Specific discrimination of three pathogenic salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray

Applied and Environmental Microbiology

Volumn 80, Issue 1, 2014, Pages 366-373

  Shin, Hwa Hui ^a   Hwang, Byeong Hee ^a   Seo, Jeong Hyun ^a   Cha, Hyung Joon ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; FOOD SAFETY; OLIGONUCLEOTIDES; BIOCONTROL; CELLS; CYTOLOGY; ESCHERICHIA COLI; GENE EXPRESSION; PROTEINS; SALMONELLA;

CARBAMOYL PHOSPHATES; CROSS REACTIVITY; NONSPECIFIC SIGNALS; OLIGONUCLEOTIDE MICROARRAY; PATHOGENIC BACTERIUM; SALMONELLA ENTERICA; SALMONELLA INFECTIONS; SPECIFIC DETECTION; BIOCONTROL AGENT; CAPSID PROTEINS; COMPARATIVE GENOMIC; GROWTH ANALYSIS; LIPOPOLYSACCHARIDES; PHAGE INFECTION; PHYLOGENETIC ANALYSIS;

SALMONELLA; BACTERIOPHAGES;

ARRAY; BACTERIUM; BIOMARKER; DISCRIMINANT ANALYSIS; GENE EXPRESSION; MORBIDITY; MORTALITY; PATHOGENICITY; ANTIGEN; BACTERIOPHAGE; CELL ORGANELLE; CLUSTER ANALYSIS; GENOME; MUTATION; PROTEIN; TEMPERATE ENVIRONMENT;

BACTERIA (MICROORGANISMS); SALMONELLA; SALMONELLA ENTERICA SUBSP. ENTERICA;

LIGASE; VIRUS DNA;

ARTICLE; CLASSIFICATION; DNA MICROARRAY; EVALUATION STUDY; FOOD CONTROL; GENETICS; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; SALMONELLA ENTERICA; SENSITIVITY AND SPECIFICITY; BACTERIOLYSIS; BACTERIOPHAGE; CHEMISTRY; DNA SEQUENCE; ISOLATION AND PURIFICATION; LYSOGENIZATION; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; SALMONELLA PHAGE; SALMONELLA TYPHIMURIUM; VIROLOGY; VIRULENCE; VIRUS CULTURE; VIRUS ENTRY; VIRUS GENE; VIRUS GENOME;

BACTERIOLOGICAL TECHNIQUES; CARBON-NITROGEN LIGASES; FOOD MICROBIOLOGY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SALMONELLA ENTERICA; SENSITIVITY AND SPECIFICITY; BACTERIOLYSIS; DNA, VIRAL; GENES, VIRAL; GENOME, VIRAL; LYSOGENY; MOLECULAR SEQUENCE DATA; MUTATION; PODOVIRIDAE; SALMONELLA PHAGES; SALMONELLA TYPHIMURIUM; SEQUENCE ANALYSIS, DNA; VIRAL PLAQUE ASSAY; VIRULENCE; VIRUS INTERNALIZATION;

EID: 84891085220     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02978-13     Document Type: Article

References (47)

