High-throughput detection of food-borne pathogenic bacteria using oligonucleotide microarray with quantum dots as fluorescent labels

International Journal of Food Microbiology

Volumn 185, Issue , 2014, Pages 27-32

  Huang, Aihua ^a,b   Qiu, Zhigang ^a   Jin, Min ^a   Shen, Zhiqiang ^a   Chen, Zhaoli ^a   Wang, Xinwei ^a   Li, Jun Wen ^a  

^a INSTITUTE OF HEALTH AND ENVIRONMENTAL MEDICINE   (China)

^b MEDICAL COLLEGE OF CHINESE PEOPLE'S ARMED POLICE FORCES   (China)

Author keywords

Bacteria; Detection; Hybridization; Microarray; Probes; Quantum dots

Indexed keywords

BIOTIN; CADMIUM SELENIDE; OLIGONUCLEOTIDE; QUANTUM DOT; RNA 16S; STREPTAVIDIN; ZINC SULFIDE;

ARTICLE; BACTERIAL STRAIN; BACTERIUM CONTAMINATION; BACTERIUM CULTURE; BACTERIUM DETECTION; COLONY FORMING UNIT; CONTROLLED STUDY; DNA MICROARRAY; FLUORESCENCE ANALYSIS; FOOD ANALYSIS; FOOD CONTAMINATION; HYBRIDIZATION; NONHUMAN; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SIMULATION; SPECIES IDENTIFICATION;

BACTERIA; DETECTION; HYBRIDIZATION; MICROARRAY; PROBES; QUANTUM DOTS;

BACTERIA; FOOD MICROBIOLOGY; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; QUANTUM DOTS; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY;

EID: 84902267920     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2014.05.012     Document Type: Article

References (54)

