Comparison of a semi-automated rep-PCR system and multilocus sequence typing for differentiation of Salmonella enterica isolates

Journal of Microbiological Methods

Volumn 81, Issue 1, 2010, Pages 11-16

  Ben Darif, Elloulu ^a   De Pinna, Elizabeth ^b   Threlfall, E John ^b   Bolton, Frederic J ^b   Upton, Mathew ^a   Fox, Andrew J ^c  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b PUBLIC HEALTH ENGLAND   (United Kingdom)

^c ROYAL PRESTON HOSPITAL   (United Kingdom)

Author keywords

Diagnostics; DiversiLab; MLST; Salmonella; Typing

Indexed keywords

ACCURACY; ARTICLE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; COMPARATIVE STUDY; CONTROLLED STUDY; DATA BASE; MICROFLUIDIC ANALYSIS; MOLECULAR EPIDEMIOLOGY; MOLECULAR LIBRARY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; ONLINE SYSTEM; POLYMERASE CHAIN REACTION; POPULATION BIOLOGY; PREDICTION; PRIORITY JOURNAL; SALMONELLA ENTERICA; SALMONELLOSIS; SEROTYPE;

AUTOMATION; BACTERIAL TYPING TECHNIQUES; DNA FINGERPRINTING; DNA, BACTERIAL; GENOTYPE; HUMANS; POLYMERASE CHAIN REACTION; SALMONELLA ENTERICA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); SALMONELLA; SALMONELLA ENTERICA;

EID: 77949273858     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.01.013     Document Type: Article

References (50)

