Construction and characterization of a highly redundant Pseudomonas aeruginosa genomic library prepared from 12 clinical isolates: Application to studies of gene distribution among populations

International Journal of Pediatric Otorhinolaryngology

Volumn 70, Issue 11, 2006, Pages 1891-1900

  Erdos, Geza ^a,b   Sayeed, Sameera ^a   Hu, Fen Ze ^a,b   Antalis, Patricia T ^a   Shen, Kai ^a   Hayes, Jay D ^a   Ahmed, Azad I ^a   Johnson, Sandra L ^a   Post, J Christopher ^a,b   Ehrlich, Garth D ^a,b  

^a ALLEGHENY SINGER RESEARCH INSTITUTE   (United States)

^b DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

Bacterial evolution; Distributed genome hypothesis; Genomic plasticity; Otitis media; Otorrhea; Supragenome

Indexed keywords

DNA FRAGMENT; GENOMIC DNA; NUCLEOTIDE; RESTRICTION ENDONUCLEASE; TRANSCRIPTOME;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIOPLANKTON; BACTERIUM ISOLATE; BIOFILM; CONTROLLED STUDY; CYSTIC FIBROSIS; GENE CONSTRUCT; GENE LIBRARY; GENETIC TRAIT; GENOME ANALYSIS; GENOME SIZE; HYDRODYNAMICS; HYPOTHESIS; MOLECULAR CLONING; MOLECULAR WEIGHT; NONHUMAN; OPPORTUNISTIC INFECTION; OTITIS MEDIA; OTORRHEA; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; QUALITY CONTROL; SEQUENCE ANALYSIS;

CHILD, PRESCHOOL; DNA, BACTERIAL; GENE EXPRESSION; GENETIC SCREENING; GENETIC TESTING; GENOME, BACTERIAL; GENOMIC LIBRARY; HUMANS; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA;

EID: 33749573638     PISSN: 01655876     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijporl.2006.06.016     Document Type: Article

References (36)

