Evaluation of automated and manual commercial DNA extraction methods for recovery of Brucella DNA from suspensions and spiked swabs

Journal of Clinical Microbiology

Volumn 47, Issue 12, 2009, Pages 3920-3926

  Dauphin, Leslie A ^a   Hutchins, Rebecca J ^b   Bost, Liberty A ^c   Bowen, Michael D ^a,d  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b Medical Staffing Network Inc   (United States)

^c EMORY UNIVERSITY   (United States)

^d NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PHOSPHATE BUFFERED SALINE;

ARTICLE; AUTOANALYSIS; BACTERIAL STRAIN; BACTERIAL VIABILITY; BACTERIUM CULTURE; BACTERIUM DETECTION; BRUCELLA; COMPARATIVE STUDY; CONTROLLED STUDY; COST BENEFIT ANALYSIS; DNA EXTRACTION; DNA ISOLATION; DNA PURIFICATION; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA PURIFICATION; SENSITIVITY ANALYSIS;

AUTOMATION; BACTERIOLOGICAL TECHNIQUES; BRUCELLA; BRUCELLA ABORTUS; BRUCELLA MELITENSIS; BRUCELLA SUIS; BRUCELLOSIS; DNA, BACTERIAL; HUMANS; POLYMERASE CHAIN REACTION; REAGENT KITS, DIAGNOSTIC; SENSITIVITY AND SPECIFICITY; SPECIES SPECIFICITY; SPECIMEN HANDLING;

BACTERIA (MICROORGANISMS); BRUCELLA; BRUCELLA MELITENSIS; BRUCELLA MELITENSIS BIOVAR ABORTUS;

EID: 71549136165     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01288-09     Document Type: Article

References (33)

