identificar proteínas.…”