1. Abubakar I., Irvine L., Aldus C.F., Wyatt G.M., Fordham R., Schelenz S., Shepstone L., Howe A., Peck M., Hunter P.R. A systematic review of the clinical, public health and cost-effectiveness of rapid diagnostic tests for the detection and identification of bacterial intestinal pathogens in faeces and food. Health Technol. Assess. 2007, 11:1-216.
2. Afghani B., Stutman H.R. Polymerase chain reaction for diagnosis of M. tuberculosis: comparison of simple boiling and a conventional method for DNA extraction. Biochem. Mol. Med. 1996, 57:14-18.
3. Call D.R., Borucki M.K., Loge F.J. Detection of bacterial pathogens in environmental samples using DNA microarrays. J. Microbiol. Methods 2003, 53:235-243.
4. Caspers M.P., Schuren F.H., van Zuijlen A.C., Brul S., Montijn R.C., Abee T., Kort R. A mixed-species microarray for identification of food spoilage bacilli. Food Microbiol. 2011, 28:245-251.
5. Chan W.C., Maxwell D.J., Gao X., Bailey R.E., Han M., Nie S. Luminescent quantum dots for multiplexed biological detection and imaging. Curr. Opin. Biotechnol. 2002, 13:40-46.
6. Chung Y., Kim J.E., Lim H.S., Kim H.K. Clinical performance of anticardiolipin and antiβ2 glycoprotein I antibodies using a new automated chemiluminescent assay: superior thrombotic prediction of combined results measured by two different methods. Blood Coagul. Fibrinolysis. 2014, 25:10-15.
7. Cremonesi P., Pisoni G., Severgnini M., Consolandi C., Moroni P., Raschetti M., Castiglioni B. Pathogen detection in milk samples by ligation detection reaction-mediated universal array method. J. Dairy Sci. 2009, 92:3027-3039.
8. de Las Rivas B., Marcobal A., Munoz R. Improved multiplex-PCR method for the simultaneous detection of food bacteria producing biogenic amines. FEMS Microbiol. Lett. 2005, 244:367-372.
9. Drost D.R., Novaes E., Boaventura-Novaes C., Benedict C.I., Brown R.S., Yin T., Tuskan G.A., Kirst M. A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence. Plant J. 2009, 58:1054-1067.
10. Fricker M., Messelhausser U., Busch U., Scherer S., Ehling-Schulz M. Diagnostic real-time PCR assays for the detection of emetic Bacillus cereus strains in foods and recent food-borne outbreaks. Appl. Environ. Microbiol. 2007, 73:1892-1898.
11. Fukushima H., Katsube K., Hata Y., Kishi R., Fujiwara S. Rapid separation and concentration of food-borne pathogens in food samples prior to quantification by viable-cell counting and real-time PCR. Appl. Environ. Microbiol. 2007, 73:92-100.
12. Gazouli M., Liandris E., Andreadou M., Sechi L.A., Masala S., Paccagnini D., Ikonomopoulos J. Specific detection of unamplified mycobacterial DNA by use of fluorescent semiconductor quantum dots and magnetic beads. J. Clin. Microbiol. 2010, 48:2830-2835.
13. Gerion D., Chen F., Kannan B., Fu A., Parak W.J., Chen D.J., Majumdar A., Alivisatos A.P. Room-temperature single-nucleotide polymorphism and multiallele DNA detection using fluorescent nanocrystals and microarrays. Anal. Chem. 2003, 75:4766-4772.
14. Gomes B.C., Franco B.D., De Martinis E.C. Microbiological food safety issues in Brazil: bacterial pathogens. Foodborne Pathog. Dis. 2013, 10:197-205.
15. Haagsma J.A., Polinder S., Stein C.E., Havelaar A.H. Systematic review of foodborne burden of disease studies: quality assessment of data and methodology. Int. J. Food Microbiol. 2013, 166:34-47.
16. Hacia J.G., Edgemon K., Fang N., Mayer R.A., Sudano D., Hunt N., Collins F.S. Oligonucleotide microarray based detection of repetitive sequence changes. Hum. Mutat. 2000, 16:354-363.
17. Hahn M.A., Tabb J.S., Krauss T.D. Detection of single bacterial pathogens with semiconductor quantum dots. Anal. Chem. 2005, 77:4861-4869.
18. Horakova K., Mlejnkova H., Mlejnek P. Evaluation of methods for isolation of DNA for polymerase chain reaction (PCR)-based identification of pathogenic bacteria from pure cultures and water samples. Water Sci. Technol. 2008, 58:995-999.
19. Huang A., Li J.W., Shen Z.Q., Wang X.W., Jin M. High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray. J. Clin. Microbiol. 2006, 44:3299-3305.
20. Jin D.Z., Wen S.Y., Chen S.H., Lin F., Wang S.Q. Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays. Mol. Cell. Probes 2006, 20:337-347.
21. Jin D., Qi H., Chen S., Zeng T., Liu Q., Wang S. Simultaneous detection of six human diarrheal pathogens by using DNA microarray combined with tyramide signal amplification. J. Microbiol. Methods 2008, 75:365-368.
22. Karlin-Neumann G., Sedova M., Falkowski M., Wang Z., Lin S., Jain M. Application of quantum dots to multicolor microarray experiments: four-color genotyping. Methods Mol. Biol. 2007, 374:239-251.
23. Kim C.J., Jeong J.K., Park M., Park T.S., Park T.C., Namkoong S.E., Park J.S. HPV oligonucleotide microarray-based detection of HPV genotypes in cervical neoplastic lesions. Gynecol. Oncol. 2003, 89:210-217.
24. Kim J.S., Lee G.G., Park J.S., Jung Y.H., Kwak H.S., Kim S.B., Nam Y.S., Kwon S.T. A novel multiplex PCR assay for rapid and simultaneous detection of five pathogenic bacteria: Escherichia coli O157:H7, Salmonella, Staphylococcus aureus, Listeria monocytogenes, and Vibrio parahaemolyticus. J. Food Prot. 2007, 70:1656-1662.
25. Kim T.K., Oh S.W., Hong S.C., Mok Y.J., Choi E.Y. Point-of-Care Fluorescence Immunoassay for Cardiac Panel Biomarkers 2014, J. Clin. Lab, Anal. 10.1002/jcla.21704.
26. Kozak G.K., MacDonald D., Landry L., Farber J.M. Foodborne outbreaks in Canada linked to produce: 2001 through 2009. J. Food Prot. 2013, 76:173-183.