1. Adak G.K., Long S.M., and O'Brien S.J. Trends in indigenous foodborne disease and deaths, England and Wales: 1992 to 2000. Gut 51 (2002) 832-841
2. Albufera U., Bhugaloo-Vial P., Issack M.I., and Jaufeerally-Fakim Y. Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis. Infect. Genet. Evol. 9 (2009) 322-327
3. Altwegg M., Hickman-Brenner F.W., and Farmer III J.J. Ribosomal RNA gene restriction patterns provide increased sensitivity for typing Salmonella typhi strains. J. Infect. Dis. 160 (1989) 145-149
4. Anderson E.S., Ward L.R., Saxe M.J., and de Sa J.D. Bacteriophage-typing designations of Salmonella typhimurium. J. Hyg. (Lond.) 78 (1977) 297-300
5. Bale J.A., d.P.E., Threlfall E.J., and Ward L.R. Kauffmann-White Scheme-2007: Salmonella Identification-Serotypes and Antigenic Formulae (2007), Health Protection Agency, London 978-0-901144-91-1.362
6. Beltran P., Musser J.M., Helmuth R., Farmer J.J., Frerichs W.M., Cravioto A., and Selander R.K. Toward a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S. cholerasuis, S. derby, S. dublin, S. enteriditis, S. heidelberg, S. infantis, S. newport, and S. typhimurium. Proc. Natl. Acad. Sci. U. S. A. 85 (1988) 7753-7757
7. Best E.L., Hampton M.D., Ethelberg S., Liebana E., Clifton-Hadley F.A., and Threlfall E.J. Drug-resistant Salmonella Typhimurium DT 120: use of PFGE and MLVA in a putative international outbreak investigation. Microb. Drug. Resist. 15 (2009) 133-138
8. Braden C.R. Salmonella enterica serotype Enteritidis and eggs: a national epidemic in the United States. Clin. Infect. Dis. 43 (2006) 512-517
9. Cangelosi G.A., Freeman R.J., Lewis K.N., Livingston-Rosanoff D., Shah K.S., Milan S.J., and Goldberg S.V. Evaluation of a high-throughput repetitive-sequence-based PCR system for DNA fingerprinting of Mycobacterium tuberculosis and Mycobacterium avium complex strains. J. Clin. Microbiol. 42 (2004) 2685-2693
10. Carraminana J.J., Humbert F., Ermel G., and Colin P. Molecular epidemiological investigation of Salmonella typhimurium strains related to an egg-borne outbreak. Res. Microbiol. 148 (1997) 633-636
11. Coburn B., Grassl G.A., and Finlay B.B. Salmonella, the host and disease: a brief review. Immunol. Cell Biol. 85 (2007) 112-118
12. Dionisi A.M., Carattoli A., Luzzi I., Magistrali C., and Pezzotti G. Molecular genotyping of Salmonella enterica Abortusovis by pulsed field gel electrophoresis. Vet. Microbiol. 116 (2006) 217-223
13. Enright M.C., and Spratt B.G. Multilocus sequence typing. Trends Microbiol. 7 (1999) 482-487
14. Fisher I.S., and Threlfall E.J. The Enter-net and Salm-gene databases of foodborne bacterial pathogens that cause human infections in Europe and beyond: an international collaboration in surveillance and the development of intervention strategies. Epidemiol. Infect. 133 (2005) 1-7
15. Foley S.L., White D.G., McDermott P.F., Walker R.D., Rhodes B., Fedorka-Cray P.J., Simjee S., and Zhao S. Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. J. Clin. Microbiol. 44 (2006) 3569-3577
16. Grundmann H., Hori S., and Tanner G. Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. J. Clin. Microbiol. 39 (2001) 4190-4192
17. Hansen D., Healy M., Reece K., Smith C., and Woods G.L. Repetitive-sequence-based PCR using the DiversiLab system for identification of Aspergillus species. J. Clin. Microbiol. 46 (2008) 1835-1839
18. Harbottle H., White D.G., McDermott P.F., Walker R.D., and Zhao S. Comparison of multilocus sequence typing, pulsed-field gel electrophoresis, and antimicrobial susceptibility typing for characterization of Salmonella enterica serotype Newport isolates. J. Clin. Microbiol. 44 (2006) 2449-2457
19. Healy M., Huong J., Bittner T., Lising M., Frye S., Raza S., Schrock R., Manry J., Renwick A., Nieto R., Woods C., Versalovic J., and Lupski J.R. Microbial DNA typing by automated repetitive-sequence-based PCR. J. Clin. Microbiol. 43 (2005) 199-207
20. Healy M., Reece K., Walton D., Huong J., Shah K., and Kontoyiannis D.P. Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR. J. Clin. Microbiol. 42 (2004) 4016-4024
21. HPA. Salmonella serotypes recorded in the HPA Salmonella data set: October to end of December 2006 Health Protection Agency (2007)
22. Hunter P.R., and Gaston M.A. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26 (1988) 2465-2466
23. Jones T.F., Ingram L.A., Fullerton K.E., Marcus R., Anderson B.J., McCarthy P.V., Vugia D., Shiferaw B., Haubert N., Wedel S., and Angulo F.J. A case-control study of the epidemiology of sporadic Salmonella infection in infants. Pediatrics 118 (2006) 2380-2387
24. Kidgell C., Reichard U., Wain J., Linz B., Torpdahl M., Dougan G., and Achtman M. Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect. Genet. Evol. 2 (2002) 39-45
25. Koeuth T., Versalovic J., and Lupski J.R. Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. Genome Res. 5 (1995) 408-418
26. Kontoyiannis D.P., Lionakis M.S., Lewis R.E., Chamilos G., Healy M., Perego C., Safdar A., Kantarjian H., Champlin R., Walsh T.J., and Raad I.I. Zygomycosis in a tertiary-care cancer center in the era of Aspergillus-active antifungal therapy: a case-control observational study of 27 recent cases. J. Infect. Dis. 191 (2005) 1350-1360
27. Kotetishvili M., Stine O.C., Kreger A., Morris Jr. J.G., and Sulakvelidze A. Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J. Clin. Microbiol. 40 (2002) 1626-1635
