Development of a high-throughput DNA microarray for drug-resistant gene detection and its preliminary application

Journal of Microbiological Methods

Volumn 89, Issue 2, 2012, Pages 110-118

  Fu, Yali ^a   Pan, Ying ^b   Pan, Mingjie ^a   Wang, Yao ^a   Liu, Wu ^c   Li, Yuexi ^a,b  

^a NANJING MEDICAL UNIVERSITY   (China)

^b Huadong Research Institute for Medicine and Biotechniques   (China)

^c Quanyi Biotechnology Limited Company   (China)

Author keywords

Drug resistant genes; Microarray; Optimization; Preliminary application

Indexed keywords

BACTERIAL DNA; DNA; OLIGONUCLEOTIDE;

ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; DNA EXTRACTION; DNA MICROARRAY; DNA SEQUENCE; DRUG SENSITIVITY; ESCHERICHIA COLI; GENE AMPLIFICATION; GENETIC ANALYSIS; GENOTYPE; HIGH THROUGHPUT SCREENING; HYBRIDIZATION; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

BACTERIA; BACTERIAL INFECTIONS; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; DRUG RESISTANCE, BACTERIAL; GENES, BACTERIAL; GENOTYPE; HIGH-THROUGHPUT SCREENING ASSAYS; HOSPITALS; HUMANS; MICROBIAL SENSITIVITY TESTS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; SENSITIVITY AND SPECIFICITY;

BACTERIA (MICROORGANISMS);

EID: 84862827057     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.02.010     Document Type: Article

References (33)

