Examination with next-generation sequencing technology of the bacterial microbiota in bronchoalveolar lavage samples after traumatic injury

Surgical Infections

Volumn 14, Issue 3, 2013, Pages 275-282

  Huebinger, Ryan M ^a   Liu, Ming Mei ^a   Dowd, Scot E ^b   Rivera Chavez, Fernando A ^a   Boynton, John ^c   Carey, Curtis ^c   Hawkins, Kenneth ^c   Minshall, Christian T ^a   Wolf, Steven E ^a   Minei, Joseph P ^a   Barber, Robert C ^d  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b MR DNA (Molecular Research LP)   (United States)

^c PARKLAND HEALTH AND HOSPITAL SYSTEM   (United States)

^d UNIVERSITY OF NORTH TEXAS HEALTH SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RNA 16S;

ADULT; ARTICLE; BACTERIAL FLORA; BACTERIAL STRAIN; BACTERIUM CULTURE; CAUCASIAN; CLINICAL ARTICLE; CLINICAL PULMONARY INFECTION SCORE; CLOSTRIDIUM; COMPARATIVE STUDY; CONTROLLED STUDY; ESCHERICHIA; FEMALE; GENE SEQUENCE; HUMAN; INJURY; INTENSIVE CARE UNIT; LENGTH OF STAY; LUNG LAVAGE; MALE; MICROBIAL DIVERSITY; MYCOPLASMA; NAMED INVENTORIES, QUESTIONNAIRES AND RATING SCALES; PRIORITY JOURNAL; SALMONELLA; STAPHYLOCOCCUS; STREPTOCOCCUS;

ADOLESCENT; ADULT; BACTERIA; BRONCHOALVEOLAR LAVAGE FLUID; DNA, BACTERIAL; FEMALE; HUMANS; INTENSIVE CARE; LINEAR MODELS; MALE; MIDDLE AGED; MOLECULAR TYPING; RESPIRATION, ARTIFICIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WOUNDS AND INJURIES;

EID: 84879392159     PISSN: 10962964     EISSN: 15578674     Source Type: Journal    
DOI: 10.1089/sur.2012.095     Document Type: Article

References (37)