1. Swaminathan B, Gerner-Smidt P, Barrett T. 2006. Focus on Salmonella. Foodborne Pathog. Dis. 3:154-156. http://dx.doi.org/10.1089/fpd.2006.3.154.
2. Voetsch AC, Van Gilder TJ, Angulo FJ, Farley MM, Shallow S, Marcus R, Cieslak PR, Deneen VC, Tauxe RV, Emerging Infections Program FoodNet Working Group. 2004. FoodNet estimate of the burden of illness caused by nontyphoidal Salmonella infections in the United States. Clin. Infect. Dis. 38:S127-S134. http://dx.doi.org/10.1086/381578.
3. Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG, LeClerc JE, Ravel J, Cebula TA. 2011. Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution. J. Bacteriol. 193:3556-3568. http://dx.doi.org/10.1128/JB.00297-11.
4. Chan K, Baker S, Kim CC, Detweiler CS, Dougan G, Falkow S. 2003. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray. J. Bacteriol. 185:553-563. http://dx.doi.org/10.1128/JB.185.2.553-563.2003.
5. Grassl GA, Finlay BB. 2008. Pathogenesis of enteric Salmonella infections. Curr. Opin. Gastroenterol. 24:22-26. http://dx.doi.org/10.1097/MOG.0b013e3282f21388.
6. Layton AN, Galyov EE. 2007. Salmonella-induced enteritis: molecular pathogenesis and therapeutic implications. Expert Rev. Mol. Med. 9:1-17.
7. Liebana E, Guns D, Garcia-Migura L, Woodward MJ, Clifton-Hadley FA, Davies RH. 2001. Molecular typing of Salmonella serotypes prevalent in animals in England: assessment of methodology. J. Clin. Microbiol. 39:3609-3616. http://dx.doi.org/10.1128/JCM.39.10.3609-3616.2001.
8. Mertes F, Biens K, Lehrach H, Wagner M, Dahl A. 2010. Highthroughput universal probe Salmonella serotyping (UPSS) by nanoPCR. J. Microbiol. Methods 83:217-223. http://dx.doi.org/10.1016/j.mimet.2010.09.005.
9. Harvey RW, Price TH. 1979. Principles of Salmonella isolation. J. Appl. Bacteriol. 46:27-56. http://dx.doi.org/10.1111/j.1365-2672.1979.tb02580.x.
10. Perales I, Audicana A. 1989. Semisolid media for isolation of Salmonella spp. from coastal waters. Appl. Environ. Microbiol. 55:3032-3033.
11. Croci L, Delibato E, Volpe G, De Medici D, Palleschi G. 2004. Comparison of PCR, electrochemical enzyme-linked immunosorbent assays, and the standard culture method for detecting Salmonella in meat products. Appl. Environ. Microbiol. 70:1393-1396. http://dx.doi.org/10.1128/AEM.70.3.1393-1396.2004.
12. Eom HS, Hwang BH, Kim DH, Lee IB, Kim YH, Cha HJ. 2007. Multiple detection of food-borne pathogenic bacteria using a novel 16S rDNAbased oligonucleotide signature chip. Biosens. Bioelectron. 22:845-853. http://dx.doi.org/10.1016/j.bios.2006.03.005.
13. Hwang BH, Cha HJ. 2010. Pattern-mapped multiple detection of 11 pathogenic bacteria using a 16S rDNA-based oligonucleotide microarray. Biotechnol. Bioeng. 106:183-192. http://dx.doi.org/10.1002/bit.22674.
14. Hwang BH, Shin HH, Seo JH, Cha HJ. 2012. Specific multiplex analysis of pathogens using a direct 16S rRNA hybridization in microarray system. Anal. Chem. 84:4873-4879. http://dx.doi.org/10.1021/ac300476k.
15. Pathirana ST, Barbaree J, Chin BA, Hartell MG, Neely WC, Vodyanoy V. 2000. Rapid and sensitive biosensor for Salmonella. Biosens. Bioelectron. 15:135-141. http://dx.doi.org/10.1016/S0956-5663(00)00067-1.
16. Call DR, Borucki MK, Loge FJ. 2003. Detection of bacterial pathogens in environmental samples using DNA microarrays. J. Microbiol. Methods 53:235-243. http://dx.doi.org/10.1016/S0167-7012(03)00027-7.
17. Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD. 1997. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63:2397-2402.
18. Schena M, Shalon D, Davis RW, Brown PO. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470. http://dx.doi.org/10.1126/science.270.5235.467.
19. Severgnini M, Cremonesi P, Consolandi C, De Bellis G, Castiglioni B. 2011. Advances in DNA microarray technology for the detection of foodborne pathogens. Food Bioprocess Technol. 4:936-953. http://dx.doi.org/10.1007/s11947-010-0430-5.
20. Call DR. 2005. Challenges and opportunities for pathogen detection using DNA microarrays. Crit. Rev. Microbiol. 31:91-99. http://dx.doi.org/10.1080/10408410590921736.
21. Chandler DP, Newton GJ, Small JA, Daly DS. 2003. Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays. Appl. Environ. Microbiol. 69:2950-2958. http://dx.doi.org/10.1128/AEM.69.5.2950-2958.2003.
22. Liu WT, Mirzabekov AD, Stahl DA. 2001. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 3:619-629. http://dx.doi.org/10.1046/j.1462-2920.2001.00233.x.
23. Peplies J, Lachmund C, Glockner FO, Manz W. 2006. A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities. Appl. Environ. Microbiol. 72:4829-4838. http://dx.doi.org/10.1128/AEM.02949-05.
24. Rudi K, Skulberg OM, Skulberg R, Jakobsen KS. 2000. Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization. Appl. Environ. Microbiol. 66:4004-4011. http://dx.doi.org/10.1128/AEM.66.9.4004-4011.2000.
