Molecular Source Tracking and Molecular Subtyping

Peter Gerner-Smidt; Eija Hyytia-Trees; Timothy J. Barrett

doi:10.1128/9781555818463.ch43

Chapter 43 : Molecular Source Tracking and Molecular Subtyping

Authors: Peter Gerner-Smidt¹, Eija Hyytia-Trees¹, Timothy J. Barrett¹

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd., Atlanta, GA 30333

Content Type: Reference

Publication Year: 2013

Category: Food Microbiology; Applied and Industrial Microbiology

Book DOI: 10.1128/9781555818463

Chapter DOI: 10.1128/9781555818463.ch43

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Molecular Source Tracking and Molecular Subtyping, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555818463/9781555816261_Chap43-1.gif /docserver/preview/fulltext/10.1128/9781555818463/9781555816261_Chap43-2.gif

Abstract:

Molecular subtyping can be used to study the population structure of a particular bacterial species, to determine the possible evolution of the subject microorganism, or to study the molecular epidemiology of a microbe. The types of methods used for subtyping and the approaches to data analysis and interpretation may vary greatly with the reason for specific subtyping. This chapter focuses almost entirely on subtyping for molecular epidemiology. Molecular epidemiology can be applied to identifying the source of a particular outbreak or to a broader understanding of the role of certain foods or processes in outbreak-related or sporadic infections. Perhaps the most easily appreciated reason for molecular subtyping is to facilitate the identification and investigation of foodborne disease outbreaks. Although the focus of this chapter is on molecular methods, it is important to consider them in the context of earlier phenotypic methods such as serotyping, phage typing, biotyping, and antimicrobial susceptibility typing. Most of these phenotypic methods have long and successful histories of use in subtyping for the same purposes for which molecular methods are now used. Although molecular methods typically provide greater strain discrimination than phenotypic methods, this is not always the case, and it is only one reason why molecular methods are generally preferred. In recent years, the main focus of subtyping method development has been on DNA sequence-based methods. Sequence-based approaches to subtyping of bacteria, such as multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA), are already being widely implemented in the surveillance of foodborne infections.

Citation: Gerner-Smidt P, Hyytia-Trees E, Barrett T. 2013. Molecular Source Tracking and Molecular Subtyping, p 1059-1077. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch43

Highlighted Text: Show | Hide

Full text loading...

Figures

Molecular Source Tracking and Molecular Subtyping

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818463.chap43-1,webId=/content/author/10.1128/9781555818463.chap43-1,properties={foaf_givenname=Peter, foaf_name=Peter Gerner-Smidt, foaf_surname=Gerner-Smidt, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818463.chap43-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818463.chap43-2,webId=/content/author/10.1128/9781555818463.chap43-2,properties={foaf_givenname=Eija, foaf_name=Eija Hyytia-Trees, foaf_surname=Hyytia-Trees, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818463.chap43-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818463.chap43-3,webId=/content/author/10.1128/9781555818463.chap43-3,properties={foaf_givenname=Timothy J., foaf_name=Timothy J. Barrett, foaf_surname=Barrett, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818463.chap43-aff1]]}]]

/content/10.1128/9781555818463.chap43.fig43-1

Figure 43.1

Example of plasmid profile analysis. Each lane contains plasmid DNA extracted from an isolate of ceftriaxone-resistant Salmonella. In this instance, plasmid DNA was separated by PFGE rather than standard gel electrophoresis for better separation of large plasmids. doi:10.1128/9781555818463.ch43f1

10.1128/9781555818463/fig43-1_thmb.gif

10.1128/9781555818463/fig43-1.gif

Figure 43.1

/content/10.1128/9781555818463.chap43.fig43-2

Figure 43.2

PFGE analysis of seven isolates of Salmonella Berta. (a) Raw data: lanes 2 to 4 and 6 to 9 contain BlnI digests of S. Berta genomic DNA, and lanes 1, 5, and 10 contain XbaI digests of a molecular weight standard strain. (b) Analyzed data: dendrogram showing relatedness of S. Berta isolates produced using BioNumerics software. doi:10.1128/9781555818463.ch43f2

10.1128/9781555818463/fig43-2_thmb.gif

10.1128/9781555818463/fig43-2.gif

Figure 43.2

/content/10.1128/9781555818463.chap43.fig43-3

Figure 43.3

Example of MLVA of E. coli O157:H7 isolates. (a and b) Electropherograms from automated DNA sequencer showing different fragment sizes at three of four sites; (c) dendrogram generated with BioNumerics software showing relatedness of isolates based on data at eight VNTR loci. doi:10.1128/9781555818463.ch43f3

