Characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16S ribosomal DNA terminal restriction fragment length polymorphism profiling

Journal of Clinical Microbiology

Volumn 42, Issue 11, 2004, Pages 5176-5183

  Rogers, G B ^a,b   Carroll, M P ^b   Serisier, D J ^b   Hockey, P M ^b   Jones, G ^b   Bruce, K D ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY HOSPITAL SOUTHAMPTON NHS FOUNDATION TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S;

ADULT; ANAEROBIC METABOLISM; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GROWTH; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; CLINICAL ARTICLE; CYSTIC FIBROSIS; HUMAN; LUNG FUNCTION; LUNG INFECTION; MOLECULAR CLONING; MORTALITY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SPECIES; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM PROFILING;

BACTERIA; BACTERIAL INFECTIONS; CYSTIC FIBROSIS; DNA, RIBOSOMAL; ECOSYSTEM; HUMANS; LUNG DISEASES; MOLECULAR SEQUENCE DATA; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPUTUM; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 8644256676     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.11.5176-5183.2004     Document Type: Article

References (41)

1. Anderson, S. G. E., A. Zomorodipour, H. H. Winkler, and C. G. Kurland. 1995. Unusual organization of the rRNA genes in Rickettsia prowazekii. J. Bacteriol. 177:4171-4175.
2. Baron, E. J., P. J. Summanen, J. Downes, M. C. Roberts, H. Wexler, and S. M. Finegold. 1989. Bilophila wadsorthia, gen. nov. and sp. nov., a unique Gram-negative anaerobic rod recovered from appendicitis specimens and human faeces. J. Gen. Microbiol. 135:3405-3411.
3. Bercovier, H., O. Kafri, and S. Sela. 1986. Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome. Biochem. Biophys. Res. Commun. 136:1136-1141.
4. Bonsell, S. Isolated knee joint infection with Neisseria meningitidis. Orthopedics 25:537-539.
5. Brook, I. 1989. Bacteriology of chronic maxillary sinusitis in adults. Ann. Otol. Rhinol. Laryngol. 98:426-428.
6. Bruce, K. D., and M. R. Hughes. 2000. Terminal restriction fragment length polymorphism monitoring of genes amplified directly from bacterial communities in soils and sediments. Mol. Biotechnol. 16:261-269.
7. Clement, B. G., L. E. Kehl, K. L. DeBord, and C. L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31:135-142.
8. Coenye, T., J. Goris, T. Spilker, P. Vandamme, and J. J. LiPuma. 2002. Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of Inquilinus limosus gen. nov., sp. nov. J. Clin. Microbiol. 40:2062-2069.
9. Coenye, T., P. Vandamme, and J. J. LiPuma. 2002. Infection by Ralstonia pickettii in cystic fibrosis patients: identification of R. Pickettii and R. mannitolilytica by polymerase chain reaction. Emerg. Infect. Dis. 8:692-696.
10. Conese, M., and B. M. Assael. 2001. Bacterial infections and inflammation in the lungs of cystic fibrosis patients. Pediatr. Infect. Dis. J. 20:207-213.
11. DeKoster, J. A., and P. S. Thorne. 1995. Bioaerosol concentrations in non-compliant, compliant, and intervention homes in the Midwest. Am. Ind. Hyg. Assoc. J. 56:573-580.
12. Duan, K., C. Dammel, J. Stein, H. Rabin, M. G. Surette. 2003. Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication. Mol. Microbiol. 50:1477-1491.
13. Dunbar, J., S. White, and L. J. Forney. 1997. Genetic diversity through the looking glass: effect of enrichment bias. Appl. Environ. Microbiol. 63:1326-1331.
14. Filler, G., J. H. Ehrich, E. Strauch, and L. Beutin. 2000. Acute renal failure in an infant associated with cytotoxic Aeromonas sobna isolated from patient's stool and from aquarium water as suspected source of infection. J. Clin. Microbiol. 38:469-470.
15. Gilljam, H., A. S. Malmborg, and B. Strandvik. 1986. Conformity of bacterial growth in sputum and contamination free endobronchial samples in patients with cystic fibrosis. Thorax 41:641-646.
16. Health Protection Agency. 2003. Standard operating procedure 8. Investigation of sputum. Issue 5.1. Standards Unit, Evaluations and Standards Laboratory, Specialist and Reference Microbiology Division, Health Protection Agency, London, United Kingdom.