25. Choi SH, Woo JH, Lee JE, Park SJ, Choo EJ, Kwak YG, Kim MN, Choi MS, Lee NY, Lee BK, Kim NJ, Jeong JY, Ryu J, Kim YS. 2005. Increasing incidence of quinolone resistance in human non-typhoid Salmonella enterica isolates in Korea and mechanisms involved in quinolone resistance. J. Antimicrob. Chemother. 56:1111-1114. http://dx.doi.org/10.1093/jac/dki369.
26. Kim S, Chun SG, Lim OY, Park MS, Kang YH, Park YH, Lee BK. 2004. Genomic relationship of Salmonella enterica serovar Typhimurium DT104 isolates from Korea and the United States. J. Microbiol. 42:14-19.
27. Hwang BH, Cha HJ. 2008. Quantitative oligonucleotide microarray data analysis with an artificial standard probe strategy. Biosens. Bioelectron. 23:1738-1744. http://dx.doi.org/10.1016/j.bios.2008.01.024.
28. Holden HM, Thoden JB, Raushel FM. 1999. Carbamoyl phosphate synthetase: an amazing biochemical odyssey from substrate to product. Cell. Mol. Life Sci. 56:507-522. http://dx.doi.org/10.1007/s000180050448.
29. Javid-Majd F, Mullins LS, Raushel FM, Stapleton MA. 2000. The differentially conserved residues of carbamoyl-phosphate synthetase. J. Biol. Chem. 275:5073-5080. http://dx.doi.org/10.1074/jbc.275.7.5073.
30. Nyunoya H, Lusty CJ. 1983. The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase. Proc. Natl. Acad. Sci. U. S. A. 80:4629-4633. http://dx.doi.org/10.1073/pnas.80.15.4629.
31. Hong J, Salo WL, Lusty CJ, Anderson PM. 1994. Carbamyl phosphate synthetase III, an evolutionary intermediate in the transition between glutamine- dependent and ammonia-dependent carbamyl phosphate synthetases. J. Mol. Biol. 243:131-140. http://dx.doi.org/10.1006/jmbi.1994.1638.
32. Lawson FS, Charlebois RL, Dillon JA. 1996. Phylogenetic analysis of carbamoyl phosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life. Mol. Biol. Evol. 13:970-977. http://dx.doi.org/10.1093/oxfordjournals.molbev.a025665.
33. Seong WJ, Kwon HJ, Kim TE, Lee DY, Park MS, Kim JH. 2012. Molecular serotyping of Salmonella enterica by complete rpoB gene sequencing. J. Microbiol. 50:962-969. http://dx.doi.org/10.1007/s12275-012-2547-x.
34. Koehler RT, Peyret N. 2005. Effects of DNA secondary structure on oligonucleotide probe binding efficiency. Comput. Biol. Chem. 29:393- 397. http://dx.doi.org/10.1016/j.compbiolchem.2005.09.002.
35. Lane S, Evermann J, Loge F, Call DR. 2004. Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays. Biosens. Bioelectron. 20:728 -735. http://dx.doi.org/10.1016/j.bios.2004.04.014.
36. Hagan MF, Chakraborty AK. 2004. Hybridization dynamics of surface immobilized DNA. J. Chem. Phys. 120:4958-4968. http://dx.doi.org/10.1063/1.1645786.
37. Lima WF, Monia BP, Ecker DJ, Freier SM. 1992. Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31:12055-12061. http://dx.doi.org/10.1021/bi00163a013.
38. Bowtell D, Sambrook J. 2003. DNA microarrays. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
39. Francois P, Charbonnier Y, Jacquet J, Utinger D, Bento M, Lew D, Kresbach GM, Ehrat M, Schlegel W, Schrenzel J. 2006. Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification. J. Microbiol. Methods 65:390-403. http://dx.doi.org/10.1016/j.mimet.2005.08.012.
40. Oaew S, Karoonuthaisiri N, Surareungchai W. 2009. Sensitivity enhancement in DNA hybridization assay using gold nanoparticle-labeled two reporting probes. Biosens. Bioelectron. 25:435-441. http://dx.doi.org/10.1016/j.bios.2009.07.031.
41. Lee G, Cho YS, Park S, Yi GR. 2011. Synthesis and assembly of anisotropic nanoparticles. Korean J. Chem. Eng. 28:1641-1650. http://dx.doi.org/10.1007/s11814-011-0183-5.
42. Lampel KA, Orlandi PA, Kornegay L. 2000. Improved template preparation for PCR-based assays for detection of food-borne bacterial pathogens. Appl. Environ. Microbiol. 66:4539-4542. http://dx.doi.org/10.1128/AEM.66.10.4539-4542.2000.
43. Layton MC, Calliste SG, Gomez TM, Patton C, Brooks S. 1997. A mixed foodborne outbreak with Salmonella heidelberg and Campylobacter jejuni in a nursing home. Infect. Control Hosp. Epidemiol. 18:115-121. http://dx.doi.org/10.1086/647565.
44. Mandal P, Biswas A, Choi K, Pal U. 2011. Methods for rapid detection of foodborne pathogens: an overview. Am. J. Food Technol. 6:87-102. http://dx.doi.org/10.3923/ajft.2011.87.102.
45. Meehan PJ, Atkeson T, Kepner DE, Melton M. 1992. A foodborne outbreak of gastroenteritis involving two different pathogens. Am. J. Epidemiol. 136:611-616.
46. Zhao CW, Ge BL, De Villena J, Studler R, Yeh E, Zhao SH, White DG, Wagner D, Meng JH. 2001. Prevalence of Campylobacter spp., Escherichia coli, and Salmonella serovars in retail chicken, turkey, pork, and beef from the Greater Washington, DC, area. Appl. Environ. Microbiol. 67:5431- 5436. http://dx.doi.org/10.1128/AEM.67.12.5431-5436.2001.
47. Nyunoya H, Broglie KE, Lusty CJ. 1985. The gene coding for carbamoylphosphate synthetase I was formed by fusion of an ancestral glutaminase gene and a synthetase gene. Proc. Natl. Acad. Sci. U. S. A. 82:2244-2246. http://dx.doi.org/10.1073/pnas.82.8.2244.