Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays

Molecular and Cellular Probes

Volumn 20, Issue 6, 2006, Pages 337-347

  Jin, Da Zhi ^a   Wen, Si Yuan ^a   Chen, Su Hong ^a   Lin, Feng ^b   Wang, Sheng Qi ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b THE FIRST PEOPLE S HOSPITAL OF WENLING   (China)

Author keywords

Detection and identification; DNA microarrays; Intestinal pathogens

Indexed keywords

BACTERIAL DNA; DNA 16S; DNA 23S;

AMPLICON; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; FECES MICROFLORA; GENE AMPLIFICATION; GENETIC SCREENING; HYBRIDIZATION; INTESTINE FLORA; MICROBIAL IDENTIFICATION; MICROORGANISM DETECTION; MOLECULAR PROBE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

BACTERIAL INFECTIONS; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; FECES; HUMANS; INTESTINES; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR PROBES; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

BACTERIA (MICROORGANISMS);

EID: 33749045848     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2006.03.005     Document Type: Article

References (42)

1. Burkhalter P.W., Muller C., Luthy J., and Candrian U. AIAC Int 78 (1995) 1531-1537
2. Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., and Solas D. Light-directed, apatiallt addressable parallel chemical synthesis. Science 251 (1991) 767-773
3. Fodor S.P., Rava R.P., Huang X.C., Pease A.C., Holmes C.P., and Adams C.L. Multiplexed biochemical assays with biological chip. Nature 364 (1993) 555-556
4. Schena M. Microarray biochip technology (2000), Eaton Publishing, Natick, MA, USA
5. Al-Khaldi S.F., Villanueva D., and Chizhikov V. Identification and characterization of Clostridium perfringens using single target DNA microarray chip. Int J Food Microbiol 91 (2004) 289-296
6. Call D.R., Brockman F.J., and Chanler D.P. Detecting and genotyping E. coli O157:H7 using multiplexed PCR and nucleic acid microarrays. Int J Food Microbiol 67 (2001) 71-80
7. Chizhikov V., Rasooly A., Chumakov K., and Levy D.D. Microarray analysis of microbial virulence factors. Appl Environ Microbiol 67 (2001) 3258-3263
8. Keramas G., Bang D.D., Lund M., Rasmussen S.E., Bunkenborg H., Telleman P., et al. Development of a sensitive DNA microarray suitable for rapid detection of campylobacter spp. Mol Cellar Probes 17 4 (2003) 187-196
9. Ko K.S., Kim J.W., Jung B.Y., Kim I.J., and Kook Y.H. Identification of bacillus anthracis by rpoB sequence analysis and multiplex PCR. J Clin Microbiol 41 7 (2003) 2908-2914
10. Wilson W.J., Strout C.L., Desantis T.Z., Stilwell J.L., Carrano A.V., and Andersen G.L. sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cellar Probes 16 (2002) 119-127
11. Jung W- S., Kim S., Hong S- I., Min N- K., Lee C- W., and Paek S- H. DNA probe chip system for multiple detection of food poisoning microorganisms. Mater Sci Eng 24 (2004) 47-51
12. Call D.R., Borucki M., and Loge F. Detection of bacterial pathogens in environmental samples using DNA microarrays. J Microbiol Methods 53 (2003) 235-243
13. Woese C.R. Bacterial evolution. Microbiol Rev 51 (1987) 221-271
14. Burgin A.B., Parodos K., Lane D.J., and Pace N.R. The excision of intervening sequences from Salmonella 23S ribosomal RNA. Cell 60 (1990) 405-414
15. Gurtler V., and Stanisich V.A. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142 (1996) 3-16
16. Hopfl P., Ludwig W., Schleifer K.H., and Larsen N. The 23S ribosomal RNA higher-order structure of Pseudomonas cepacia and other prokaryotes. Eur J Biochem 185 (1989) 355-364
17. Ludwig W., Kirchhof G., Klugbauer N., et al. Complete 23S ribosomal RNA sequences of Gram-positive bacteria with a low DNA G+C content. Syst Appl Microbiol 15 (1992) 487-501
18. Ludwig W., Rossello-Mora R., Aznar R., Klugbauer S., Spring S., Reetz K., et al. Comparative sequence analysis of 23S rRNA from proteobacteria. Syst Appl Microbiol 18 (1995) 164-188
19. Roller C., Ludwig W., and Schleifer K.H. Gram-positive bacteria with a high DNA G+C content are characterized by a common insertion within their 23S rRNA genes. J Gen Microbiol 138 (1992) 1167-1175
20. Greisen K., Loeffelholz M., Purohit A., and Leong D. PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. J Clin Microbiol 32 (1994) 335-351