27. Lee L.Y., Ong S.L., Hu J.Y., Ng W.J., Feng Y., Tan X., Wong S.W. Use of semiconductor quantum dots for photostable immunofluorescence labeling of Cryptosporidium parvum. Appl. Environ. Microbiol. 2004, 70:5732-5736.
28. Leporati M., Bua R.O., Mariano F., Carignano P., Stella M., Biancone L., Vincenti M. Determination by LC-MS/MS of colistins A and B in plasma and ultrafiltrate from critically ill patients undergoing continuous venovenous hemodiafiltration. Ther. Drug. Monit. 2014, 36:182-191.
29. Liang R.Q., Li W., Li Y., Tan C.Y., Li J.X., Jin Y.X., Ruan K.C. An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 2005, 33:e17.
30. Liu Y.J., Zhang C.M., Wang X.C., Lu Y.J., Zuo L.L. Detection of enteric pathogenic bacteria from surface waters by quantitative polymerase chain reaction (QPCR). Huan Jing Ke Xue 2008, 29:1175-1180.
31. Llop P., Caruso P., Cubero J., Morente C., Lopez M.M. A simple extraction procedure for efficient routine detection of pathogenic bacteria in plant material by polymerase chain reaction. J. Microbiol. Methods 1999, 37:23-31.
32. Lopez I., Pardo M.A. Evaluation of a real-time polymerase chain reaction (PCR) assay for detection of anisakis simplex parasite as a food-borne allergen source in seafood products. J. Agric. Food. Chem. 2010, 58:1469-1477.
33. Mao H., Li Y., Pei X., He C., Qu L. Rapid detection of three foodborne pathogenic bacteria by multiplex polymerase chain reaction-capillary electrophoresis with laser induced fluorescence detector. Se Pu 2007, 25(4):473-477.
34. Maruyama N., Segawa T., Kinoshita N., Ichihara A. Novel sandwich ELISA for detecting the human soluble (pro)renin receptor. Front. Biosci. (Elite Ed). 2013, (5):583-590.
35. Naravaneni R., Jamil K. Rapid detection of food-borne pathogens by using molecular techniques. J. Med. Microbiol. 2005, 54:51-54.
36. Panicker G., Call D.R., Krug M.J., Bej A.K. Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarrays. Appl. Environ. Microbiol. 2004, 70:7436-7444.
37. Park J.H., Kim I.J., Kang H.C., Shin Y., Park H.W., Jang S.G., Ku J.L., Lim S.B., Jeong S.Y., Park J.G. Oligonucleotide microarray-based mutation detection of the K-ras gene in colorectal cancers with use of competitive DNA hybridization. Clin. Chem. 2004, 50:1688-1691.
38. Pasquini G., Barba M., Hadidi A., Faggioli F., Negri R., Sobol I., Tiberini A., Caglayan K., Mazyad H., Anfoka G., Ghanim M., Zeidan M., Czosnek H. Oligonucleotide microarray-based detection and genotyping of Plum pox virus. J. Virol. Methods 2008, 147:118-126.
39. Pathak S., Choi S.K., Arnheim N., Thompson M.E. Hydroxylated quantum dots as luminescent probes for in situ hybridization. J. Am. Chem. Soc. 2001, 123:4103-4104.
40. Peplies J., Glockner F.O., Amann R. Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 2003, 69:1397-1407.
41. Priest F.G., Kaji D.A., Rosato Y.B., Canhos V.P. Characterization of Bacillus thuringiensis and related bacteria by ribosomal RNA gene restriction fragment length polymorphisms. Microbiology 1994, 140:1015-1022.
42. Rasooly A., Herold K.E. Food microbial pathogen detection and analysis using DNA microarray technologies. Foodborne Pathog. Dis. 2008, 5:531-550.
43. Resch-Genger U., Grabolle M., Cavaliere-Jaricot S., Nitschke R., Nann T. Quantum dots versus organic dyes as fluorescent labels. Nat. Methods 2008, 5:763-775.
44. Sawada N., Iwamura Y., Shimizu T., Hayashi H. Detection and identification of pathogenic bacteria by polymerase chain reaction with primers from DNA sequence of ribosomal RNA. Nihon Saikingaku Zasshi 1992, 47:607-616.
45. Shingyoji M., Gerion D., Pinkel D., Gray J.W., Chen F. Quantum dots-based reverse phase protein microarray. Talanta 2005, 67:472-478.
46. Suo B., He Y., Paoli G., Gehring A., Tu S.I., Shi X. Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Mol. Cell. Probes 2010, 24:77-86.
47. Takaishi Y., Morii H., Miki T. The benzoyl-DL arginine-naphthylamide (BANA) test and polymerase chain reaction measurement of pathogenic bacteria can assess the severity of periodontal disease. Int. J. Tissue React. 2003, 25:19-24.
48. Tan C.Y., Liang R.Q., Ruan K.C. Application of quantum dot to life science. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 2002, 34:1-5.
49. Tiberini A., Tomassoli L., Barba M., Hadidi A. Oligonucleotide microarray-based detection and identification of 10 major tomato viruses. J. Virol. Methods 2010, 168:133-140.
50. Versalovic J., Kapur V., Koeuth T., Mazurek G.H., Whittam T.S., Musser J.M., Lupski J.R. DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction. Arch. Pathol. Lab. Med. 1995, 119:23-29.
51. Wang X.W., Zhang L., Jin L.Q., Jin M., Shen Z.Q., An S., Chao F.H., Li J.W. Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens. Appl. Microbiol. Biotechnol. 2007, 76:225-233.
52. Wang M., Cao B., Gao Q., Sun Y., Liu P., Feng L., Wang L. Detection of Enterobacter sakazakii and other pathogens associated with infant formula powder by use of a DNA microarray. J. Clin. Microbiol. 2009, 47:3178-3184.
53. Xiao Y., Barker P.E. Semiconductor nanocrystal probes for human metaphase chromosomes. Nucleic Acids Res. 2004, 32:e28.
54. Zhao Y., Ye M., Chao Q., Jia N., Ge Y., Shen H. Simultaneous detection of multifood-borne pathogenic bacteria based on functionalized quantum dots coupled with immunomagnetic separation in food samples. J. Agric. Food. Chem. 2009, 57:517-524.