1. Stover C.K., Pham X.Q., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., et al. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406 6799 (2000) 959-964
2. Romling U., and Tummler B. The impact of two-dimensional pulsed-field gel electrophoresis techniques for the consistent and complete mapping of bacterial genomes: refined physical map of Pseudomonas aeruginosa PAO1. Nucleic Acids Res. 19 12 (1991) 3199-3206
3. Romling U., Schmidt K.D., and Tummler B. Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats. J. Mol. Biol. 271 3 (1997) 386-404
4. Claus H., Rotlich H., and Filip Z. DNA fingerprints of Pseudomonas spp. using rotating field electrophoresis. Microb. Releases 1 1 (1992) 11-16
5. Lewis D.A., Jones A., Parkhill J., Speert D.P., Govan J.R., Lipuma J.J., Lory S., Webb A.K., and Mahenthiralingam E. Identification of DNA markers for a transmissible Pseudomonas aeruginosa cystic fibrosis strain. Am. J. Respir. Cell Mol. Biol. 33 1 (2005) 56-64
6. He J., Baldini R.L., Deziel E., Saucier M., Zhang Q., Liberati N.T., Lee D., Urbach J., Goodman H.M., and Rahme L.G. The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proceedings of the National Academy of Sciences of the United States of America, vol. 101(8) (2004) 2530-2535
7. Dubois V., Arpin C., Noury P., Andre C., Coulange L., and Quentin C. Prolonged outbreak of infection due to TEM-21-producing strains of Pseudomonas aeruginosa and enterobacteria in a nursing home. J. Clin. Microbiol. 43 8 (2005) 4129-4138
8. Erdos G., Sayeed S., Antalis P., Hu F.Z., Hayes J., Goodwin J., et al. Development and characterization of a pooled Haemophilus influenzae genomic library for the evaluation of gene expression changes associated with mucosal biofilm formation in otitis media. Int. J. Pediatr. Otorhinolaryngol. 67 7 (2003) 749-755
9. Shen K., Wang X., Post J.C., and Ehrlich G.D. Molecular and translational research. In: Rosenfeld R., Bluestone C.D., and Hamilton B.C. (Eds). Evidence-based Otitis Media. 2nd ed. (2003), Decker Inc. Chapter 7
10. Ehrlich G.D., Hu F.Z., and Post J.C. Role for biofilms in infectious disease. In: Ghannoum M., and O'Toole G.A. (Eds). Microbial Biofilms (2004), ASM Press, Washington, DC 332-358
11. Pedersen S.S., Hoiby N., Espersen F., and Koch C. Role of alginate in infection with mucoid Pseudomonas aeruginosa in cystic fibrosis. Thorax 47 1 (1992) 6-13
12. Singh P.K., Schaefer A.L., Parsek M.R., Moninger T.O., Welsh M.J., and Greenberg E.P. Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms. Nature 407 6805 (2000) 762-764
13. Davies D.G., Parsek M.R., Pearson J.P., Iglewski B.H., Costerton J.W., and Greenberg E.P. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280 5361 (1998) 295-298
14. O'Toole G.A., and Kolter R. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol. Microbiol. 30 2 (1998) 295-304
15. Nakagawa T., Yadohisa O., Komune S., and Uemura T. A 16-year survey of changes in bacterial isolates associated with chronic suppurative otitis media. Eur. Arch. Otorhinolaryngol. 251 Suppl. 1 (1994) S27-S32
16. Kenna M.A., White G.W., Wadowsky R.M., Post J.C., and Ehrlich G.D. Bacteriology of otorrhea: polymerase chain reaction versus cultures. Proceedings of the Sixth International Symposium on Recent Advances in Otitis Media (1996) 428-430
17. Melaku A., and Lulseged S. Chronic suppurative otitis media in a children's hospital in Addis Ababa. Ethiopia. Ethiop. Med. J. 37 4 (1999) 237-246
18. Bluestone C.D., and Klein J.O. Intratemporal complications and sequelae of otitis media. In: Bluestone C.D., Stool S.E., and Kenna M.A. (Eds). Pediatric Otolaryngology. 3rd ed. (1996), W.B. Saunders, Philadelphia 583-647
19. Eimas P.D., and Kavanagh J.F. Otitis media, hearing loss, and child development: a NICHD conference summary. Public Health Rep. 101 3 (1986) 289-293
20. Daly K.A., Hunter L.L., and Giebink G.S. Chronic otitis media with effusion. Pediatr. Rev. 20 3 (1999) 85-93 quiz 94
21. Teele D.W., Klein J.O., Chase C., Menyuk P., and Rosner B.A. Otitis media in infancy and intellectual ability, school achievement, speech, and language at age 7 years. Greater Boston Otitis Media Study Group. J. Infect. Dis. 162 3 (1990) 685-694
22. Bennett K.E., Haggard M.P., Silva P.A., and Stewart I.A. Behaviour and developmental effects of otitis media with effusion into the teens. Arch. Dis. Child. 85 2 (2001) 91-95
23. Haggard M.P., Birkin J.A., Browning G.G., Gatehouse S., and Lewis S. Behavior problems in otitis media. Pediatr. Infect. Dis. J. 13 1 Suppl. 1 (1994) S43-S50 discussion S50-S44
24. Seed B., Parker R.C., and Davidson N. Representation of DNA sequences in recombinant DNA libraries prepared by restriction enzyme partial digestion. Gene 19 2 (1982) 201-209
25. Woo T.H., Cheng A.F., and Ling J.M. An application of a simple method for the preparation of bacterial DNA. Biotechniques 13 5 (1992) 696-698
26. T. Nishijyo, D. Haas, Y. Itoh, The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa. Mol. Microbiol. 200;40(4):917-31.
27. Whiteley M., Bangera M.G., Bumgarner R.E., Parsek M.R., Teitzel G.M., Lory S., et al. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413 6858 (2001) 860-864
28. Wagner V.E., Bushnell D., Passador L., Brooks A.I., and Iglewski B.H. Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment. J. Bacteriol. 185 7 (2003) 2080-2095
29. Firoved A.M., and Deretic V. Microarray analysis of global gene expression in mucoid Pseudomonas aeruginosa. J. Bacteriol. 185 3 (2003) 1071-1081
30. Malloff C.A., Fernandez R.C., and Lam W.L. Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer. J. Mol. Biol. 312 1 (2001) 1-5
31. Nesbo C.L., Nelson K.E., and Doolittle W.F. Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima. J. Bacteriol. 184 16 (2002) 4475-4488
32. Shen K., Antalis P., Gladitz J., Sayeed S., Ahmed A., Yu S., Hayes J., Johnson S., Dice B., Dopico R., Keefe R., Janto B., Chong W., Goodwin J., Wadowsky R.M., Erdos G., Post J.C., Ehrlich G.D., and Hu F.Z. Identification, distribution, and expression of novel (nonRd) genes in ten clinical isolates of nontypeable Haemophilus influenzae. Infect. Immun. 73 (2005) 3479-3491
33. Shen K., Antalis P., Gladitz J., Dice B., Janto B., Keefe R., Hayes J., Ahmed A., Dopico R., Ehrlich N., Jocz J., Kropp J., Yu S., Nistico L., Greenberg D.P., Barbadora K., Post J.C., Ehrlich G.D., and Hu F.Z. Characterization, distribution and expression of novel genes among eight clinical isolates of Streptococcus pneumoniae. Infect. Immun. 74 1 (2006) 321-330
34. Ehrlich G.D., Hu F.Z., Shen K., Stoodley P., and Post J.C. Bacterial plurality as a general mechanism driving persistence in chronic infections. Clin. Orthop. Relat. Res. 437 (2005) 20-24
35. Bonten M.J., Bergmans D.C., Speijer H., and Stobberingh E.E. Characteristics of polyclonal endemicity of Pseudomonas aeruginosa colonization in intensive care units. Implications for infection control. Am. J. Respir. Crit. Care Med. 160 4 (1999) 1212-1219
36. Pirnay J.P., De Vos D., Cochez C., Bilocq F., Pirson J., Struelens M., et al. Molecular epidemiology of Pseudomonas aeruginosa colonization in a burn unit: persistence of a multidrug-resistant clone and a silver sulfadiazine-resistant clone. J. Clin. Microbiol. 41 3 (2003) 1192-1202