The Use of DNA Methods to Characterize Biofilm Infection - Antibiofilm Agents: From Diagnosis to Treatment and Prevention - page 27

Mutz KO, Heilkenbrinker A, Lonne M, Walter JG, Stahl F (2013) Transcriptome analysis using
next-generation sequencing. Curr Opin Biotechnol 24:22-30. doi: 10.1016/j.copbio.2012.09.
004 , S0958-1669(12)00131-0 [pii]
O'Meara S, Al-Kurdi D, Ologun Y, Ovington LG (2010) Antibiotics and antiseptics for venous leg
ulcers. Cochrane Database Syst Rev: CD003557. doi: 10.1002/14651858.CD003557.pub3
Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J (2009) Metagenomic
pyrosequencing and microbial identification. Clin Chem 55:856-866. doi: 10.1373/clinchem.
2008.107565 , clinchem.2008.107565 [pii]
Post JC, Aul JJ, White GJ, Wadowsky RM, Zavoral T, Tabari R, Kerber B, Doyle WJ, Ehrlich GD
(1996) PCR-based detection of bacterial DNA after antimicrobial treatment is indicative of
persistent, viable bacteria in the chinchilla model of otitis media. Am J Otolaryngol 17:106-
111
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009)
Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods
6:639-641. doi: 10.1038/nmeth.1361 , nmeth.1361 [pii]
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced
amplicons. BMC Bioinformatics 12:38. doi: 10.1186/1471-2105-12-38 , 1471-2105-12-38 [pii]
Ramsey MM, Rumbaugh KP, Whiteley M (2011) Metabolite cross-feeding enhances virulence in
a model polymicrobial infection. PLoS Pathog 7:e1002012. doi: 10.1371/journal.ppat.1002012
Reddington K, Tuite N, Barry T, O'Grady J, Zumla A (2013) Advances in multiparametric
molecular diagnostics technologies for respiratory tract infections. Curr Opin Pulm Med 19
(3):298-304. doi: 10.1097/MCP.0b013e32835f1b32
Rhoads DD, Wolcott RD, Sun Y, Dowd SE (2012a) Comparison of culture and molecular
identification of bacteria in chronic wounds. Int J Mol Sci 13:2535-2550. doi: 10.3390/
ijms13032535 , ijms-13-02535 [pii]
Rhoads DD, Cox SB, Rees EJ, Sun Y, Wolcott RD (2012b) Clinical identification of bacteria in
human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing. BMC Infect
Dis 12:321. doi: 10.1186/1471-2334-12-321 , 1471-2334-12-321 [pii]
Siami G, Christou N, Eiseman I, Tack KJ (2001) Clinafloxacin versus piperacillin-tazobactam in
treatment of patients with severe skin and soft tissue infections. Antimicrob Agents Chemother
45:525-531. doi: 10.1128/AAC.45.2.525-531.2001
Sibley CD, Grinwis ME, Field TR, Eshaghurshan CS, Faria MM, Dowd SE, Parkins MD, Rabin
HR, Surette MG (2011) Culture enriched molecular profiling of the cystic fibrosis airway
microbiome. PLoS One 6:e22702. doi: 10.1371/journal.pone.0022702 , PONE-D-11-00492
[pii]
Stauffer SH, Birkenheuer AJ, Levy MG, Marr H, Gookin JL (2008) Evaluation of four DNA
extraction methods for the detection of Tritrichomonas foetus in feline stool specimens by
polymerase chain reaction. J Vet Diagn Invest 20:639-641, 20/5/639 [pii]
Stephenson MF, Mfuna L, Dowd SE, Wolcott RD, Barbeau J, Poisson M, James G, Desrosiers M
(2010) Molecular characterization of the polymicrobial flora in chronic rhinosinusitis. J
Otolaryngol Head Neck Surg 39:182-187
Takahashi N (2003) Acid-neutralizing activity during amino acid fermentation by Porphyromonas
gingivalis, Prevotella intermedia and Fusobacterium nucleatum. Oral Microbiol Immunol
18:109-113, 054 [pii]
Tuttle MS, Mostow E, Mukherjee P, Hu FZ, Melton-Kreft R, Ehrlich GD, Dowd SE, Ghannoum
MA (2011) Characterization of bacterial communities in venous insufficiency wounds by use
of conventional culture and molecular diagnostic methods. J Clin Microbiol 49:3812-3819.
doi: 10.1128/JCM.00847-11 , JCM.00847-11 [pii]
Verhoeven PO, Grattard F, Carricajo A, Lucht F, Cazorla C, Garraud O, Pozzetto B, Berthelot P
(2012) Quantification by real-time PCR assay of Staphylococcus aureus load: a useful tool for
rapidly identifying persistent nasal carriers. J Clin Microbiol 50:2063-2065. doi: 10.1128/JCM.
00157-12 , JCM.00157-12 [pii]