Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung

American Journal of Respiratory Cell and Molecular Biology

Volumn 46, Issue 2, 2012, Pages 127-131

  Willner, Dana ^a,c   Haynes, Matthew R ^a   Furlan, Mike ^a   Hanson, Nicole ^a   Kirby, Breeann ^a   Lim, Yan Wei ^a   Rainey, Paul B ^d,e   Schmieder, Robert ^a,b   Youle, Merry ^f   Conrad, Douglas ^g,h   Rohwer, Forest ^a,i  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d MASSEY UNIVERSITY   (New Zealand)

^e MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^f Rainbow Rock   (United States)

^g UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^h VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

ⁱ Center for Microbial Sciences   (United States)

Author keywords

Antibiotic resistance; Cystic fibrosis; Metagenomics; Viruses

Indexed keywords

ADULT; ANELLOVIRUS; ANTIBIOTIC RESISTANCE; ARTICLE; AUTOPSY; BACTERIOPHAGE; BIOFILM; CYSTIC FIBROSIS; DISEASE SEVERITY; EXPLANT; GENETIC CODE; HERPES VIRUS; HUMAN; HUMAN TISSUE; LUNG PARENCHYMA; LUNG TRANSPLANTATION; METAGENOMICS; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PHENOTYPE; PREDATION;

BACTERIOPHAGES; CYSTIC FIBROSIS; DNA VIRUSES; DRUG RESISTANCE, MICROBIAL; HUMANS; VIRUS DISEASES;

DNA VIRUSES; EUKARYOTA; PAPILLOMAVIRIDAE;

EID: 84856629583     PISSN: 10441549     EISSN: None     Source Type: Journal    
DOI: 10.1165/rcmb.2011-0253OC     Document Type: Article

References (33)

1. Brody AS, Klein JS, Molina PL, Quan J, Bean JA, Wilmott RW. High-resolution computed tomography in young patients with cystic fibrosis: distribution of abnormalities and correlation with pulmonary function tests. J Pediatr 2004;145:32-38. (Pubitemid 38962449)
2. Meyer K, Sharma A. Regional variability of lung inflammation in cystic fibrosis. Am J Respir Crit Care Med 1997;156:1536-1540. (Pubitemid 27505521)
3. Gurney JW, Habbe TG, Hicklin J. Distribution of disease in cystic fibrosis. Chest 1997;112:357-362.
4. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B, et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS ONE 2011;6:e16384.
5. Willner D, Haynes M, Furlan M, Schmieder R, Lim YW, Rainey P, Rohwer F, Conrad D. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J (In press)
6. Liu B, Pop M. ARDB: Antibiotic Resistance Genes Database. Nucleic Acids Res 2009;37:D443-D447.
7. Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res 2009;19:1639-1645.
8. Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 2009;25:2730-2731.
9. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999;9:868-877. (Pubitemid 29488446)
10. Hyatt D, Chen G-L, LoCascio P, Land M, Larimer F, Hauser L. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119.
11. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52:696-704. (Pubitemid 37365050)
12. Huelsenbeck JP, Ronquist F. MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 2001;17:754-755. (Pubitemid 32851390)
13. Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, Salamon P, Felts B, Nulton J, Mahaffy J, Rohwer F. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 2005;6:41.
14. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010;466:334-338.
15. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and noncystic fibrosis individuals. PLoS ONE 2009;4:e7370.
16. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, et al. Functional metagenomic profiling of nine biomes. Nature 2008;452:629-632. (Pubitemid 351483360)
17. Webb JS, Lau M, Kjelleberg S. Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development. J Bacteriol 2004; 186:8066-8073. (Pubitemid 39552518)
18. Chien M, Morozova I, Shi S, Sheng H, Chen J, Gomez SM, Asamani G, Hill K, Nuara J, Feder M, et al. The genomic sequence of the accidental pathogen Legionella pneumophila. Science 2004;305:1966-1968. (Pubitemid 39287997)
19. Payne DJ, Du W, Bateson JH. Beta-lactamase epidemiology and the utility of established and novel beta-lactamase inhibitors. Expert Opin Investig Drugs 2000;9:247-261. (Pubitemid 30032310)
20. Doolittle MM, Cooney JJ, Caldwell DE. Tracing the interaction of bacteriophage with bacterial biofilms using fluorescent and chromogenic probes. J Ind Microbiol 1996;16:331-341.
21. van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, Carroll MP, Parkhill J, Bruce KD. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J 2011;5:780-791.
22. Costa C, Delsedime L, Solidoro P, Curtoni A, Bergallo M, Libertucci D, Baldi S, Rinaldi M, Cavallo R. Herpesviruses detection by quantitative real-time polymerase chain reaction in bronchoalveolar lavage and transbronchial biopsy in lung transplant: viral infections and histopathological correlation. Transplant Proc 2010;42:1270-1274.
23. Puchhammer-Stöckl E. Herpesviruses and the transplanted lung: looking at the air side. J Clin Virol 2008;43:415-418.
24. Antonsson A, Forslund O, Ekberg H, Sterner G, Hansson BG. The ubiquity and impressive genomic diversity of human skin papillomaviruses suggest a commensalic nature of these viruses. J Virol 2000;74:11636-11641. (Pubitemid 32222312)
25. Ruan S-Y, Chen K-Y, Yang P-C. Recurrent respiratory papillomatosis with pulmonary involvement: a case report and review of the literature. Respirology 2009;14:137-140.
26. Klein F, Amin Kotb WFM, Petersen I. Incidence of human papilloma virus in lung cancer. Lung Cancer 2009;65:13-18.
27. Berkhout R, Tieben L, Smits H, Bavinck J, Vermeer B, ter Schegget J. Nested PCR approach for detection and typing of epidermodysplasia verruciformis-associated human papillomavirus types in cutaneous cancers from renal transplant recipients. J Clin Microbiol 1995;33: 690-695.
28. Pifferi M, Maggi F, Caramella D, De Marco E, Andreoli E, Meschi S, Macchia P, Bendinelli M, Boner AL. High torquetenovirus loads are correlated with bronchiectasis and peripheral airflow limitation in children. Pediatr Infect Dis J 2006;25:804-808. (Pubitemid 44325782)
29. Blahová J, Králiková K, Krcméry V, Schäfer V. Bacteriophages transducing antibiotic resistance from a cluster of lysogenic strains of Pseudomonas aeruginosa isolated from patients. J Chemother 2001;13: 331-333. (Pubitemid 32575145)
30. Colomer-Lluch M, Jofre J, Muniesa M. Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples. PLoS ONE 2011;6:e17549.
31. Foweraker JE, Laughton CR, Brown DF, Bilton D. Comparison of methods to test antibiotic combinations against heterogeneous populations of multi-resistant Pseudomonas aeruginosa from patients with acute infective exacerbations in cystic fibrosis. Antimicrob Agents Chemother 2009;53:4809-4815.
32. Mukhopadhyay S, Staddon GE, Eastman C, Palmer M, Davies ER, Carswell F. The quantitative distribution of nebulized antibiotic in the lung in cystic fibrosis. Respir Med 1994;88:203-211. (Pubitemid 24130571)
33. Goerke C, Köller J, Wolz C. Ciprofloxacin and trimethoprim cause phage induction and virulence modulation in Staphylococcus aureus. Antimicrob Agents Chemother 2006;50:171-177. (Pubitemid 43042918)