10.1128/9781555818463/fig43-3a_thmb.gif

10.1128/9781555818463/fig43-3a.gif

Figure 43.3

/content/10.1128/9781555818463.chap43.fig43-4

Figure 43.4

Molecular identification of serotype in Salmonella by the Luminex platform. The data represent identification of serotype based on reactivity with DNA probes corresponding to specific serotype antigens coupled to fluorescent microspheres. The results are expressed as the ratio of median fluorescent intensity for test versus negative control samples (P/N ratio). (a) Results of the O antigen assay; probes detect sequences specific for common O groups or for serotype Paratyphi A; (b) results of the H antigen assay; probes detect specific H epitopes; (c) interpretation of data based on the Kauffmann-White scheme. (Courtesy J. McQuiston, CDC.) doi:10.1128/9781555818463.ch43f4

10.1128/9781555818463/fig43-4_thmb.gif

10.1128/9781555818463/fig43-4.gif

Figure 43.4

References

/content/book/10.1128/9781555818463.chap43

1. Amon, J. J.,, R. Devasia,, G. Xia,, O. V. Nainan,, S. Hall,, B. Lawson,, J. S. Wolthuis,, P. D. Macdonald,, C. W. Shepard,, I. T. Williams,, G. L. Armstrong,, J. A. Gabel,, P. Erwin,, L. Sheeler,, W. Kuhnert,, P. Patel,, G. Vaughan,, A. Weltman,, A. S. Craig,, B. P. Bell,, and A. Fiore. 2005. Molecular epidemiology of foodborne hepatitis A outbreaks in the United States, 2003. J. Infect. Dis. 192: 1323– 1330.

2. Barrett, T. J.,, P. Gerner-Smidt,, and B. Swaminathan. 2006. Interpretation of pulsed-field gel electrophoresis patterns in foodborne disease investigations and surveillance. Foodborne Pathog. Dis. 3: 20– 31.

3. Barrett, T. J.,, H. Lior,, J. H. Green,, R. Khakhria,, J. G. Wells,, B. P. Bell,, K. D. Greene,, J. Lewis,, and P. M. Griffin. 1994. Laboratory investigation of a multistate food-borne outbreak of Escherichia coli O157:H7 by using pulsed-field gel electrophoresis and phage typing. J. Clin. Microbiol. 32: 3013– 3017.

4. Ben-Darif, E.,, E. De Pinna,, E. J. Threlfall,, F. J. Bolton,, M. Upton,, and A. J. Fox. 2010. Comparison of a semi-automated rep-PCR system and multilocus sequence typing for differentiation of Salmonella enterica isolates. J. Microbiol. Methods 81: 11– 16.

5. Bender, J. B.,, C. W. Hedberg,, D. J. Boxrud,, J. M. Besser,, J. H. Wicklund,, K. E. Smith,, and M. T. Osterholm. 2001. Use of molecular subtyping in surveillance for Salmonella enterica serotype Typhimurium. N. Engl. J. Med. 344: 189– 195.

6. Bentley, D. R.,, S. Balasubramanian,, H. P. Swerdlow,, G. P. Smith,, J. Milton,, C. G. Brown,, K. P. Hall,, D. J. Evers,, C. L. Barnes,, H. R. Bignell,, J. M. Boutell,, J. Bryant,, R. J. Carter,, R. Keira Cheetham,, A. J. Cox,, D. J. Ellis,, M. R. Flatbush,, N. A. Gormley,, S. J. Humphray,, L. J. Irving,, M. S. Karbelashvili,, S. M. Kirk,, H. Li,, X. Liu,, K. S. Maisinger,, L. J. Murray,, B. Obradovic,, T. Ost,, M. L. Parkinson,, M. R. Pratt,, I. M. Rasolonjatovo,, M. T. Reed,, R. Rigatti,, C. Rodighiero,, M. T. Ross,, A. Sabot,, S. V. Sankar,, A. Scally,, G. P. Schroth,, M. E. Smith,, V. P. Smith,, A. Spiridou,, P. E. Torrance,, S. S. Tzonev,, E. H. Vermaas,, K. Walter,, X. Wu,, L. Zhang,, M. D. Alam,, C. Anastasi,, I. C. Aniebo,, D. M. Bailey,, I. R. Bancarz,, S. Banerjee,, S. G. Barbour,, P. A. Baybayan,, V. A. Benoit,, K. F. Benson,, C. Bevis,, P. J. Black,, A. Boodhun,, J. S. Brennan,, J. A. Bridgham,, R. C. Brown,, A. A. Brown,, D. H. Buermann,, A. A. Bundu,, J. C. Burrows,, N. P. Carter,, N. Castillo,, E. C. M. Chiara,, S. Chang,, R. Neil Cooley,, N. R. Crake,, O. O. Dada,, K. D. Diakoumakos,, B. Dominguez-Fernandez,, D. J. Earnshaw,, U. C. Egbujor,, D. W. Elmore,, S. S. Etchin,, M. R. Ewan,, M. Fedurco,, L. J. Fraser,, K. V. Fuentes Fajardo,, W. Scott Furey,, D. George,, K. J. Gietzen,, C. P. Goddard,, G. S. Golda,, P. A. Granieri,, D. E. Green,, D. L. Gustafson,, N. F. Hansen,, K. Harnish,, C. D. Haudenschild,, N. I. Heyer,, M. M. Hims,, J. T. Ho,, A. M. Horgan, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53– 69.

