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The Airway Microbiome in Cystic Fibrosis: Challenges for Therapy

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The Airway Microbiome in Cystic Fibrosis: Challenges for Therapy Review The airway microbiome in cystic fibrosis: challenges for therapy Although cystic fibrosis pulmonary infection is polymicrobial, routine laboratory methods focus on the detection of a small number of known pathogens. Recently, the use of strict anaerobic culture techniques and molecular technologies have identified other potential pathogens including anaerobic bacteria. Determining the role of all bacteria in a complex bacterial community and how they interact is extremely important; individual bacteria may affect how the community develops, possess virulence factors, produce quorum-sensing signals, stimulate an immune response or transfer antibiotic resistance genes, which could all contribute to disease progression. There are many challenges to managing cystic fibrosis lung infection but as knowledge about the airway microbiome continues to increase, this may lead to advances in the therapeutic management of the disease. 1,2 KEYWORDS: anaerobic bacteria n antibiotics n cystic fibrosis n microbiome Laura J Gillanders , n polymicrobial J Stuart Elborn1,3, Deirdre F Gilpin1,2, Cystic fibrosis pulmonary infection: why some CF patients improve clinically even T Schneiders3 a polymicrobial disease though they harbor P. aeruginosa isolates that & Michael M Tunney†1,2 Over the past 50 years, life expectancy for cystic are resistant to the antibiotics administered [18]. 1CF & Airways Microbiology Research fibrosis (CF) patients has increased dramatically It is vital to determine what bacteria con- Group, Queen’s University, Belfast, UK, with one of the most important interventions tribute directly to the deterioration in clinical 2School of Pharmacy, Queen’s University Belfast, UK being antibiotic treatment directed against pul- status of CF patients; individual community 3Centre for Infection & Immunity, monary infection. Antibiotic regimens have been members may not be pathogenic but when Queen’s University, Belfast, UK †Author for correspondence: developed for prophylaxis, eradication of initial part of an array of microorganisms they may Tel.: +44 289 097 2087 infection and control of chronic infection and interact and contribute to the overall burden of Fax: +44 289 024 7794 [email protected] exacerbations [201]. Until recently, a small num- pathogenesis in CF. Furthermore, studying the ber of bacteria, such as Pseudomonas aeruginosa, airway microbiome in CF and how it changes Staphylococcus aureus and Burkholderia cepa- over time is important to determine what is usu- cia complex were implicated as the predomi- ally present in the CF lung and what contributes nant pathogens in CF pulmonary disease. For to maintenance of clinical stability for the CF example, between the ages of 24 and 31 years patient. Better understanding of the microbiome approximately 65% of CF patients are chroni- in the CF lung and how it changes may enable cally infected with P. aeruginosa [201]. As a result, t reatment to be optimized. routine diagnostic laboratories focused on detec- tion of these well-characterized CF pathogens [1]. Characterization of the CF ‘cultured’ However, evidence now indicates that the bac- microbiome terial community within the CF lung is highly Routine culture focuses on detection of the diverse with aerobes, facultative and obligate known CF-associated pathogens. However, by anaerobes, including oropharyngeal flora, all using quantitative aerobic and anaerobic culture, present [2–14]. It has also been proposed that the studies have attempted to detect the entire cul- combination of species colonizing the lungs dif- ture microbiome [5,8]. The accurate identification fers between individuals [3,11,12]. CF lung infec- of all CF pathogens is important to guide treat- tion is not only chronic but it is also polymi- ment of the infection and understand the occur- crobial. The presence of bacteria, not identified rence and distribution of the bacteria. There are by culture methods, in a complex polymicrobial a number of methods available that can identify community may be a plausible explanation as to bacteria and these can be broadly categorized why some CF patients fail to respond clinically to into two groups: standard antibiotic therapy whilst others possess Phenotypic identification lung inflammation in the absence of the known pathogens [15–17]. In addition, it may also explain Molecular identification 10.2217/THY.11.81 © 2011 Future Medicine Ltd Therapy (2011) 8(6), 645–660 ISSN 1475-0708 645 Review Gillanders, Elborn, Gilpin, Schneiders & Tunney The airway microbiome in cystic fibrosis: challenges for therapy Review nPhenotypic identification directly detect bacteria in clinical samples, such Phenotypic