Prediction system for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis fingerprints

Journal of Clinical Microbiology

Volumn 50, Issue 5, 2012, Pages 1524-1532

  Zou, Wen ^a   Lin, Wei Jiun ^b   Hise, Kelley B ^c   Chen, Hung Chia ^a   Keys, Christine ^d   Chen, James J ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b FENG CHIA UNIVERSITY   (Taiwan)

^c NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

^d CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; EPIDEMIC; INTERMETHOD COMPARISON; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RANDOM FOREST; SALMONELLA; SEROTYPING; SUPPORT VECTOR MACHINE; VALIDATION PROCESS;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA FINGERPRINTING; ELECTROPHORESIS, GEL, PULSED-FIELD; GENOTYPE; HUMANS; MOLECULAR TYPING; SALMONELLA; SEROTYPING;

EID: 84860009557     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00111-12     Document Type: Article

References (27)

1. Baek S, Tsai CA, Chen JJ. 2009. Development of biomarker classifiers from high-dimensional data. Brief Bioinform. 10:537-546.
2. Ben-Darif E, et al. 2010. Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes. J. Clin. Microbiol. 48:1055-1060.
3. Breiman L. 2001. Random forests. Machine Learning. 45:5-32. (Pubitemid 32933532)
4. Centers for Disease Control and Prevention. 2008. Salmonella: annual summary, 2006. U.S. Department of Health and Human Services, CDC, Atlanta, GA. http://www.cdc.gov/ncidod/dbmd/phlisdata/salmtab/2006 / SalmonellaAnnualSummary2006.pdf.
5. Fang H, et al. 2010. An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. BMC Bioinformatics 11(Suppl. 6):S4.
6. Fitzgerald C, et al. 2007. Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups. J. Clin. Microbiol. 45:3323-3334. (Pubitemid 47585658)
7. Foley SL, Zhao S, Walker RD. 2007. Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens. Foodborne Pathog. Dis. 4:253-276. (Pubitemid 47518165)
8. Garaizar J, et al. 2000. Suitability of PCR fingerprinting, infrequent-restriction- site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar Enteritidis. Appl. Environ. Microbiol. 66:5273-5281. (Pubitemid 32217130)
9. Gaul SB, et al. 2007. Use of pulsed-field gel electrophoresis of conserved XbaI fragments for identification of swine Salmonella serotypes. J. Clin. Microbiol. 45:472-476.
10. Gerner-Smidt P, et al. 2006. PulseNet U. S. A.: a five-year update. Foodborne Pathog. Dis. 3:9-19.
11. Grimont PAD, Weill FX. 2007. Antigenic formulae of the Salmonella serovars, 9th ed. World Health Organization Collaborating Center for Reference and Research on Salmonella, Institut Pasteur, Paris, France.
12. Guibourdenche M, et al. 2010. Supplement 2003-2007 (no. 47) to the White-Kauffmann-Le Minor scheme. Res. Microbiol. 161:26-29.
13. Jaccard P. 1901. Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull. Soc. Vaudoise Sci. Nat. 37:547-579.
14. Kauffmann F, Edwards PR. 1952. Classification and nomenclature of Enterobacteriaceae. Int. Bull. Bacteriol. Nomencl. Taxon. 2:2-8.
15. Kotetishvili M, Stine OC, Kreger A, Morris JG, Jr, Sulakvelidze A. 2002. Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J. Clin. Microbiol. 40:1626-1635. (Pubitemid 34493130)
16. Kumar S, Balakrishna K, Batra HV. 2006. Detection of Salmonella enterica serovar Typhi (S. Typhi) by selective amplification of invA, viaB, fliC-D and prt genes by polymerase chain reaction in mutiplex format. Lett. Appl. Microbiol. 42:149-154.
17. Lee JW, Lee JB, Park M, Song SH. 2005. An extensive comparison of recent classification tools applied to microarray data. Comput. Stat. Data Anal. 48:869-885.
18. Liebana E, et al. 2001. Molecular typing of Salmonella serotypes prevalent in animals in England: assessment of methodology. J. Clin. Microbiol. 39:3609-3616. (Pubitemid 32954510)
19. Moon H, et al. 2006. Classification methods for the development of genomic signatures from high-dimensional data. Genome Biol. 7:R121. http://genomebiology.com/content/7/12/R121.
20. Painter JA, et al. 2009. Recipes for foodborne outbreaks: a scheme for categorizing and grouping implicated foods. Foodborne Pathog. Dis. 6:1259-1264.
21. Tenover FC, et al. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:2233-2239.
22. Threlfall EJ, et al. 1999. Pulsed field gel electrophoresis identifies an outbreak of Salmonella enterica serotype Montevideo infection associated with a supermarket hot food outlet. Commun. Dis. Public Health 2:207-209.
23. Vapnik V. 1995. The nature of statistical learning theory. Springer, New York, NY.
24. Wattiau P, Boland C, Bertrand S. 2011. Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives. Appl. Environ. Microbiol. 77:7877-7885.
25. Wise MG, et al. 2009. Predicting Salmonella enterica serotypes by repetitive sequence-based PCR. J. Microbiol. Methods 76:18-24.
26. Wonderling L, et al. 2003. Use of pulsed-field gel electrophoresis to characterize the heterogeneity and clonality of Salmonella isolates obtained from the carcasses and feces of swine at slaughter. Appl. Environ. Microbiol. 69:4177-4182. (Pubitemid 36870079)
27. Zou W, et al. 2010. Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes. J. Clin. Microbiol. 48:3122-3126.