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

Department of Biotechnology, Chemistry, and Environmental Engineering, Faculty of Engineering and Science, Aalborg University, Aalborg, Denmark.
Journal of clinical microbiology (Impact Factor: 3.99). 12/2011; 49(12):4352-5. DOI: 10.1128/JCM.06092-11
Source: PubMed


Patients suffering from cystic fibrosis (CF) develop chronic lung infection. In this study, we investigated the microorganisms
present in transplanted CF lungs (n = 5) by standard culturing and 16S rRNA gene analysis. A correspondence between culturing and the molecular methods was observed.
In conclusion, standard culturing seems reliable for the identification of the dominating pathogens.

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Available from: Per Halkjær Nielsen
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    • "The increased prevalence of A. xylosoxidans in the lungs of CF patients is believed to be related to several factors: The prolonged life expectancy, which leads to an extended evolutionary pressure on the existing microbiota of the CF lungs in response to heavy and continued antibiotic treatment is believed to be one of the underlying reasons that pathogens such as A. xylosoxidans are emerging in connection with CF lung infection [11,87,88]. Another factor is the increased accuracy with which Achromobacter xylosoxidans and other emerging Gram-negative pathogens of the CF lungs are identified [2,89]. "
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    ABSTRACT: Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.
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    • "The abundance of P. aeruginosa was found to vary considerably between the patients and also between the different samples from a single patient, which is to be expected based on our previous findings of a heterogeneous distribution of microcolonies. Samples from patients 1 and 5 generally did not contain quantifiable amounts of P. aeruginosa (not shown), which corresponded to our previous results using 16S rRNA gene analysis and culturing (Rudkjøbing et al., 2011). Only a single sample from patient 1 contained P. aeruginosa genes above the limit of detection, and the normalized results show that P. aeruginosa constituted a very small percentage of all bacteria present (Table 1). "
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    ABSTRACT: Patients suffering from cystic fibrosis (CF) develop chronic lung infections because of highly viscous mucus, where bacteria can form biofilms. In this study, we investigated the microorganisms present in the lungs of end-stage and non-end-stage patients using standard culturing techniques and molecular methods. Tissue and sputum samples (n = 34) from explanted lungs of five end-stage patients were examined along with routine expectorates (n = 15) from 13 patients with non-end-stage CF, representing earlier stages of chronic lung infections. Previously, using peptide nucleic acid (PNA) fluorescence in situ hybridization (FISH), we have shown that Pseudomonas aeruginosa was the sole pathogen in end-stage CF lungs (Pediatr Pulmonol 2009, 44: 547). In this study, this tendency was supported by the results of real-time PCR, confirming previous results obtained by standard culturing and 16S rRNA gene analysis (J Clin Microbiol 2011, 49: 4352). Conversely, the non-end-stage patients were found to harbor several species by culturing. PNA FISH confirmed heterogeneous microbiota and showed that the bacteria were located in monospecies aggregates with no apparent physical interaction between the different microcolonies. In conclusion, standard culturing identifies the dominating pathogens, which seem to reside in monospecies microcolonies. The possibility of signaling between the distinct microcolonies still has to be verified and elucidated.
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