7. Best, E. L.,, A. J. Fox,, J. A. Frost,, and F. J. Bolton. 2005. Real-time single-nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes. J. Med. Microbiol. 54: 919– 925.

8. Borucki, M. K.,, S. H. Kim,, D. R. Call,, S. C. Smole,, and F. Pagotto. 2004. Selective discrimination of Listeria monocytogenes epidemic strains by a mixed-genome DNA microarray compared to discrimination by pulsed-field gel electrophoresis, ribotyping, and multilocus sequence typing. J. Clin. Microbiol. 42: 5270– 5276.

9. Boxrud, D.,, K. Pederson-Gulrud,, J. Wotton,, C. Medus,, E. Lyszkowicz,, J. Besser,, and J. M. Bartkus. 2007. Comparison of multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and phage typing for subtype analysis of Salmonella enterica serotype Enteritidis. J. Clin. Microbiol. 45: 536– 543.

10. Bruun, T.,, G. Sorensen,, L. P. Forshell,, T. Jensen,, K. Nygard,, G. Kapperud,, B. A. Lindstedt,, T. Berglund,, A. Wingstrand,, R. F. Petersen,, L. Muller,, C. Kjelso,, S. Ivarsson,, M. Hjertqvist,, S. Lofdahl,, and S. Ethelberg. 2009. An outbreak of Salmonella Typhimurium infections in Denmark, Norway and Sweden, 2008. Euro Surveill. 14( 10):pii 19147.

11. Bustamante, A. V.,, A. M. Sanso,, P. M. Lucchesi,, and A. E. Parma. 2011. Genetic diversity of O157:H7 and non-O157 verocytotoxigenic Escherichia coli from Argentina inferred from multiple-locus variable-number tandem repeat analysis (MLVA). Int. J. Med. Microbiol. 300: 212– 217.

12. Carle, G. F.,, M. Frank,, and M. V. Olson. 1986. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science 232: 65– 68.

13. Centers for Disease Control and Prevention. 29 October 2007, posting date. Investigation of outbreak of human infections caused by Salmonella I 4,[5],12:i:-. http://www.cdc.gov/salmonella/4512eyeminus.html. Accessed September 14, 2012.

14. Centers for Disease Control and Prevention. 2009. Multistate outbreak of Salmonella infections associated with peanut butter and peanut butter-containing products—United States, 2008-2009. MMWR Morb. Mortal. Wkly. Rep. 58: 85– 90.

15. Chu, G.,, D. Vollrath,, and R. W. Dacis. 1986. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Anal. Biochem. 234: 1582– 1585.

16. Clark, C. G.,, L. Bryden,, W. R. Cuff,, P. L. Johnson,, F. Jamieson,, B. Ciebin,, and G. Wang. 2005. Use of the Oxford multilocus sequence typing protocol and sequencing of the flagellin short variable region to characterize isolates from a large outbreak of waterborne Campylobacter sp. strains in Walkerton, Ontario, Canada. J. Clin. Microbiol. 43: 2080– 2091.

17. Clawson, M. L.,, J. E. Keen,, T. P. Smith,, L. M. Durso,, T. G. McDaneld,, R. E. Mandrell,, M. A. Davis,, and J. L. Bono. 2009. Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms. Genome Biol. 10: R56.

18. Cook, K. A.,, T. E. Dobbs,, G. Hlady,, J. G. Wells,, T. J. Barrett,, N. D. Puhr,, G. A. Lancette,, D. W. Bodager,, B. L. Toth,, C. A. Genese,, A. K. Highsmith,, K. E. Pilot,, L. Finelli,, and D. L. Swerdlow. 1998. Outbreak of Salmonella serotype Hartford infections associated with unpasteurized orange juice. JAMA 280: 1504– 1509.

19. de Boer, P.,, J. A. Wagenaar,, R. P. Achterberg,, J. P. van Putten,, L. M. Schouls,, and B. Duim. 2002. Generation of Campylobacter jejuni genetic diversity in vivo. Mol. Microbiol. 44: 351– 359.