17. Hiraishi, A., M. Iwasaki, and H. Shinjo. 2000. Terminal restriction pattern analysis of 16S rRNA genes for the characterization of bacterial communities of activated sludge. J. Biosci. Bioeng. 90:148-156.
18. http://rdp.cme.msu.edu/html/.
19. http://www.ncbi.nlm.nih.gov/blast/.
20. Jackson, R., and P. B. Pencharz. 2003. Cystic fibrosis. Best Pract. Res. Clin. Gastroenterol. 17:213-235.
21. Kasten, M. J., J. E. Rosenblatt, and D. R. Gustafson. 1992. Bilophila wadsworthia bacteraemia in two patients with hepatic abscesses. J. Clin. Microbiol. 30:2502-2503.
22. Konstan, M. W., and M. Berger. 1993. Infection and inflammation of the lung in cystic fibrosis, p. 219-276. In P. B. Davis (ed.), Lung biology in health and disease, vol. 64. Cystic fibrosis. Marcel Dekker. New York, N.Y.
23. Konstan, M. W., K. A. Hillard, T. M. Norwell, and M. Berger. 1994. Bronchoalveolar lavage findings in cystic fibrosis patients with stable, clinically mild lung disease suggests ongoing infection and inflammation. Am. J. Respir. Crit. Care Med. 150:448-454.
24. Liu, W., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
25. Magurran, A. E. 1988. Ecological diversity and its measurement. Croom Helm. London, United Kingdom.
26. Moore, W. E., and L. V. Holdeman. 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27:961-979.
27. Muhlebach, M. S., P. W. Stewart, M. W. Leigh, and T. L. Noah. 1999. Quantitation of inflammatory responses to bacteria in young cystic fibrosis and control patients. Am. J. Respir. Crit. Care Med. 160:186-191.
28. Peet, R. K. 1974. The measurement of species diversity. Annu. Rev. Ecol. Syst. 5:285-307.
29. Poulin, R. 1996. Patterns in the evenness of gastrointestinal helminth communities. Int. J. Parasitol. 26:181-186.
30. Rainey, F. A., N. L. Ward-Rainey, P. H. Janssen, and H. Hippe. 1996. Clostridium paradoxum DSM 7308(T) contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiology 142:2087-2095.
31. Ramsey, B. W. 1996. Management of pulmonary disease in patients with cystic fibrosis. N. Engl. J. Med. 180:179-188.
32. Ritchie, N. J., M. E. Schutter, R. P. Dick, and D. D. Myrold. 2000. Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl. Environ. Microbiol. 66:1668-1675.
33. Rock, T. D. 1987. The study of microorganisms in situ: progress and problems. Symp. Soc. Gen. Microbiol. 41:1-17.
34. Rogers, G. B., C. A. Hart, J. R. Mason, M. Hughes, M. J. Walshaw, and K. D. Bruce. 2003. Bacterial diversity in cystic fibrosis lung infections 16S ribosomal DNA (rDNA) length heterogeneity PCR and 16S rDNA terminal restriction fragment length polymorphism profiling. J. Clin. Microbiol. 41:3548-3558.
35. Smith, J. J., S. M. Travis, E. P. Greenberg, and M. J. Welsh. 1996. Cystic fibrosis airway epithelia fail to kill bacteria because of abnormal airway surface fluid. Cell 85:229-236.
36. Thomassen, M. J., J. D. Klinger, S. J. Badger, D. W. Heeckeren, and R. C. Stern. 1984. Cultures of thoracotomy specimens confirm usefulness of sputum cultures in cystic fibrosis. J. Pediatr. 104:352-356.
37. Thomson, R. B. 1999. Laboratory diagnosis of respiratory infections. Curr. Opin. Infect. Dis. 12:115-119.
38. Tiquia, S. M., J. Lloyd, D. A. Herms, H. A. J. Hoitink, and F. C. Michel, Jr. 2002. Effects of mulching and fertilization on soil nutrients, microbial activity and rhizosphere bacterial community structure determined by analysis of TRFLPs of PCR-amplified 16S rRNA genes. Appl. Soil Ecol. 21:31-48.
39. Torsvik, V., Goskyr, J., and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
40. Von Wintzingerode, F., U. B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
41. Worlitzsch, D., R. Tarran, M. Ulrich, U. Schwab, A. Cekici, K. C. Meyer, P. Birrer, G. Bellon, J. Berger, T. Weiss, K. Botzenhart, J. R. Yankaskas, S. Randell, R. C. Boucher, and G. During. 2002. Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J. Clin. Investig. 109:317-325.