1. Eagye KJ, Nicolau DP, Kuti JL. Impact of superinfection on hospital length of stay and costs in patients with ventilatorassociated pneumonia. Semin Respir Crit Care Med 2009; 30:116-123.
2. Boyce JM, Potter-Bynoe G, Dziobek L, Solomon SL. Nosocomial pneumonia in Medicare patients. Hospital costs and reimbursement patterns under the prospective payment system. Arch Intern Med 1991;151:1109-1114.
3. Dietrich ES, Demmler M, Schulgen G, et al. Nosocomial pneumonia:Acost-of-illness analysis. Infection 2002;30:61-67.
4. Labelle AJ, Arnold H, Reichley RM, et al. A comparison of culture-positive and culture-negative health-care-associated pneumonia. Chest 2010;137:1130-1137.
5. Caliendo AM. Multiplex PCR and emerging technologies for the detection of respiratory pathogens. Clin Infect Dis 2011; 52:S326-S330.
6. Dowd SE, Sun Y, Secor PR, et al. Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 2008;8:43.
7. Hamady M, Walker JJ, Harris JK, et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008;5:235-237.
8. Ley RE, Backhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005;102:11070-11075.
9. Koren O, Spor A, Felin J, et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci USA 2011;108:4592-4598.
10. Ley RE, Lozupone CA, Hamady M, et al. Worlds within worlds: Evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008;6:776-788.
11. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 2008;105:17994-17999.
12. Wolcott RD, Gontcharova V, Sun Y, et al. Bacterial diversity in surgical site infections: Not just aerobic cocci any more. J Wound Care 2009;18:317-323.
13. Hilty M, Burke C, Pedro H, et al. Disordered microbial communities in asthmatic airways. PLoS One 2010;5:e8578.
14. Erb-Downward JR, Thompson DL, Han MK, et al. Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One 2011;6:e16384.
15. Zhou Y, Lin P, LiQ, et al. Analysis of themicrobiota of sputum samples from patients with lower respiratory tract infections. Acta Biochim Biophys Sin (Shanghai) 2010;42:754-761.
16. Pugin J. Clinical signs and scores for the diagnosis of ventilator-associated pneumonia. Minerva Anestesiol 2002; 68:261-265.
17. Pugin J, Auckenthaler R, Mili N, et al. Diagnosis of ventilator- associated pneumonia by bacteriologic analysis of bronchoscopic and nonbronchoscopic "blind" bronchoalveolar lavage fluid. Am Rev Respir Dis 1991;143:1121-1129.
18. Minei JP, Nathens AB, West M, et al. Inflammation and the host response to injury, a large-scale collaborative project: Patient-oriented research core-standard operating procedures for clinical care. II. Guidelines for prevention, diagnosis and treatment of ventilator-associated pneumonia (VAP) in the trauma patient. J Trauma 2006;60:1106-1113.
19. Edrington TS, Dowd SE, Farrow RF, et al. Development of colonic microflora as assessed by pyrosequencing in dairy calves fed waste milk. J Dairy Sci 2012;95:4519-4525.
20. Hume ME, Hernandez CA, Barbosa NA, et al. Molecular identification and characterization of ileal and cecal fungus communities in broilers given probiotics, specific essential oil blends, and under mixed Eimeria infection. Foodborne Pathog Dis 2012;9:853-860.
21. Suchodolski JS, Dowd SE, Wilke V, et al. 16S rRNA Gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease. PLoS One 2012;7:e39333.
22. Nagy-Szakal D, Ross MC, Dowd SE, et al. Maternal micronutrients can modify colonic mucosal microbiota maturation in murine offspring. Gut Microbes 2012;3:426-433.
23. Hooda S, Boler BM, Serao MC, et al. 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber. J Nutrition 2012;142:1259-1265.
24. Dowd SE, Zaragoza J, Rodriguez JR, et al. Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). BMC Bioinformatics 2005;6:93.
25. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009;37:D141-D145.
26. Dowd SE, Wolcott RD, Sun Y, et al. Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS One 2008;3:e3326.
27. Sun Y, Wolcott RD, Dowd SE. Tag-encoded FLX amplicon pyrosequencing for the elucidation of microbial and functional gene diversity in any environment. Methods Mol Biol 2011;733:129-141.
28. Kuczynski J, Stombaugh J, Walters WA, et al. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics 2011 Dec;Chapter 10:Unit 10.7.
29. Shannon CE, Weaver W. The mathematical theory of communication. Urbana, II: University of Illinois Press, 1949.
30. Chao A. Non-parametric estimation of the number of classes in a population. Scand J Stat 1984;11:265-270.
31. Thomson RB. Specimen collection, transport, and processing: Bacteriology. In: Murray PR, Baron EJ, Jorgensen JH, et al., eds. Manual of Clinical Microbiology. Washington, DC: ASM Press, 2007, 309-310.
32. Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res 2012;160:258-266.
33. Venkatachalam V, Hendley JO, Willson DF. The diagnostic dilemma of ventilator-associated pneumonia in critically ill children. Pediatr Crit Care Med 2011;12:286-296.
34. Gomez R, Murray CK, Hospenthal DR, et al. Causes of mortality by autopsy findings of combat casualties and civilian patients admitted to a burn unit. J Am Coll Surg 2009;208:348-354.
35. Agarwal J, Awasthi S, Rajput A, et al. Atypical bacterial pathogens in community-acquired pneumonia in children: A hospital-based study. Trop Doct 2009;39:109-111.
36. Muir MT, Cohn SM, Louden C, et al. Novel toxin assays implicate Mycoplasma pneumoniae in prolonged ventilator course and hypoxemia. Chest 2011;139:305-310.
37. Kumar A, Ellis P, Arabi Y, et al. Initiation of inappropriate antimicrobial therapy results in a fivefold reduction of survival in human septic shock. Chest 2009;136:1237-1248.