20. de Haan, C. P.,, R. I. Kivisto,, M. Hakkinen,, J. Corander,, and M. L. Hanninen. 2010. Multilocus sequence types of Finnish bovine Campylobacter jejuni isolates and their attribution to human infections. BMC Microbiol. 10: 200.

21. de Valk, H. A.,, J. F. Meis,, S. Bretagne,, J. M. Costa,, B. A. Lasker,, S. A. Balajee,, A. C. Pasqualotto,, M. J. Anderson,, L. Alcazar-Fuoli,, E. Mellado,, and C. H. Klaassen. 2009. Interlaboratory reproducibility of a microsatellite-based typing assay for Aspergillus fumigatus through the use of allelic ladders: proof of concept. Clin. Microbiol. Infect. 15: 180– 187.

22. Dingle, K. E.,, F. M. Colles,, D. R. Wareing,, R. Ure,, A. J. Fox,, F. E. Bolton,, H. J. Bootsma,, R. J. Willems,, R. Urwin,, and M. C. Maiden. 2001. Multilocus sequence typing system for Campylobacter jejuni. J. Clin. Microbiol. 39: 14– 23.

23. Dingle, K. E.,, N. D. McCarthy,, A. J. Cody,, T. E. Peto,, and M. C. Maiden. 2008. Extended sequence typing of Campylobacter spp., United Kingdom. Emerg. Infect. Dis. 14: 1620– 1622.

24. Doumith, M.,, C. Cazelet,, N. Simoes,, L. Frangeul,, C. Jacquet,, F. Kunst,, P. Martin,, P. Cossart,, P. Glaser,, and C. Buchrieser. 2004. New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect. Immun. 72: 1072– 1083.

25. Dressman, D.,, H. Yan,, G. Traverso,, K. W. Kinzler,, and B. Vogelstein. 2003. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl. Acad. Sci. USA 100: 8817– 8822.

26. Ducey, T. F.,, B. Page,, T. Usgaard,, M. K. Borucki,, K. Pupedis,, and T. J. Ward. 2007. A single-nucleotide-polymorphism-based multilocus genotyping assay for subtyping lineage I isolates of Listeria monocytogenes. Appl. Environ. Microbiol. 73: 133– 147.

27. Dyet, K. H.,, I. Robertson,, E. Turbitt,, and P. E. Carter. 2011. Characterization of Escherichia coli O157:H7 in New Zealand using multiple-locus variable-number tandem-repeat analysis. Epidemiol. Infect. 139: 464– 471.

28. Fakhr, M. K.,, L. K. Nolan,, and C. M. Logue. 2005. Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium. J. Clin. Microbiol. 43: 2215– 2219.

29. Farlow, J.,, K. L. Smith,, J. Wong,, M. Abrams,, M. Lytle,, and P. Keim. 2001. Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis. J. Clin. Microbiol. 39: 3186– 3192.

30. Fedurco, M.,, A. Romieu,, S. Williams,, I. Lawrence,, and G. Turcatti. 2006. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res. 34: e22.

31. Fisher, I. S. 1999. The Enter-net international surveillance network—how it works. Euro Surveill. 4: 52– 55.

32. Fisher, I. S. 1995. Salm-Net: a network for human Salmonella surveillance in Europe. Euro Surveill. Sep:7-8.

33. Fitzgerald, C.,, M. Collins,, S. van Duyne,, M. Mikoleit,, T. Brown,, and P. Fields. 2007. Multiplex, bead-basedsuspension array for molecular determination of common Salmonella serogroups. J. Clin. Microbiol. 45: 3323– 3334.

34. Foley, S. L.,, S. Simiee,, J. Meng,, D. G. White,, P. F. McDermott,, and S. Zhao. 2004. Evaluation of molecular typing methods for Escherichia coli O157:H7 isolates from cattle, food, and humans. J. Food Prot. 67: 651– 657.

35. Frye, J. G.,, T. Jesse,, F. Long,, G. Rondeau,, S. Porwollik,, M. McClelland,, C. R. Jackson,, M. Englen,, and P. J. Fedorka-Cray. 2006. DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int. J. Antimicrob. Agents 27: 138– 151.

36. Frye, J. G.,, R. L. Lindsey,, G. Rondeau,, S. Porwollik,, F. Long,, M. McClelland,, C. R. Jackson,, M. D. Englen,, R. J. Meinersmann,, M. E. Berrang,, J. A. Davis,, J. B. Barrett,, J. B. Turpin,, S. N. Thitaram,, and P. J. Fedorka-Cray. 2010. Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database. Microb. Drug Resist. 16: 9– 19.

37. Garaizar, J.,, A. Rementeria,, and S. Porwollik. 2006. DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? FEMS Immunol. Med. Microbiol. 47: 178– 189.