28. Lau S.H., Cheesborough J., Kaufmann M.E., Woodford N., Dodgson A.R., Dodgson K.J., Bolton E.J., Fox A.J., and Upton M. Rapid identification of uropathogenic Escherichia coli of the O25:H4-ST131 clonal lineage using the DiversiLab repetitive sequence-based PCR system. Clin. Microbiol. Infect. (2009)
29. Liu Y., Lee M.A., Ooi E.E., Mavis Y., Tan A.L., and Quek H.H. Molecular typing of Salmonella enterica serovar Typhi isolates from various countries in Asia by a multiplex PCR assay on variable-number tandem repeats. J. Clin. Microbiol. 41 (2003) 4388-4394
30. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., Zhang Q., Zhou J., Zurth K., Caugant D.A., Feavers I.M., Achtman M., and Spratt B.G. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 3140-3145
31. Olive D.M., and Bean P. Principles and applications of methods for DNA-based typing of microbial organisms. J. Clin. Microbiol. 37 (1999) 1661-1669
32. Pang T., Altwegg M., Martinetti G., Koh C.L., and Puthucheary S. Genetic variation among Malaysian isolates of Salmonella typhi as detected by ribosomal RNA gene restriction patterns. Microbiol. Immunol. 36 (1992) 539-543
33. Pitout J.D., Campbell L., Church D.L., Wang P.W., Guttman D.S., and Gregson D.B. Using a commercial DiversiLab semiautomated repetitive sequence-based PCR typing technique for identification of Escherichia coli clone ST131 producing CTX-M-15. J. Clin. Microbiol. 47 (2009) 1212-1215
34. Popoff M.R., Marvaud J.C., and Raffestin S. Mechanism of action and therapeutic uses of botulinum and tetanus neurotoxins. Ann. Pharm. Fr. 59 (2001) 176-190
35. Pounder J.I., Williams S., Hansen D., Healy M., Reece K., and Woods G.L. Repetitive-sequence-PCR-based DNA fingerprinting using the Diversilab system for identification of commonly encountered dermatophytes. J. Clin. Microbiol. 43 (2005) 2141-2147
36. Reche M.P., Echeita M.A., de los Rios J.E., Usera M.A., Jimenez P.A., Rojas A.M., Colas J., and Rodriguez I. Comparison of phenotypic and genotypic markers for characterization of an outbreak of Salmonella serotype Havana in captive raptors. J. Appl. Microbiol. 94 (2003) 65-72
37. Robinson D.A., Hollingshead S.K., Musser J.M., Parkinson A.J., Briles D.E., and Crain M.J. The IS1167 insertion sequence is a phylogenetically informative marker among isolates of serotype 6B Streptococcus pneumoniae. J. Mol. Evol. 47 (1998) 222-229
38. Schmieger H. Molecular survey of the Salmonella phage typing system of Anderson. J. Bacteriol. 181 (1999) 1630-1635
39. Scott F., Threlfall J., Stanley J., and Arnold C. Fluorescent amplified fragment length polymorphism genotyping of Salmonella Enteritidis: a method suitable for rapid outbreak recognition. Clin. Microbiol. Infect. 7 (2001) 479-485
40. Sivapalasingam S., Barrett E., Kimura A., Van Duyne S., De Witt W., Ying M., Frisch A., Phan Q., Gould E., Shillam P., Reddy V., Cooper T., Hoekstra M., Higgins C., Sanders J.P., Tauxe R.V., and Slutsker L. A multistate outbreak of Salmonella enterica serotype Newport infection linked to mango consumption: impact of water-dip disinfestation technology. Clin. Infect. Dis. 37 (2003) 1585-1590
41. Stern M.J., Ames G.F., Smith N.H., Robinson E.C., and Higgins C.F. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37 (1984) 1015-1026
42. Sukhnanand S., Alcaine S., Warnick L.D., Su W.L., Hof J., Craver M.P., McDonough P., Boor K.J., and Wiedmann M. DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes. J. Clin. Microbiol. 43 (2005) 3688-3698
43. Te Witt R., Kanhai V., and van Leeuwen W.B. Comparison of the DiversiLab system, pulsed-field gel electrophoresis and multi-locus sequence typing for the characterization of epidemic reference MRSA strains. J. Microbiol. Methods 77 (2009) 130-133
44. Threlfall E.J., Hampton M.D., Chart H., and Rowe B. Use of plasmid profile typing for surveillance of Salmonella enteritidis phage type 4 from humans, poultry and eggs. Epidemiol. Infect. 112 (1994) 25-31
45. Threlfall E.J., Hampton M.D., Ward L.R., and Rowe B. Application of pulsed-field gel electrophoresis to an international outbreak of Salmonella agona. Emerg. Infect. Dis. 2 (1996) 130-132
46. Torpdahl M., Skov M.N., Sandvang D., and Baggesen D.L. Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism. J. Microbiol. Methods 63 (2005) 173-184
47. Versalovic J., Koeuth T., and Lupski J.R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19 (1991) 6823-6831
48. Weigel R.M., Qiao B., Teferedegne B., Suh D.K., Barber D.A., Isaacson R.E., and White B.A. Comparison of pulsed field gel electrophoresis and repetitive sequence polymerase chain reaction as genotyping methods for detection of genetic diversity and inferring transmission of Salmonella. Vet. Microbiol. 100 (2004) 205-217
49. Wise M.G., Healy M., Reece K., Smith R., Walton D., Dutch W., Renwick A., Huong J., Young S., Tarrand J., and Kontoyiannis D.P. Species identification and strain differentiation of clinical Candida isolates using the DiversiLab system of automated repetitive sequence-based PCR. J. Med. Microbiol. 56 (2007) 778-787
50. Wise M.G., Siragusa G.R., Plumblee J., Healy M., Cray P.J., and Seal B.S. Predicting Salmonella enterica serotypes by repetitive sequence-based PCR. J. Microbiol. Methods 76 (2009) 18-24