Assessment of microbial diversity in biofilms recovered from endotracheal tubes using culture dependent and independent approaches

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Vandecandelaere, Ilse ^a   Matthijs, Nele ^a   van Nieuwerburgh, Filip ^a   Deforce, Dieter ^a   Vosters, Peter ^b   de Bus, Liesbet ^b   Nelis, Hans J ^a   Depuydt, Pieter ^b   Coenye, Tom ^a  

^a GHENT UNIVERSITY   (Belgium)

^b GHENT UNIVERSITY HOSPITAL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACTINOBACTERIA; ARTICLE; ARTIFICIAL VENTILATION; BACTERIAL FLORA; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BETAPROTEOBACTERIA; BIOFILM; CANDIDA; CLOSTRIDIA; CORRELATION ANALYSIS; CULTURE MEDIUM; ENDOTRACHEAL TUBE; EPSILONPROTEOBACTERIA; FIRMICUTES; FUSOBACTERIA; GAMMAPROTEOBACTERIA; GENE AMPLIFICATION; GENE LIBRARY; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; KOCURIA VARIANS; LACTIC ACID BACTERIUM; MICROBIAL DIVERSITY; MICROBIOLOGICAL EXAMINATION; MOUTH FLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PEPTOSTREPTOCOCCUS; PHYLOGENY; POLYMERASE CHAIN REACTION; PREVOTELLA; PSEUDOMONAS AERUGINOSA; PYROSEQUENCING; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS; VENTILATOR ASSOCIATED PNEUMONIA; ENDOTRACHEAL INTUBATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; CANDIDA; CLOSTRIDIA; EPSILONPROTEOBACTERIA; FIRMICUTES; FUSOBACTERIA; GAMMAPROTEOBACTERIA; KOCURIA VARIANS; PEPTOSTREPTOCOCCUS; PREVOTELLA; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS;

ACTINOBACTERIA; BETAPROTEOBACTERIA; BIOFILMS; CANDIDA; EPSILONPROTEOBACTERIA; FUSOBACTERIA; GAMMAPROTEOBACTERIA; INTUBATION, INTRATRACHEAL; PNEUMONIA, VENTILATOR-ASSOCIATED; PSEUDOMONAS AERUGINOSA; RNA, RIBOSOMAL, 16S; STAPHYLOCOCCUS AUREUS;

EID: 84861898547     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038401     Document Type: Article

References (65)