38. Gardiner, K.,, W. Laas,, and D. Patterson. 1986. Fractionation of large mammalian DNA restriction fragments using vertical pulsed-field gradient gel electrophoresis. Somat. Cell. Mol. Genet. 12: 185– 195.

39. Gerner-Smidt, P.,, K. Hise,, J. Kincaid,, S. Hunter,, S. Rolando,, E. Hyytia-Trees,, E. M. Ribot,, and B. Swaminathan. 2006. PulseNet USA: a five-year update. Foodborne Pathog. Dis. 3: 9– 19.

40. Gilmour, M. W.,, M. Graham,, G. Van Domselaar,, S. Tyler,, H. Kent,, K. M. Trout-Yakel,, O. Larios,, V. Allen,, B. Lee,, and C. Nadon. 2011. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 11: 120.

41. Graves, L. M.,, S. B. Hunter,, A. R. Ong,, D. Schoonmaker-Bopp,, K. Hise,, L. Kornstein,, W. E. DeWitt,, P. S. Hayes,, E. Dunne,, P. Mead,, and B. Swaminathan. 2005. Microbiological aspects of the investigation that traced the 1998 outbreak of listeriosis in the United States to contaminated hot dogs and establishment of molecular subtyping-based surveillance for Listeria monocytogenes in the PulseNet network. J. Clin. Microbiol. 43: 2350– 2355.

42. Grimont, P. A. D.,, and F.-X. Weill. 2007. Antigenic formulae of the Salmonella serovars, 9th ed. WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur, Paris, France.

43. Gudmundsdottir, S.,, B. Gudbjornsdottir,, H. L. Lauzon,, H. Einarsson,, K. G. Kristinsson,, and M. Kristjansson. 2005. Tracing Listeria monocytogenes isolates from cold-smoked salmon and its processing environment in Iceland using pulsed-field gel electrophoresis. Int. J. Food Microbiol. 101: 41– 51.

44. Harrington, C. S.,, F. M. ThomsonCarter,, and P. E. Carter. 1997. Evidence for recombination in the flagellin locus of Campylobacter jejuni: implications for the flagellin gene typing scheme. J. Clin. Microbiol. 35: 2386– 2392.

45. Hassan, W. M.,, S. Y. Wang,, and R. D. Ellender. 2005. Methods to increase fidelity of repetitive extragenic palindromic PCR fingerprint-based bacterial source tracking efforts. Appl. Environ. Microbiol. 71: 512– 518.

46. Healy, M.,, J. Huong,, T. Bittner,, M. Lising,, S. Frye,, S. Raza,, R. Schrock,, J. Manry,, A. Renwick,, R. Nieto,, C. Woods,, J. Versalovic,, and J. R. Lupski. 2005. Microbial DNA typing by automated repetitive-sequence-based PCR. J. Clin. Microbiol. 43: 199– 207.

47. Hedberg, C. W.,, K. E. Smith,, J. M. Besser,, D. J. Boxrud,, T. W. Hennessy,, J. B. Bender,, F. A. Anderson,, and M. T. Osterholm. 2001. Limitations of pulsed-field gelelectrophoresis for the routine surveillance of Campylobacter infections. J. Infect. Dis. 184: 242– 244.

48. Holmberg, S. D.,, I. K. Wachsmuth,, F. W. Hickman-Brenner,, and M. L. Cohen. 1984. Comparison of plasmid profile analysis, phage typing, and antimicrobial susceptibility testing in characterizing Salmonella Typhimurium isolates from outbreaks. J. Clin. Microbiol. 19: 100– 104.

49. Hommais, F.,, S. Pereira,, C. Acquaviva,, P. Escobar-Paramo,, and E. Denamur. 2005. Single-nucleotide polymorphism phylotyping of Escherichia coli. Appl. Environ. Microbiol. 71: 4784– 4792.

50. Horby, P. W.,, S. J. O’Brien,, G. K. Adak,, C. Graham,, J. I. Hawker,, P. Hunter,, C. Lane,, A. J. Lawson,, R. T. Mitchell,, M. H. Reacher,, E. J. Threlfall,, and L. R. Ward. 2003. A national outbreak of multi-resistant Salmonella enterica serovar Typhimurium definitive phage type (DT) 104 associated with consumption of lettuce. Epidemiol. Infect. 130: 169– 178.

51. Hyytia-Trees, E.,, P. Lafon,, P. Vauterin,, and E. M. Ribot. 2010. Multilaboratory validation study of standardized multiple-locus variable-number tandem repeat analysis protocol for Shiga toxin-producing Escherichia coli O157: a novel approach to normalize fragment size data between capillary electrophoresis platforms. Foodborne Pathog. Dis. 7: 129– 136.

