Evaluation of commercial kits for extraction of DNA and RNA from Clostridium difficile

Anaerobe

Volumn 18, Issue 6, 2012, Pages 608-613

  Metcalf, Devon ^a   Weese, J Scott ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Clostridium difficile; DNA extraction; RNA extraction

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; NUCLEIC ACID; VIRULENCE FACTOR;

ARTICLE; BACTERIUM IDENTIFICATION; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; DNA EXTRACTION; DNA EXTRACTION KIT; DNA ISOLATION; GENERAL DEVICE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA EXTRACTION; RNA EXTRACTION KIT; RNA ISOLATION;

CLOSTRIDIUM DIFFICILE; DNA, BACTERIAL; MOLECULAR BIOLOGY; RNA, BACTERIAL; SPECIMEN HANDLING;

CLOSTRIDIUM DIFFICILE;

EID: 84870383460     PISSN: 10759964     EISSN: 10958274     Source Type: Journal    
DOI: 10.1016/j.anaerobe.2012.10.003     Document Type: Article

References (27)

1. Pépin J., Valiquette L., Alary M., Villemure P., Pelletier A., Forget K., et al. Clostridium difficile-associated diarrhea in a region of Quebec from 1991-2003: a changing pattern of disease severity. CMAJ 2004, 171:466-472.
2. McDonald L., Owings M., Jernigan D. Clostridium difficile infection in patients discharged from US short-stay hospitals, 1996-2003. Emerg Infect Dis 2006, 12:409-415.
3. Freeman J., Bauer M., Baines S., Corver J., Fawley W., Goorhuis B., et al. The changing epidemiology of Clostridium difficile infections. Clin Microbiol Rev 2010, 23:529-549.
4. Fahle G., Fischer S. Comparison of six commercial DNA extraction kits for recovery of cytomegalovirus DNA from spiked human specimens. J Clin Microbiol 2000, 38:3860-3863.
5. Heap J., Pennington O., Cartman S., Minton N. The ClosTron: a universal gene knock-out system for the genus Clostridium. J Microbiol Methods 2007, 70:452-464.
6. Cartman S., Kelly M., Heeg D., Heap J., Minton N. Precise manipulation of the Clostridium difficile chromosome reveals a lack of association between the tcdC genotype and toxin production. Appl Environ Microbiol 2012, 78:4638-4690.
7. Fleige S., Pfaffl M. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006, 27:126-139.
8. Derveaux S., Vandesompele J., Hellemans J. How to do successful gene expression analysis using real-time PCR. Methods 2010, 50:227-230.
9. Rump L., Asamoah B., Gonzalez-Escalona N. Comparison of commercial RNA extraction kits for preparation of DNA-free total RNA from Salmonella cells. BMC Res Notes 2010, 27:3-11.
10. Kim S., Jeong H., Kim Y., Song S., Lee J., Oh S., et al. Evaluation of DNA extraction methods and their clinical application for direct detection of causative bacteria in continuous ambulatory peritoneal dialysis culture fluids from patients with peritonitis by using broad-range PCR. Ann Lab Med 2012, 32:119-125.
11. Pitcher D., Saunders N., Owen R. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 1989, 8:151-156.
12. Popham D., Setlow P. The cortical peptidoglycan from spores of Bacillus megaterium and Bacillus subtilis is not highly cross-linked. J Bacteriol 1993, 175:2767-2769.
13. Aslan K., Previte M., Zhang Y., Gallagher T., Baillie L., Geddes C. Extraction and detection of DNA from Bacillus anthracis spores and the vegetative cells within 1 min. Anal Chem 2008, 80:4125-4132.
14. Rantakokko-Jalava K., Jalava J. Optimal DNA isolation method for detection of bacteria in clinical specimens by broad-range PCR. J Clin Microbiol 2002, 40:4211-4212.
15. Metcalf D., Sharif S., Weese J.S. Evaluation of candidate reference genes in Clostridium difficile for gene expression normalization. Anaerobe 2010, 16:439-443.
16. ® stabilization solution: product guidelines 2006, Invitrogen Life Technologies Inc., Burlington, ON. http://tools.invitrogen.com/content/sfs/manuals/7020MF.pdf.
17. Bertolo L., Boncheff A., Ma Z., Chen Y., Wakeford T., Friendship R., et al. Clostridium difficile carbohydrates: glucan in spores, PSII common antigen in cells, immunogenicity of PSII in swine and synthesis of a dual C. difficile-ETEC conjugate vaccine. Carbohydr Res 2012, 354:79-86.
18. MacCannell D., Louie T., Gregson D., Laverdiere M., Labbe A.-C., Laing F., et al. Molecular analysis of Clostridium difficile PCR ribotype 027 isolates from Eastern and Western Canada. J Clin Microbiol 2006, 44:2147-2152.
19. Kuijper E., Coignard B., Brazier J., Suetens C., Drudy D., Wiuff C., et al. Update of Clostridium difficile-associated disease due to PCR ribotype 027 in Europe. Euro Surveill 2007, 12:E1-E2.
20. Goorhuis A., Bakker D., Corver J., Debast S., Harmanus C., Notermans D., et al. Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078. Clin Infect Dis 2008, 47:1162-1170.
21. Dhalluin A., Bourgeois I., Pestel-Caron M., Camiade E., Raux G., Courtin P., et al. Acd, a peptidoglycan hydrolase of Clostridium difficile with N-acetylglucosamidase activity. Microbiology 2005, 151:2343-2351.
22. Carter G., Purdy S., Williams P., Minton N. Quorum sensing in Clostridium difficile: analysis of a luxS-type signalling system. J Med Microbiol 2005, 54:119-127.
23. Govind R., Vediyappan G., Rolfe R., Dupuy B., Fralick J. Bacteriophage-mediated toxin gene regulation in Clostridium difficile. J Virol 2009, 83:12037-12045.
24. Sargent M. A procedure for isolating high quality DNA from spores of Bacillus subtilis 168. J Gen Microbiol 1980, 116:511-514.
25. Brisco M., Latham S., Bartley P., Morley A. Incorporation of measurement of DNA integrity into qPCR assays. Biotechniques 2010, 49:893-897.
26. See M., Staggs S., Dubey J., Villegas E. Evaluation of four RNA extraction methods for gene expression analyses of Cryptosporidium parvum and Toxoplasma gondii. J Microbiol Methods 2012, 89:185-192.
27. Fraga D., Meulia T., Fenster S. Real-time PCR 2008, Curr Prot Ess Lab Tech, 10.3: p. 1-34.