Five commercial DNA extraction systems tested and compared on a stool sample collection

Diagnostic Microbiology and Infectious Disease

Volumn 69, Issue 3, 2011, Pages 240-244

  Persson, Søren ^a   de Boer, Richard F ^b   Kooistra Smid, Anna M D ^b   Olsen, Katharina E P ^a  

^a STATENS SERUM INSTITUT   (Denmark)

^b Laboratory for Infectious Diseases ^*  (Netherlands)

Author keywords

Commercial kits; DNA extraction; DNA purification; Gastrointestinal pathogens; Stool

Indexed keywords

BACTERIAL DNA;

ANALYTICAL EQUIPMENT; ARTICLE; BACTERIAL VIRULENCE; BACTERIUM CULTURE; CAMPYLOBACTER JEJUNI; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; DIARRHEA; DNA EXTRACTION SYSTEM; DNA PURIFICATION; ESCHERICHIA COLI; FECES ANALYSIS; HUMAN; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; OUTCOME ASSESSMENT; PRIORITY JOURNAL; PROCESS OPTIMIZATION; SALMONELLA ENTERICA; SENSITIVITY AND SPECIFICITY;

CAMPYLOBACTER JEJUNI; CLOSTRIDIUM DIFFICILE; DNA, BACTERIAL; ESCHERICHIA COLI; FECES; HUMANS; MOLECULAR TYPING; POLYMERASE CHAIN REACTION; SALMONELLA ENTERICA;

EID: 79951879778     PISSN: 07328893     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2010.09.023     Document Type: Article

References (31)