1. Depuydt P, Myny D, Blot S, (2006) Nosocomial pneumonia: aetiology, diagnosis and treatment. Curr Opin Pulm Med 12: 192-197.
2. Augustyn B, (2007) Ventilator-associated pneumonia: risk factors and prevention. Crit Care Nurse 27: 32-36.
3. Heo SM, Haase EM, Lesse AJ, Gill SR, Scannapieco FA, (2008) Genetic relationships between respiratory pathogens isolated from dental plaque and bronchoalveolar lavage fluid from patients in the intensive care unit undergoing mechanical ventilation. Clin Infect Dis 47: 1562-1570.
4. Adair CG, Gorman SP, Feron BM, Byers LM, Jones DS, et al. (1999) Implications of endotracheal tube biofilm for ventilator-associated pneumonia. Intensive Care Med 25: 1072-1076.
5. Bauer TT, Torres A, Ferrer R, Heyer CM, Schultze-Werninghaus G, Rasche K, (2002) Biofilm formation in endotracheal tubes. Association between pneumonia and the persistence of pathogens. Monaldi Arch Chest Dis 57: 84-87.
6. Inglis TJ, Millar MR, Jones JG, Robinson DA, (1989) Tracheal tube biofilm as a source of bacterial colonization of the lung. J Clin Microbiol 27: 2014-2018.
7. Sottile FD, Marrie TJ, Prough DS, Hobgood CD, Gower GJ, et al. (1986) Nosocomial pulmonary infection: possible etiologic significance of bacterial adhesion to endotracheal tubes. Crit Care Med 14: 265-270.
8. Cairns S, Thomas JG, Hooper SJ, Wise MP, Frost PJ, et al. (2011) Molecular analysis of microbial communities in endotracheal tube biofilms. PLoS ONE 6 (3): e14759.
9. Edwards C, (2000) Problems posed by natural environments for monitoring microorganisms. Mol Biotechnol 15: 211-223.
10. Luna CM, Sibila O, Agusti C, Torres A, (2009) Animal models of ventilator-associated pneumonia. Eur Respir J 33: 182-188.
11. American Thoracic Society, Infectious diseases society of America (2005) Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. Am J Respir Crit Care Med 171: 388-416.
12. Depuydt P, Benoit D, Vogelaers D, Claeys G, Verschraegen G, et al. (2006) Outcome in bacteremia associated with nosocomial pneumonia and the impact of pathogen prediction by tracheal surveillance cultures. Intensive Care Med 32: 1773-1781.
13. Depuydt P, Benoit D, Vogelaers D, Decruyenaere J, Vandijck D, et al. (2008) Systematic surveillance cultures as a tool to predict involvement of multidrug antibiotic resistant bacteria in ventilator-associated pneumonia. Intensive Care Med 34: 675-682.
14. Joseph NM, Sistla S, Dutta TK, Badhe AS, Parija SC, (2010) Ventillator-associated pneumonia: a review. Eur J Intern Med 21: 360-368.
15. Blot S, Depuydt P, Vandijck D, Vandewoude K, Peleman R, et al. (2008) Predictive value of surveillance cultures and subsequent bacteremia with extended-spectrum beta-lactamase-producing Enterobacteriaceae. Clin Infect Dis 46: 481-482.
16. Blot S, Depuydt P, Vogelaers D, (2008) Maximizing rates of empiric appropriate antibiotic therapy with minimized use of broad-spectrum agents: are surveillance cultures the key? Intensive Care Med 34: 2130-2133.
17. Esteban J, Molina-Manso D, Spiliopoulou I, Cordero-Ampuero J, Fernández-Roblas R, et al. (2010) Biofilm development by clinical isolates of Staphylococcus spp. from retrieved orthopedic prostheses. Acta Orthop 81: 674-679.
18. Costerton JW, Post JC, Ehrlich GD, Hu FZ, Kreft R, et al. (2011) New methods for the detection of orthopedic and other biofilm infections. FEMS Immunol Med Microbiol 61: 133-140.
19. Perkins SD, Woeltje KF, Angenent LT, (2010) Endotracheal tube biofilm inoculation of oral flora and subsequent colonization of opportunistic pathogens. Int J Med Microbiol 300: 503-511.
20. Bahrani-Mougeot FK, Paster BJ, Coleman S, Barbuto S, Brennan MT, et al. (2007) Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia. J Clin Microbiol 45: 1588-1593.
21. Zemanick ET, Sagel SD, Harris JK, (2011) The airway microbiome in cystic fibrosis and implications for treatment. Curr Opin Pediatr 23: 319-324.
22. Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, et al. (2008) Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 177: 995-1001.
23. Park DR, (2005) The microbiology of ventilator-associated pneumonia. Respir Care 50: 742-765.
24. Baron EJ, Thomson RB Jr, (2011) Specimen collection, transport, and processing: bacteriology. In J. Versalovic (ed.), Manual of Clinical Microbiology, 10th ed. ASM press, Washington, DC.
25. Pereira EM, Schuenck RP, Malvar KL, Iorio NL, Matos PD, et al. (2010) Staphylococcus aureus, Staphylococcus epidermidis and Staphylococcus haemolyticus: methicillin-resistant isolates are detected directly in blood cultures by multiplex PCR. Microbiol Res 165: 243-249.
26. Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JR, et al. (1999) Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 49: 405-413.
27. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
28. Palatinzky M, Nikolausz M, Svab D, Marialigeti K, (2011) Preferential ligation during TA-cloning of multitemplate PCR products - A factor causing bias in microbial community structure analysis. J Microbiol Methods 85: 131-136.
29. Joly E, (1996) Preparation of plasmid DNA by alkaline lysis. Meth Mol Biol 58, 256-263.
30. Simpson EH, (1949) Measurement of diversity. Nature 163: 688.
31. Good IJ, (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40: 237-264.
32. Schloss PD, Westcott RL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
33. Carbon C, (2000) MRSA and MRSE: is there an answer? Clin Microbiol Infect 6: 17-22.
34. Ziebuhr W, Hennig S, Eckart M, Kränzler H, Batzilla C, et al. (2006) Nosocomial infections by Staphylococcus epidermidis: how a commensal bacterium turns into a pathogen. Int J Antimicrob Agents 28: 14-20.