21. Helps C.R., Harbour D.A., and Corry J.E. PCR-based 16S ribosomal DNA detection technique for Clostridium estertheticum causing spoilage in vacuum-packed chill-stored beef. Int J Food Microbiol 52 (1999) 57-65
22. Madico G., Quinn T.C., Boman J., and Gaydos C.A. Touchdown enzyme time release-PCR for detection and identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci using the 16S and 16S-23S spacer rRNA genes. J Clin Microbiol 38 (2000) 1085-1093
23. Siqueira J.F., Rocas I.N., Favieri A., and Santos K.R. Detection of Treponema denticola in endodontic infections by 16S rRNA gene-directed polymerase chain reaction. Oral Microbiol Immunol 15 (2000) 335-337
24. Matar G.M., Koehler J.E., Malcolm G., Lambert-Fair M.A., Tappero J., Hunter S.B., et al. Identification of Bartonella species directly in clinical specimens by PCR-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment. J Clin Microbiol 37 (1999) 4045-4047
25. Anthony R.M., Brown T.J., and French G.L. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 38 2 (2000) 781-788
26. Hong B.-X., Jiang L.-F., Hu Y.-S., and Fang D.-Y. Application of oligonucleotide array technology for the rapid detection of pathogenic bacteria of foodborne infections. J Microbiol Methods 58 (2004) 403-411
27. Frahm E., Heiber I., Hoffmann S., Koob C., Meier H., Ludwig W., et al. Application of 23S rDNA-targeted oligonucleotide probes specific for enterococci to water hygiene control. Syst Appl Microbiol 21 (1998) 450-453
28. Straub J.A., Hertel C., and Hammes W.P. A 23S rDNA-targeted polymerase chain reaction-based system for detection of Staphylococcus aureus in meat starter cultures and dairy products. J Food Prot 62 (1999) 1150-1156
29. Gu X.X., Rossau R., Jannes G., Ballard R., Laga M., and Van Dyck E. The rrs (16S)-rrl (23S) ribosomal intergenic spacer region as a target for the detection of Haemophilus ducreyi by a heminested-PCR assay. Microbiology 144 (1998) 1013-1019
30. Hamid M.E., Roth A., Landt O., Kroppenstedt R.M., Goodfellow M., and Mauch H. Differentiation between Mycobacterium farcinogenes and Mycobacterium senegalense species based on 16S-23S ribosomal DNA internal transcribed spacer sequences. J Clin Microbiol 40 (2002) 707-711
31. Nubel U., Schmidt P.M., Reiss E., Bier F., Beyer W., and Nanmann D. Oligonucleotide microarray for identification of bacillus anthracis based on intergenic transcribed spacers in ribosomal DNA. FEMS Microbiol Lett 240 2 (2004) 215-223
32. Sasaki Y., Yamamoto K., Amimoto K., Kojima A., Ogikubo Y., Norimatsu M., et al. Amplification of the 16S-23S rDNA spacer region for rapid detection of Clostridium chauvoei and Clostridium septicum. Res Vet Sci 71 (2001) 227-229
33. Evans A.S. Bacterial infections of humans (1998), Plenum Medical Book Company, New York, NY
34. Miliotis M.D. International handbook of foodborne pathogens (2003), Marcel Dekker, New York, Basel
35. Wang R.-F., Beggs M.L., Robertson L.H., and Ceriglia C.E. Design and evaluation of oligonucleotide-microarray method for the detection of human intentinal bacteria in fecal samples. FEMS Microbiol Lett 213 (2002) 175-182
36. Wen S.-Y., Wang H., Sun O.-J., and Wang S.-Q. Rapid detection of the known SNPs of CYP 2C9 using oligonucleotide microarray. World J Gastroenterol 9 6 (2003) 1342-1346
37. In: Holt J.G., Krieg N.R., Sneath P.H.A., Staley J.T., and Williams S.T. (Eds). Bergey's manual of determinative bacteriology. 9th ed (1994), Williams & Wilkins, Baltimore, MD
38. Lane S., Evermann J., Loge F., and Call D.R. Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays. Biosensors Bioelectron 20 (2004) 728-735
39. Warsen A.E., Krug M.J., LaFrentz S., Stanek D.R., Loge F.J., and Call D.R. Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays. Appl Environ Microbiol 70 7 (2004) 4216-4221
40. Carman R.J., Tassell R.L., and Van Wilkins T.D. The normal intestinal microflora: ecology, variability and stability. Vet Hum Toxicol 35 1 (1993) 11-14
41. Drasar B.S., and Duerden B.I. Anaerobes in the normal flora of man. In: Duerden B.I., and Drasar B.S. (Eds). Anaerobes in human disease (1991), Wiley-Liss, New York, NY 162-179
42. Drasar B.S., and Roberts A.K. Control of the large bowel microflora. In: Hill M.J., and Marsh B.S. (Eds). Human microbial ecology (1990), CRC Press, Boca Raton, FL 95-100