Development of a multiple-run high-resolution melting assay for Salmonella spp. genotyping. HRM application for Salmonella spp. subtyping

Diagnostic Microbiology and Infectious Disease

Volumn 71, Issue 3, 2011, Pages 192-200

  Bratchikov, Maksim ^a   Mauricas, Mykolas ^a  

^a State Research Institute Centre for Innovative Medicine   (Lithuania)

Author keywords

CRISPR; Error evaluation; Error minimization; Genotyping; High resolution melting (HRM); Multiple run; Normalization; Reference sample; Rotor Gene; Salmonella spp.; Subtyping; Syto9; VNTR

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; FLUORESCENCE; GENE AMPLIFICATION; GENOTYPE; HIGH RESOLUTION MELTING ANALYSIS; NONHUMAN; PRIORITY JOURNAL; REPRODUCIBILITY; SALMONELLA; SEROTYPE; SUBTYPING;

BACTERIAL TYPING TECHNIQUES; GENOTYPING TECHNIQUES; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SALMONELLA; SENSITIVITY AND SPECIFICITY;

EID: 80053914398     PISSN: 07328893     EISSN: 18790070     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2011.06.012     Document Type: Article

References (23)

1. Bolotin A., Quinquis B., Sorokin A., Ehrlich S.D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 2005, 151:2551-2561.
2. Cho S., Boxrud D.J., Bartkus J.M., Whittam T.S., Saeed M. Multiple-locus variable-number tandem repeat analysis of Salmonella enteritidis isolates from human and non-human sources using a single multiplex PCR. FEMS Microbiol. Lett. 2007, 275:16-23.
3. Dillon J.R., Rahman M., Yeung K. Discriminatory power of typing schemes based on Simpson's index of diversity for Neisseria gonorrhoeae. J. Clin. Microbiol. 1993, 31:2831-2833.
4. Gundry C.N., Vandersteen J.G., Reed G.H., Pryor R.J., Chen J., Wittwer C.T. Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin. Chem. 2003, 49:396-406.
5. Hu H., Lan R., Reeves P.R. Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar typhimurium reveals phage-type-specific markers and potential for microarray typing. J. Clin. Microbiol. 2002, 40:3406-3415.
6. Janda J.M., Abbott S.L. The Enterobacteriaceae 2006, ASM Press, Washington. DC. 2nd ed.
7. Jeoffreys N.J., James G.S., Chiew R., Gilbert G.L. Practical evaluation of molecular subtyping and phage typing in outbreaks of infection due to Salmonella enterica serotype typhimurium. Pathology 2001, 33:66-72.
8. Lillestol R.K., Redder P., Garrett R.A., Brugger K. A putative viral defence mechanism in archaeal cells. Archaea 2006, 2:59-72.
9. Lindstedt B.A., Heir E., Gjernes E., Kapperud G. DNA Fingerprinting of Salmonella enterica subsp. enterica serovar typhimurium with emphasis on phage type DT104 based on variable number of tandem repeat loci. J. Clin. Microbiol. 2003, 41:1469-1479.
10. Millemann Y., Lesage M.C., Chaslus-Dancla E., Lafont J.P. Value of plasmid profiling, ribotyping, and detection of IS200 for tracing avian isolates of Salmonella typhimurium and S. enteritidis. J. Clin. Microbiol. 1995, 33:173-179.
11. Makarova K.S., Grishin N.V., Shabalina S.A., Wolf Y.I., Koonin E.V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct. 2006, 1:7.
12. Mojica F.J., Diez-Villasenor C., Garcia-Martinez J., Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 2005, 60:174-182.
13. Nastasi A., Mammina C. Epidemiological evaluation by PCR ribotyping of sporadic and outbreak-associated strains of Salmonella enterica serotype typhimurium. Res. Microbiol. 1995, 146:99-106.
14. Navarro A., Eslava C., Garcia T., Leon L.A., Licona D., Leon L., Zarco L.A., Cravioto A. Common epitopes in LPS of different enterobacteriaceae are associated with an immune response against Escherichia coli O157 in bovine serum samples. J. Med. Microbiol. 2007, 56:1447-1454.
15. Popoff M.Y., Bockemuhl J., Gheesling L.L. Supplement 2002 (no. 46) to the Kauffmann-White scheme. Res. Microbiol. 2004, 155:568-570.
16. Pourcel C., Salvignol G., Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 2005, 151:653-663.
17. Price E.P., Smith H., Huygens F., Giffard P.M. High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni. Appl. Environ. Microbiol. 2007, 73:3431-3436.
18. Rundlof T., Weintraub A., Widmalm G. Structural determination of the O antigenic polysaccharide from Escherichia coli O35 and cross-reactivity to Salmonella arizonae O62. Eur. J. Biochem. 1998, 258:139-143.
19. Slinger R., Bellfoy D., Desjardins M., Chan F. High-resolution melting assay for the detection of gyrA mutations causing quinolone resistance in Salmonella enterica serovars typhi and paratyphi. Diagn. Microbiol. Infect. Disease 2007, 57:455-458.
20. Tang T.H., Bachellerie J.P., Rozhdestvensky T., Bortolin M.L., Huber H., Drungowski M., Elge T., Brosius J., Huttenhofer A. Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Natl. Acad. Sci. USA 2002, 99:7536-7541.
21. Wittwer C.T., Reed G.H., Gundry C.N., Vandersteen J.G., Pryor R.J. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem. 2003, 49:853-860.
22. Woo Y.K., Lee S.H. Genetic diversity of multi-resistant Salmonella enterica serotype typhimurium isolates from animals and humans. J. Microbiol. 2006, 44:106-112.
23. Zavadskas E., Turskis Z. A new logarithmic normalization method in games theory. Informatica 2008, 19:303-314.