1. Anjum M.F., Mafura M., Slickers P., Ballmer K., Kuhnert P., Woodward M.J., Ehricht R. Pathotyping Escherichia coli by using miniaturized DNA microarrays. Appl. Environ. Microbiol. 2007, 73(17):5692-5697.
2. Boerlin P., Reid-Smith R.J. Antimicrobial resistance: its emergence and transmission. Anim. Health Res. Rev. 2008, 9:115-126.
3. Call D.R., Bakko M.K., Krug M.J., Roberts M.C. Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob. Agents Chemother. 2003, 47:3290-3295.
4. Cassone M., D' Andrea M.M., Iannelli F., Oggioni M.R., Rossolini G.M., Pozzi G. DNA microarray for detection of macrolide resistance genes. Antimicrob. Agents Chemother. 2006, 50(6):2038-2041.
5. Clinical Laboratory Standards Institute Performance Standards for Antimicrobial Disk Susceptibility Tests; Approved Standard-9th ed. CLSI Document M2-A9 2006, 26:1.
6. Cockerill F.R. Genetic methods for assessing antimicrobial resistance. Antimicrob. Agents Chemother. 1999, 43(2):199-212.
7. Dudda-Subramanya R., Lucchese G., Kanduc D., Sinha A.A. Clinical applications of DNA microarray analysis. J. Exp. Ther. Oncol. 2003, 3(6):297-304.
8. Figueiredo-Costa S. Impact of antimicrobial resistance on the treatment and outcome of patients with sepsis. Shock 2008, 30:23-29.
9. Frye J.G., Jesse T., Long F., Rondeau G., Porwollik S., McClelland M., Jackson C.R., Englen M., Fedorka-Cray P.J. DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int. J. Antimicrob. Agents 2006, 27(2):138-151.
10. Frye J.G., Lindsey R.L., Rondeau G., Porwollik S., Long F., McClelland M., Jackson C.R., Englen M.D., Meinersmann R.J., Berrang M.E., Davis J.A., Barrett J.B., Turpin J.B., Thitaram S.N., Fedorka-Cray P.J. Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database. Microb. Drug Resist. 2010, 16(1):9-19.
11. Garneau P., Labrecque O., Maynard C., Messier S., Masson L., Archambault M., Harel J. Use of a bacterial antimicrobial resistance gene microarray for the identification of resistant Staphylococcus aureus. Zoonoses Public Health. 2010, 57(1):94-99.
12. Giammarinaro P., Leroy S., Chacornac J.P., Delmas J., Talon R. Development of a new oligonucleotide array to identify staphylococcal strains at species level. J. Clin. Microbiol. 2005, 43:3673-3680.
13. Hamels S., Gala J.L., Dufour S., Vannuffel P., Zammatteo N., Remacle J. Consensus PCR and microarray for diagnosis of the genus Staphylococcus, species, and methicillin resistance. Biotechniques 2001, 31(6):1364-1366. 1368, 1370-1372.
14. Lazzari S., Allegranzi B., Concia E. Making hospitals safer: the need for a global strategy for infection control in healthcare settings. World Hosp. Health Serv. 2004, 40:32. 34, 36-42.
15. Ma M., Wang H., Yu Y., Zhang D., Liu S. Detection of antimicrobial resistance genes of pathogenic Salmonella from swine with DNA microarray. J. Vet. Diagn. Invest. 2007, 19:161-167.
16. Majtan T., Majtanova L., Timko J., Majtan V. Oligonucleotide microarray for molecular characterization and genotyping of Salmonella spp. strains. J. Antimicrob. Chemother. 2007, 60:937-946.
17. Martineau F., Picard F.J., Lansac N., Ménard C., Roy P.H., Ouellette M., Bergeron M.G. Correlation between the resistance genotype determined by multiplex PCR assays and the antibiotic susceptibility patterns of Staphylococcus aureus and Staphylococcus epidermidis. Antimicrob. Agents Chemother. 2000, 44(2):231-238.
18. Martinez J.L., Baquero F. Mutation frequencies and antibiotic resistance. Antimicrob. Agents Chemother. 2000, 44(7):1771-1777.
19. Palka-Santini M., Cleven B.E., Eichinger L., Krönke M., Krut O. Large scale multiplex PCR improves pathogen detection by DNA microarrays. BMC Microbiol. 2009, 3(9):1-6.
20. Perreten V., Vorlet-Fawer L., Slickers P., Ehricht R., Kuhnert P., Frey J. Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J. Clin. Microbiol. 2005, 43(5):2291-2302.
21. Peterson G., Bai J., Nagaraja T.G., Narayanan S. Diagnostic microarray for human and animal bacterial diseases and their virulence and antimicrobial resistance genes. J. Microbiol. Methods 2010, 80(3):223-230.
22. Pittet Didier, Allegranzi Benedetta, Storr Julie, Donaldson Liam Clean care is safer care: the global patient safety challenge 2005-2006. Int. J. Infect. Dis. 2006, 10:419-424.
23. Schena M. Microarray Analysis 2003, 19-23:297-303. John Wilev&Sons, Inc., New York.
24. Shchepinov M.S., Case-Green S.C., Southern E.M. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 1997, 25(6):1155-1161.
25. Strommenger B., Schmidt C., Werner G., Roessle-Lorch B., Bachmann T.T., Witte W. DNA microarray for the detection of therapeutically relevant antibiotic resistance determinants in clinical isolates of Staphylococcus aureus. Mol. Cell. Probes 2007, 21(3):161-170.
26. Uda A., Tanabayashi K., Fujita O., Hotta A., Yamamoto Y., Yamada A. Comparison of whole genome amplification methods for detecting pathogenic bacterial genomic DNA using microarray. Jpn. J. Infect. Dis. 2007, 60(6):355-361.
27. Van Hoek A.H., Scholtens I.M., Cloeckaert A., Aarts H.J. Detection of antibiotic resistance genes in different Salmonella serovars by oligonucleotide microarray analysis. J. Microbiol. Methods 2005, 62(1):13-23.
28. Volokhov D., Chizhikov V., Chumakov K., Rasooly A. Microarray analysis of erythromycin resistance determinants. J. Appl. Microbiol. 2003, 95:787-798.
29. Wang D., Gao H., Zhang R., Ma X., Zhou Y., Cheng J. Single nucleotide polymorphism discrimination assisted by improved base stacking hybridization using oligonucleotide microarrays. Biotechniques 2003, 35(2):300-302. 304, 306.
30. Weinstein R.A. Nosocomial infection update. Emerg. Infect. Dis. 1998, 4:416-420.
31. Wilson K. Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol. 1997, 2.4.1-2.4.5.
32. World Health Organization The global patient safety challenge 2005-2006. Clean Care is Safer Care 2005, World Health Organization, Geneva, Switzerland.
33. Zou W., Frye J.G., Chang C.W., Liu J., Cerniglia C.E., Nayak R. Microarray analysis of antimicrobial resistance genes in Salmonella enterica from preharvest poultry environment. J. Appl. Microbiol. 2009, 107(3):906-914.