52. Jackson, S. A.,, M. K. Mammel,, I. R. Patel,, T. Mays,, T. J. Albert,, J. E. LeClerc,, and T. A. Cebula. 2007. Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays. Forensic Sci. Int. 168: 183– 199.

53. Karagiannis, I.,, T. Sideroglou,, K. Gkolfinopoulou,, A. Tsouri,, D. Lampousaki,, E. N. Velonakis,, E. V. Scoulica,, K. Mellou,, T. Panagiotopoulos,, and S. Bonovas. 2010. A waterborne Campylobacter jejuni outbreak on a Greek island. Epidemiol. Infect. 138: 1726– 1734.

54. Keim, P.,, L. B. Price,, A. M. Klevytska,, K. L. Smith,, J. M. Schupp,, R. Okinaka,, P. J. Jackson,, and M. E. Hugh-Jones. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J. Bacteriol. 182: 2928– 2936.

55. Kotetishvili, M.,, O. C. Stine,, A. Kreger,, J. G. Morris, Jr.,, and A. Sulakvelidze. 2002. Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J. Clin. Microbiol. 40: 1626– 1635.

56. Latreille, P.,, S. Norton,, B. S. Goldman,, J. Henkhaus,, N. Miller,, B. Barbazuk,, H. B. Bode,, C. Darby,, Z. Du,, S. Forst,, S. Gaudriault,, B. Goodner,, H. Goodrich-Blair,, and S. Slater. 2007. Optical mapping as a routine tool for bacterial genome sequence finishing. BMC Genomics 8: 321.

57. Leader, B. T.,, J. G. Frye,, J. Hu,, P. J. Fedorka-Cray,, and D. S. Boyle. 2009. High-throughput molecular determination of Salmonella enterica serovars by use of multiplex PCR and capillary electrophoresis analysis. J. Clin. Microbiol. 47: 1290– 1299.

58. Levy, D. D.,, B. Sharma,, and T. A. Cebula. 2004. Single-nucleotide polymorphism mutation spectra and resistance to quinolones in Salmonella enterica serovar Enteritidis with a mutator phenotype. Antimicrob. Agents Chemother. 48: 2355– 2263.

59. Liljebjelke, K. A.,, C. L. Hofacre,, T. Liu,, D. G. White,, S. Ayers,, S. Young,, and J. J. Maurer. 2005. Vertical and horizontal transmission of Salmonella within integrated broiler production system. Foodborne Pathog. Dis. 2: 90– 102.

60. Lindsey, R. L.,, J. G. Frye,, P. J. Fedorka-Cray,, T. J. Welch,, and R. J. Meinersmann. 2011. An oligonucleotide microarray to characterize multidrug resistant plasmids. J. Microbiol. Methods 81: 96– 100.

61. Lindstedt, B. A.,, L. T. Brandal,, L. Aas,, T. Vardund,, and G. Kapperud. 2007. Study of polymorphic variable-number of tandem repeats loci in the ECOR collection and in a set of pathogenic Escherichia coli and Shigella isolates for use in a genotyping assay. J. Microbiol. Methods 69: 197– 205.

62. Lindstedt, B. A.,, M. Torpdahl,, E. M. Nielsen,, T. Vardund,, L. Aas,, and G. Kapperud. 2007. Harmonization of the multiple-locus variable-number tandem repeat analysis method between Denmark and Norway for typing Salmonella Typhimurium isolates and closer examination of the VNTR loci. J. Appl. Microbiol. 102: 728– 735.

63. Lindstedt, B. A.,, T. Vardund,, L. Aas,, and G. Kapperud. 2004. Multiple-locus variable-number tandem-repeats analysis of Salmonella enterica subsp. enterica serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis. J. Microbiol. Methods 59: 163– 172.

64. Lowell, J. L.,, D. M. Wagner,, B. Atshabar,, M. F. Antolin,, A. J. Vogler,, P. Keim,, M. C. Chu,, and K. L. Gage. 2005. Identifying sources of human exposure to plague. J. Clin. Microbiol. 43: 650– 656.

65. Lu, Z.,, D. Lapen,, A. Scott,, A. Dang,, and E. Topp. 2005. Identifying host sources of fecal pollution: diversity of Escherichia coli in confined dairy and swine production systems. Appl. Environ. Microbiol. 71: 5992– 5998.

66. Malorny, B.,, E. Junker,, and R. Helmuth. 2008. Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis. BMC Microbiol. 8: 84.

67. Manning, G.,, B. Duim,, T. Wassenaar,, J. A. Wagenaar,, A. Ridley,, and D. G. Newell. 2001. Evidence for a genetically stable strain of Campylobacter jejuni. Appl. Environ. Microbiol. 67: 1185– 1189.