1. Aabo S., Rasmussen O.F., Rossen L., Sorensen P.D., Olsen J.E. Salmonella identification by the polymerase chain reaction. Mol. Cell. Probes 1993, 7:171-178.
2. Abu Al-Soud W., Radstrom P. Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 1998, 64:3748-3753.
3. Abu Al-Soud W., Radstrom P. Effects of amplification facilitators on diagnostic PCR in the presence of blood, feces, and meat. J. Clin. Microbiol. 2000, 38:4463-4470.
4. Akane A., Matsubara K., Nakamura H., Takahashi S., Kimura K. Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J. Forensic. Sci. 1994, 39:362-372.
5. Argyros F.C., Ghosh M., Huang L., Masubuchi N., Cave D.R., Grubel P. Evaluation of a PCR primer based on the isocitrate dehydrogenase gene for detection of Helicobacter pylori in feces. J. Clin. Microbiol. 2000, 38:3755-3758.
6. Barken K.B., Haagensen J.A., Tolker-Nielsen T. Advances in nucleic acid-based diagnostics of bacterial infections. Clin. Chim. Acta 2007, 384:1-11.
7. Best E.L., Powell E.J., Swift C., Grant K.A., Frost J.A. Applicability of a rapid duplex real-time PCR assay for speciation of Campylobacter jejuni and Campylobacter coli directly from culture plates. FEMS Microbiol. Lett. 2003, 229:237-241.
8. Blom M., Meyer A., Gerner-Smidt P., Gaarslev K., Espersen F. Evaluation of Statens Serum Institut enteric medium for detection of enteric pathogens. J. Clin. Microbiol. 1999, 37:2312-2316.
9. Brownie J., Shawcross S., Theaker J., Whitcombe D., Ferrie R., Newton C., Little S. The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res. 1997, 25:3235-3241.
10. de Boer R.F., Wijma J.J., Schuurman T., Moedt J., Dijk-Alberts B.G., Ott A., Kooistra-Smid A.M., van Duynhoven Y.T. Evaluation of a rapid molecular screening approach for the detection of toxigenic Clostridium difficile in general and subsequent identification of the tcdC Delta117 mutation in human stools. J Microbiol Methods 2010, 83:59-65.
11. Espy M.J., Uhl J.R., Sloan L.M., Buckwalter S.P., Jones M.F., Vetter E.A., Yao J.D., Wengenack N.L., Rosenblatt J.E., Cockerill F.R., Smith T.F. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin. Microbiol. Rev. 2006, 19:165-256.
12. Kreader C.A. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol. 1996, 62:1102-1106.
13. Lantz P.A., Matsson M., Wadström T., Rådström P. Removal of PCR inhibitors from human faecal samples through the use of an aqueous two-phase system for sample preparation prior to PCR. J. Microbiol. Methods 1997, 28:159-167.
14. Lou Q., Chong S.K., Fitzgerald J.F., Siders J.A., Allen S.D., Lee C.H. Rapid and effective method for preparation of fecal specimens for PCR assays. J. Clin. Microbiol. 1997, 35:281-283.
15. Malorny B., Paccassoni E., Fach P., Bunge C., Martin A., Helmuth R. Diagnostic real-time PCR for detection of Salmonella in food. Appl. Environ. Microbiol. 2004, 70:7046-7052.
16. Markoulatos P., Siafakas N., Moncany M. Multiplex polymerase chain reaction: a practical approach. J. Clin. Lab. Anal. 2002, 16:47-51.
17. Monteiro L., Bonnemaison D., Vekris A., Petry K.G., Bonnet J., Vidal R., Cabrita J., Megraud F. Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J. Clin. Microbiol. 1997, 35:995-998.
18. Oikarinen S., Tauriainen S., Viskari H., Simell O., Knip M., Virtanen S., Hyoty H. PCR inhibition in stool samples in relation to age of infants. J. Clin. Virol. 2009, 44:211-214.
19. Okamoto H., Takano E., Sugao T., Kage K., Okamoto E., Nishimura N., Ueda K. Direct amplification of Escherichia coli O157 vero toxin genes from human faeces by the polymerase chain reaction. Ann. Clin. Biochem. 1999, 36(Pt 5):642-648.
20. Persson S., Olsen K.E.P. Multiplex PCR for identification of Campylobacter coli and Campylobacter jejuni from pure cultures and directly on stool samples. J. Med. Microbiol. 2005, 54:1043-1047.
21. Persson S., Olsen K.E.P., Scheutz F., Krogfelt K.A., Gerner-Smidt P. A method for fast and simple detection of major diarrhoeagenic Escherichia coli in the routine diagnostic laboratory. Clin. Microbiol. Infect. 2007, 13:516-524.
22. Persson S., Torpdahl M., Olsen K.E.P. New multiplex PCR method for the detection of Clostridium difficile toxin A (tcdA) and toxin B (tcdB) and the binary toxin (cdtA/cdtB) genes applied to a Danish strain collection. Clin. Microbiol. Infect. 2008, 14:1057-1064.
23. Schuurman T., de Boer R.F., van Zanten E., van Slochteren K.R., Scheper H.R., Dijk-Alberts B.G., Moller A.V., Kooistra-Smid A.M. Feasibility of a molecular screening method for detection of Salmonella enterica and Campylobacter jejuni in a routine community-based clinical microbiology laboratory. J. Clin. Microbiol. 2007, 45:3692-3700.
24. Schuurman T., Roovers A., van der Zwaluw W.K., van Zwet A.A., Sabbe L.J., Kooistra-Smid A.M., van Duynhoven Y.T. Evaluation of 5'-nuclease and hybridization probe assays for the detection of shiga toxin-producing Escherichia coli in human stools. J. Microbiol. Methods 2007, 70:406-415.
25. Stacy-Phipps S., Mecca J.J., Weiss J.B. Multiplex PCR assay and simple preparation method for stool specimens detect enterotoxigenic Escherichia coli DNA during course of infection. J. Clin. Microbiol. 1995, 33:1054-1059.
26. Vu D.T., Sethabutr O., Von Seidlein L., Tran V.T., Do G.C., Bui T.C., Le H.T., Lee H., Houng H.S., Hale T.L., Clemens J.D., Mason C., Dang D.T. Detection of Shigella by a PCR assay targeting the ipaH gene suggests increased prevalence of shigellosis in Nha Trang, Vietnam. J. Clin. Microbiol. 2004, 42:2031-2035.
27. Weaver J.W., Rowe M.T. Effect of non-target cells on the sensitivity of the PCR for Escherichia coli O157:H7. Lett. Appl. Microbiol. 1997, 25:109-112.
28. Whitehouse C.A., Hottel H.E. Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol. Cell. Probes 2007, 21:92-96.
29. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 1997, 63:3741-3751.
30. Yang Y.G., Song M.K., Park S.J., Kim S.W. Direct detection of Shigella flexneri and Salmonella typhimurium in human feces by real-time PCR. J. Microbiol. Biotechnol. 2007, 17:1616-1621.
31. Yu Z., Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 2004, 36:808-812.