1. Al Dahouk, S., H. Tomaso, K. Nockler, and H. Neubauer. 2004. The detection of Brucella spp. using PCR-ELISA and real-time PCR assays. Clin. Lab. 50:387-394.
2. Bricker, B. J., D. R. Ewalt, and S. M. Halling. 2003. Brucella "HOOF-Prints": strain typing by multi-locus analysis of variable number tandem repeats (VNTRs). BMC Microbiol. 3:15.
3. CDC and NIH. 2007. Biosafety in microbiological and biomedical laboratories, 5th ed. U.S. Government Printing Office, Washington, DC.
4. Christopher, G. W., M. B. Agan, T. J. Cieslak, and P. E. Olson. 2005. History of U.S. military contributions to the study of bacterial zoonoses. Mil. Med. 170:39-48.
5. Dauphin, L. A., and M. D. Bowen. 2009. A simple method for the rapid removal of Bacillus anthracis spores from DNA preparations. J. Microbiol. Methods 76:212-214.
6. Dauphin, L. A., B. D. Moser, and M. D. Bowen. 2009. Evaluation of five commercial nucleic acid extraction kits for their ability to inactivate Bacillus anthracis spores and comparison of DNA yields from spores and spiked environmental samples. J. Microbiol. Methods 76:30-37.
7. Dauphin, L. A., K. W. Stephens, S. C. Eufinger, and M. D. Bowen. 2009. Comparison of five commercial DNA extraction kits for the recovery of Yersinia pestis DNA from bacterial suspensions and spiked environmental samples. J. Appl. Microbiol. doi:10.1111/j.1365-2762.2009.04404.x.
8. Debeaumont, C., P. A. Falconnet, and M. Maurin. 2005. Real-time PCR for detection of Brucella spp. DNA in human serum samples. Eur. J. Clin. Microbiol. Infect. Dis. 24:842-845.
9. Foster, J. T., R. T. Okinaka, R. Svensson, K. Shaw, B. K. De, R. A. Robison, W. S. Probert, L. J. Kenefic, W. D. Brown, and P. Keim. 2008. Real-time PCR assays of single-nucleotide polymorphisms defining the major Brucella clades. J. Clin. Microbiol. 46:296-301.
10. Gee, J. E., B. K. De, P. N. Levett, A. M. Whitney, R. T. Novak, and T. Popovic. 2004. Use of 16S rRNA gene sequencing for rapid confirmatory identification of Brucella isolates. J. Clin. Microbiol. 42:3649-3654. (Pubitemid 39045694)
11. Greenfield, R. A., D. A. Drevets, L. J. Machado, G. W. Voskuhl, P. Cornea, and M. S. Bronze. 2002. Bacterial pathogens as biological weapons and agents of bioterrorism. Am. J. Med. Sci. 323:299-315.
12. Halling, S. M., B. D. Peterson-Burch, B. J. Bricker, R. L. Zuerner, Z. Qing, L. L. Li, V. Kapur, D. P. Alt, and S. C. Olsen. 2005. Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J. Bacteriol. 187:2715-2726.
13. Heller, M. B., M. L. Bunning, M. E. France, D. M. Niemeyer, L. Peruski, T. Naimi, P. M. Talboy, P. H. Murray, H. W. Pietz, J. Kornblum, W. Oleszko, and S. T. Beatrice. 2002. Laboratory response to anthrax bioterrorism, New York City, 2001. Emerg. Infect. Dis. 8:1096-1102.
14. Hinić, V., I. Brodard, A. Thomann, Z. Cvetnic, P. V. Makaya, J. Frey, and C. Abril. 2008. Novel identification and differentiation of Brucella melitensis, B. abortus, B. suis, B. ovis, B. canis, and B. neotomae suitable for both conventional and real-time PCR systems. J. Microbiol. Methods 75:375-378.
15. Kiratisin, P., C. D. Fukuda, A. Wong, F. Stock, J. C. Preuss, L. Ediger, T. N. Brahmbhatt, S. H. Fischer, D. P. Fedorko, F. G. Witebsky, and V. J. Gill. 2002. Large-scale screening of nasal swabs for Bacillus anthracis: descriptive summary and discussion of the National Institutes of Health's experience. J. Clin. Microbiol. 40:3012-3016.
16. Knepp, J. H., M. A. Geahr, M. S. Forman, and A. Valsamakis. 2003. Comparison of automated and manual nucleic acid extraction methods for detection of enterovirus RNA. J. Clin. Microbiol. 41:3532-3536.
17. Le Flèche, P., I. Jacques, M. Grayon, S. Al Dahouk, P. Bouchon, F. Denoeud, K. Nockler, H. Neubauer, L. A. Guilloteau, and G. Vergnaud. 2006. Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay. BMC Microbiol. 6:9. (Pubitemid 44104881)
18. Luna, V. A., D. King, C. Davis, T. Rycerz, M. Ewert, A. Cannons, P. Amuso, and J. Cattani. 2003. Novel sample preparation method for safe and rapid detection of Bacillus anthracis spores in environmental powders and nasal swabs. J. Clin. Microbiol. 41:1252-1255.
19. Manchester, K. L. 1995. Value of A260/A280 ratios for measurement of purity of nucleic acis. BioTechniques 19:209-210.
20. McDonnell, G. E. 2007. Antisepsis, disinfection, and sterilization: types, action, and resistance. ASM Press, Washington, DC.
21. Murray, P. R., E. J. Baron, J. H. Jorgensen, M. L. Landry, and M. A. Pfaller. 2007. Manual of clinical microbiology, 9th ed. ASM Press, Washington, DC.
22. Newby, D. T., T. L. Hadfield, and F. F. Roberto. 2003. Real-time PCR detection of Brucella abortus: a comparative study of SYBR green I, 5′-exonuclease, and hybridization probe assays. Appl. Environ. Microbiol. 69:4753-4759.
23. Pappas, G., N. Akritidis, M. Bosilkovski, and E. Tsianos. 2005. Brucellosis. N. Engl. J. Med. 352:2325-2336.
24. Pappas, G., P. Panagopoulou, L. Christou, and N. Akritidis. 2006. Category B potential bioterrorism agents: bacteria, viruses, toxins, and foodborne and waterborne pathogens. Infect. Dis. Clin. N. Am. 20:395-421, x.
25. Paulsen, I. T., R. Seshadri, K. E. Nelson, J. A. Eisen, J. F. Heidelberg, T. D. Read, R. J. Dodson, L. Umayam, L. M. Brinkac, M. J. Beanan, S. C. Daugherty, R. T. Deboy, A. S. Durkin, J. F. Kolonay, R. Madupu, W. C. Nelson, B. Ayodeji, M. Kraul, J. Shetty, J. Malek, S. E. Van Aken, S. Riedmuller, H. Tettelin, S. R. Gill, O. White, S. L. Salzberg, D. L. Hoover, L. E. Lindler, S. M. Halling, S. M. Boyle, and C. M. Fraser. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. USA 99:13148-13153.
26. Probert, W. S., K. N. Schrader, N. Y. Khuong, S. L. Bystrom, and M. H. Graves. 2004. Real-time multiplex PCR assay for detection of Brucella spp., B. abortus, and B. melitensis. J. Clin. Microbiol. 42:1290-1293. (Pubitemid 38332870)
27. Queipo-Ortuño, M. I., F. Tena, J. D. Colmenero, and P. Morata. 2008. Comparison of seven commercial DNA extraction kits for the recovery of Brucella DNA from spiked human serum samples using real-time PCR. Eur. J. Clin. Microbiol. Infect. Dis. 27:109-114.
28. Rantakokko-Jalava, K., and J. Jalava. 2002. Optimal DNA isolation method for detection of bacteria in clinical specimens by broad-range PCR. J. Clin. Microbiol. 40:4211-4217.
29. Rose, L., B. Jensen, A. Peterson, S. N. Banerjee, and M. J. Srduino. 2004. Swab materials and Bacillus anthracis spore recovery from nonporous surfaces. Emerg. Infect. Dis. 10:1023-1029.
30. Rotz, L. D., A. S. Khan, S. R. Lillibridge, S. M. Ostroff, and J. M. Hughes. 2002. Public health assessment of potential biological terrorism agents. Emerg. Infect. Dis. 8:225-230.
31. Schuurman, T., R. de Boer, R. Patty, M. Kooistra-Smid, and A. van Zwet. 2007. Comparative evaluation of in-house manual, and commercial semi-automated and automated DNA extraction platforms in the sample preparation of human stool specimens for a Salmonella enterica 5′-nuclease assay. J. Microbiol. Methods 71:238-245. (Pubitemid 350151516)
32. Schuurman, T., A. van Breda, R. de Boer, M. Kooistra-Smid, M. Beld, P. Savelkoul, and R. Boom. 2005. Reduced PCR sensitivity due to impaired DNA recovery with the MagNA Pure LC total nucleic acid isolation kit. J. Clin. Microbiol. 43:4616-4622.
33. Verger, J. M., F. Grimont, P. A. Grimont, and M. Grayon. 1987. Taxonomy of the genus Brucella. Ann. Inst. Pasteur Microbiol. 138:235-238.