68. Manning, S. D.,, A. S. Motiwala,, A. C. Springman,, W. Qi,, D. W. Lacher,, L. M. Ouellette,, J. M. Mladonicky,, P. Somsel,, J. T. Rudrik,, S. E. Dietrich,, W. Zhang,, B. Swaminathan,, D. Alland,, and T. S. Whittam. 2008. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc. Natl. Acad. Sci. USA 105: 4868– 4873.

69. Margulies, M.,, M. Egholm,, W. E. Altman,, S. Attiya,, J. S. Bader,, L. A. Bemben,, J. Berka,, M. S. Braverman,, Y. J. Chen,, Z. Chen,, S. B. Dewell,, L. Du,, J. M. Fierro,, X. V. Gomes,, B. C. Godwin,, W. He,, S. Helgesen,, C. H. Ho,, G. P. Irzyk,, S. C. Jando,, M. L. Alenquer,, T. P. Jarvie,, K. B. Jirage,, J. B. Kim,, J. R. Knight,, J. R. Lanza,, J. H. Leamon,, S. M. Lefkowitz,, M. Lei,, J. Li,, K. L. Lohman,, H. Lu,, V. B. Makhijani,, K. E. McDade,, M. P. McKenna,, E. W. Myers,, E. Nickerson,, J. R. Nobile,, R. Plant,, B. P. Puc,, M. T. Ronan,, G. T. Roth,, G. J. Sarkis,, J. F. Simons,, J. W. Simpson,, M. Srinivasan,, K. R. Tartaro,, A. Tomasz,, K. A. Vogt,, G. A. Volkmer,, S. H. Wang,, Y. Wang,, M. P. Weiner,, P. Yu,, R. F. Begley,, and J. M. Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 326– 327.

70. McQuiston, J. R.,, R. J. Waters,, B. A. Dinsmore,, M. L. Mikoleit,, and P. I. Fields. 2010. Molecular determination of H-antigens of Salmonella using a microsphere based liquid array. J. Clin. Microbiol. 49: 565– 573.

71. Meinersmann, R. J.,, L. O. Helsel,, P. I. Fields,, and K. L. Hiett. 1997. Discrimination of Campylobacter jejuni isolates by fla gene sequencing. J. Clin. Microbiol. 35: 2810– 2814.

72. Metzker, M. L. 2005. Emerging technologies in DNA sequencing. Genome Res. 15: 1767– 1776.

73. Metzker, M. L. 2010. Sequencing technologies—the next generation. Nat. Rev. Genet. 11: 31– 46.

74. Michaud, S.,, S. Menard,, and R. D. Arbeit. 2005. Role of real-time molecular typing in the surveillance of Campylobacter enteritis and comparison of pulsed-field gel electrophoresis profiles from chicken and human isolates. J. Clin. Microbiol. 43: 1105– 1111.

75. Miller, W. G.,, M. D. Englen,, S. Kathariou,, I. V. Wesley,, G. Wang,, L. Pittenger-Alley,, R. M. Siletz,, W. Muraoka,, P. J. Fedorka-Cray,, and R. E. Mandrell. 2006. Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals. Microbiology 152: 245– 255.

76. Murphy, M.,, D. Corcoran,, J. F. Buckley,, M. O’Mahony,, P. Whyte,, and S. Fanning. 2007. Development and application of multiple-locus variable number of tandem repeat analysis (MLVA) to subtype a collection of Listeria monocytogenes. Int. J. Food Microbiol. 115: 187– 194.

77. Nachamkin, I.,, K. Bohachick,, and C. M. Patton. 1993. Flagellin gene typing of Campylobacter jejuni by restriction fragment length polymorphism analysis. J. Clin. Microbiol. 31: 1531– 1536.

78. Noller, A. C.,, M. C. McEllistrem,, and L. H. Harrison. 2004. Genotyping primers for fully automated multilocus variable-number tandem repeat analysis of Escherichia coli O157:H7. J. Clin. Microbiol. 42: 3908.

79. Noller, A. C.,, M. C. McEllistrem,, O. C. Stine,, J. G. Morris, Jr.,, D. J. Boxrud,, B. Dixon,, and L. H. Harrison. 2003. Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis. J. Clin. Microbiol. 41: 675– 679.

80. Olsvik, O.,, H. Sorum,, K. Birkness,, K. Wachsmuth,, M. Fjolstad,, J. Lassen,, K. Fossum,, and J. C. Feeley. 1985. Plasmid characterization of Salmonella Typhimurium transmitted from animals to humans. J. Clin. Microbiol. 22: 336– 338.

81. Parveen, S.,, R. L. Murphree,, L. Edmiston,, C. W. Kaspar,, K. M. Portier,, and M. L. Tamplin. 1997. Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay. Appl. Environ. Microbiol. 63: 2607– 2612.