identification is dependent on isola- as sputum (Table 1). This use of culture-inde- tion of bacteria on media using the optimum pendent approaches in which DNA is extracted growth conditions to obtain a pure culture. directly from patient samples, may result in Following growth, colony morphology can be detection of unculturable bacteria. observed, Gram staining performed and various Although the success of molecular methods for biochemical and physiological properties inves- bacterial detection has been well documented, tigated. Commercial kits and automated tech- traditional phenotypic methods using cultured nologies have been developed for standardization bacteria remain fundamentally important, for whilst increasing the ease and reducing the time example antimicrobial susceptibility testing to that is required to carry out these identification determine appropriate treatment of an infection. tests. Furthermore, pure cultures are essential Therefore, it is likely that a combination of tra- for antibiotic susceptibility testing, to guide ditional culture and molecular approaches will selection of the most appropriate treatment for be more frequently used in the future to detect the patient. Clinical microbiology laboratories and identify all CF pathogens. that employ phenotypic identification of bacte- ria encounter several problems when a disease is Characterization of the CF polymicrobial including: microbiome Time required to culture and identify all the Various culture-independent molecular bacteria; approaches have been developed to enable char- acterization of bacterial diversity and identifica- Media currently in use may not support tion based on DNA extracted directly from the growth of all potential pathogens with media clinical sample. Both cultivation and molecular continually needing to be developed; characterization techniques and analysis can be Organisms capable of rapid growth in vitro labor intensive and time consuming. Before the such as P. aeruginosa can mask growth of, or latter could be used in routine clinical practice, out-compete other less abundant bacteria on laboratories would need to acquire the necessary the same plate [19]. Certain bacteria are also equipment and expertise. difficult to identify with newly emerging bac- teria absent in databases associated with com- nMolecular characterization mercial identification kits. Furthermore, rou- techniques used in CF studies tine culture only enables a semi-quantitative A single study has reported on the use of tempo- estimation of bacterial load [12]. ral temperature gradient gel electrophoresis [14]. As an alternative to conventional phenotypic Temporal temperature gradient gel electrophore- identification, matrix-assisted laser desorption sis is a technique based on electrophoretic sepa- ionization time-of-flight mass spectrometry has ration of hypervariable regions, such as V3 or been developed to identify bacteria based on pro- V6 variable regions of the 16S rRNA genes [14]. duction of a unique spectral fingerprint. This Following size separation of the DNA mixture, spectroscopic technique has been used to iden- the bacterial species are identified by sequenc- tify bacteria cultured from CF respiratory sam- ing [14]. This method is not ideal for routine ples including the nonfermenting Gram-negative use as it is expensive, labor intensive and slow. bacilli such as P. aeruginosa, Stenotrophomonas Nevertheless, is more sensitive than conventional maltophilia, Achromobacter xylosoxidans and microbiological culture [14]. Burkholderia cenocepacia [20–22] and to help iden- A more popular approach has involved termi- tify Prevotella spp. [23]. Although, matrix-assisted nal restriction fragment length polymorphism laser desorption ionization time-of-flight mass (T-RFLP) and this has provided a useful tool spectrometry has been reported as being a rapid to explore the bacterial diversity in CF samples and reproducible method, novel bacteria will [3,4,11–13]. This PCR-based fingerprinting tech- possess a spectrum that will not match those nique involves amplification of the 16S rRNA deposited in the database [21,22]. Nevertheless, it gene followed by digestion of the PCR product has been suggested that expanding the reference with specific restriction endonucleases [11]. A spectra should be straightforward [21]. T-RFLP profile is generated after the gene frag- ments are separated by gel electrophoresis [11]. nMolecular identification The length of the terminal restriction fragment Molecular methods have been used to identify can then be assigned to a bacterial species [11]. An bacteria grown as pure cultures and also to advantage of T-RFLP is that the mixed bacterial 646 Therapy (2011) 8(6) future science group Review Gillanders, Elborn, Gilpin, Schneiders & Tunney The airway microbiome in cystic fibrosis: challenges for therapy Review
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