35. Albertson D, Natsios GA, Gleckman R, (1978) Septic shock with Micrococcus luteus. Arch Int Med 138: 487-488.
36. Decraene V, Ready D, Pratten J, Wilson M, (2008) Air-borne microbial contamination of surfaces in a UK dental clinic. J Gen Appl Microbiol 54: 195-203.
37. Ouziz RJ, Widlitz A, Beckmann J, Camanga D, Alfie J, et al. (2004) Micrococcus-associated central venous catheter infection in patients with pulmonary arterial hypertension. Chest 126: 90-94.
38. Chang EP, Chiang DH, Lin ML, Chen TL, Wang FD, et al. (2009) Clinical characteristics and predictors of mortality in patients with Enterobacter aerogenes bacteremia. J Microbiol Immunol Infect 42: 329-335.
39. Narayan SA, Kool JL, Vakololoma M, Steer AC, Mejia A, et al. (2009) Investigation and control of an outbreak of Enterobacter aerogenes bloodstream infection in a neonatal intensive care unit in Fiji. Infect Control Hosp Epidemiol 30: 797-800.
40. Song EH, Park KH, Jang EY, Lee EJ, Chong YP, et al. (2010) Comparison of the clinical and microbiologic characteristics of patients with Enterobacter cloacae and Enterobacter aerogenes bacteremia: a prospective observation study. Diagn Microbiol Infect Dis 66: 436-440.
41. Decré D, Verdet C, Emirian A, Le Gourrierec T, Petit JC, et al. (2011) Emerging severe and fatal infections due to Klebsiella pneumoniae in two French university hospitals. J Clin Microbiol 49: 3012-3014.
42. Mancini F, Carniato A, Ciervo A, (2009) Pneumonia caused by Shigella sonnei in man returned from India. Emerg Infect Dis 15: 1874-1876.
43. Czosnowski QA, Wood GC, Magnotti LJ, Croce LA, Swanson JM, et al. (2011) Clinical and microbiological outcome in trauma patients treated for Stenotrophomonas maltophilia ventilator-associated pneumonia. Pharmacotherapy 31: 338-345.
44. Ryan MP, Adley CC, (2010) Sphingomonas paucimobilis: a persistent Gram-negative nosocomial infectious organism. J Hosp Infect 75: 153-157.
45. Toyoshima M, Chida K, Suda T, (2010) Fulminant community-acquired pneumonia probably caused by Acinetobacter lwoffi. Respirology 15: 867-868.
46. Abbott SL, Janda M, Farmer JJ III, (2011) Vibrio and related organisms. In J. Versalovic (ed.), Manual of Clinical Microbiology, 10th ed. ASM press, Washington, DC.
47. Becker K, von Eiff C, (2011) Staphylococcus, Micrococcus and other catalase-positive cocci. In J. Versalovic (ed.), Manual of Clinical Microbiology, 10th ed. ASM press, Washington, DC.
48. Conville PS, Witebsky FG, (2011) Nocardia, Rhodococcus, Gordonia, Actinomadura, Streptomyces, and other Actinomycetes. In J. Versalovic (ed.), Manual of Clinical Microbiology, 10th ed. ASM press, Washington, DC.
49. Funke G, von Graevenitz A, Carridge JE III, Bernard KA, (1997) Clinical microbiology of coryneform bacteria. Clin Microbiol Rev 10: 125-159.
50. Ruoff KL, (2011) Aerococcus, Abiotrophia, and other aerobic catalase-negative, Gram-positive cocci. In J. Versalovic (ed.), Manual of Clinical Microbiology, 10th ed. ASM press, Washington, DC.
51. Savini V, Catavitello C, Masciarelli G, Astolfi D, Balbinot A, et al. (2010) Drug sensitivity and clinical impact of the genus Kocuria. J Med Microbiol 59: 1395-1402.
52. Vaneechoutte ML, Dijskhoorn L, Nemec A, Kämpfer P, Wauters G, (2011) Acinetobacter, Chryseobacterium, Moraxella, and other nonfermentative Gram-negative rods. In J. Versalovic (ed.), Manual of Clinical Microbiology, 10th ed. ASM press, Washington, DC.
53. Zbinden R, von Graevenitz A, (2011) Actinobacillus, Capnocytophaga, Eikenella, Kingella, Pasteurella, and other fastidious or rarely encountered Gram-negative rods. In J. Versalovic (ed.), 10th ed. ASM press, Washington, DC.
54. Argimon S, Caufield PW, (2011) Distribution of putative virulence genes in Streptococcus mutans strains does not correlate with caries experience. J Clin Microbiol 49: 984-992.
55. Dewhirst FE, Che T, Izard J, Paster BJ, Tanner ACR, et al. (2010) The human oral microbiome. J Bacteriol 192: 5002-5017.
56. Mahenthiralingam E, Marchbank A, Drevinek P, Garaiova I, Plummer S, (2009) Use of colony-based bacterial strain typing for tracking the fate of Lactobacillus strains during human consumption. BMC Microbiol 9: 251.
57. Sookkhee S, Chulasira M, Prachyabrued W, (2001) Lactic acid bacteria from healthy oral cavity of Thai volunteers: inhibition of oral pathogens. J App Microbiol 90: 172-179.
58. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, et al. (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods 79: 266-271.
59. Schloss PD, (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16 S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.
60. Watanabe T, Matsuura M, Seto K, (1986) Enumeration, isolation, and species identification of mycoplasmas in saliva sampled from the normal and pathological human oral cavity and antibody response to an oral mycoplasma (Mycoplasma salivarium). J Clin Microbiol 23: 1034-1038.
61. Bouza E, Burillo A, (2009) Advances in the prevention and management of ventilator-associated pneumonia. Curr Opin Infect Dis 22: 345-351.
62. Takeshita T, Tomioka M, Shimazaki Y, Matsuyama M, Koyano, Matsuda K, et al, (2010) Microflora characterization of the tongue coating and associated risk for pneumonia-related health problems in institutionalized older adults. J Am Geriatr Soc 58: 1050-1057.
63. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
64. Zhao J, Carmody LA, Kalikin LM, Li J, Petroscino JF, et al. (2012) Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS ONE 7 (3): e33127.
65. Nseir S, Jozefowicz E, Cavestri B, Sendid B, Di Pompeo C, et al. (2007) Impact of antifungal treatment on Candida-Pseudomonas interactions: a preliminary retrospective case-control study. Intensive Care Med 33: 137-142.