82. Pelludat, C.,, R. Prager,, H. Tschape,, W. Rabsch,, J. Schuchhardt,, and W. D. Hardt. 2005. Pilot study to evaluate microarray hybridization as a tool for Salmonella enterica serovar Typhimurium strain differentiation. J. Clin. Microbiol. 43: 4092– 4106.

83. Pezzoli, L.,, R. Elson,, C. L. Little,, H. Yip,, I. Fisher,, R. Yishai,, E. Anis,, L. Valinsky,, M. Biggerstaff,, N. Patel,, H. Mather,, D. J. Brown,, J. E. Coia,, W. van Pelt,, E. M. Nielsen,, S. Ethelberg,, E. de Pinna,, M. D. Hampton,, T. Peters,, and J. Threlfall. 2008. Packed with Salmonella—investigation of an international outbreak of S. Senftenberg infection linked to contamination of prepacked basil in 2007. Foodborne Pathog. Dis. 5: 661– 668.

84. Ramisse, V.,, P. Houssu,, E. Hernandez,, F. Denoeud,, V. Hilaire,, O. Lisanti,, F. Ramisse,, J. D. Cavallo,, and G. Vergnaud. 2004. Variable number of tandem repeats in Salmonella enterica subsp. enterica for typing purposes. J. Clin. Microbiol. 42: 5722– 5730.

85. Revazishvili, T.,, M. Kotetishvili,, O. C. Stine,, A. S. Kreger,, J. G. Morris,, and A. Sulakvelidze. 2004. Comparative analysis of multilocus sequence typing and pulsed-field gel electrophoresis for characterizing Listeria monocytogenes strains isolated from environmental and clinical sources. J. Clin. Microbiol. 42: 276– 285.

86. Riley, L. W.,, R. S. Remis,, S. D. Helgerson,, H. B. McGee,, J. G. Wells,, B. R. Davis,, R. J. Hebert,, E. S. Olcott,, L. M. Johnson,, N. T. Hargrett,, P. A. Blake,, and M. L. Cohen. 1983. Hemorrhagic colitis associated with a rare Escherichia coli serotype. N. Engl. J. Med. 308: 681– 685.

87. Ross, I. L.,, and M. W. Heuzenroeder. 2005. Discrimination within phenotypically closely related definitive types of Salmonella enterica serovar Typhimurium by the multiple amplification of phage locus typing technique. J. Clin. Microbiol. 43: 1604– 1611.

88. Roussel, S.,, B. Felix,, C. Colaneri,, M. L. Vignaud,, T. T. Dao,, M. Marault,, and A. Brisabois. 2010. Semi-automated repetitive-sequence-based polymerase chain reaction compared to pulsed-field gel electrophoresis for Listeria monocytogenes subtyping. Foodborne Pathog. Dis. 7: 1005– 1012.

89. Sails, A. D.,, B. Swaminathan,, and P. I. Fields. 2003. Utility of multilocus sequence typing as an epidemiological tool for investigation of outbreaks of gastroenteritis caused by Campylobacter jejuni. J. Clin. Microbiol. 41: 4733– 4739.

90. Sauders, B. D.,, E. D. Fortes,, D. L. Morse,, N. Dumas,, J. A. Kiehlbauch,, Y. Schukken,, J. R. Hibbs,, and M. Wiedmann. 2003. Molecular subtyping to detect human listeriosis clusters. Emerg. Infect. Dis. 9: 672– 680.

91. Savelkoul, P. H. M.,, H. J. M. Aarts,, J. deHaas,, L. Dijkshoorn,, B. Duim,, M. Otsen,, J. L. W. Rademaker,, L. Schouls,, and J. A. Lenstra. 1999. Amplified-fragment length polymorphism analysis: the state of an art. J. Clin. Microbiol. 37: 3083– 3091.

92. Schwartz, D. C.,, W. Saffran,, J. Welsh,, R. Haas,, M. Goldenberg,, and C. R. Cantor. 1983. New techniques for purifying large DNAs and studying their properties and packaging. Cold Spring Harb. Symp. Quant. Biol. 47( Pt. 1): 189– 195.

93. Selander, R. K.,, D. A. Caugant,, H. Ochman,, J. M. Musser,, M. N. Gilmour,, and T. S. Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51: 873– 884.

94. Sheppard, S. K.,, F. Colles,, J. Richardson,, A. J. Cody,, R. Elson,, A. Lawson,, G. Brick,, R. Meldrum,, C. L. Little,, R. J. Owen,, M. C. Maiden,, and N. D. McCarthy. 2010. Host association of Campylobacter genotypes transcends geographic variation. Appl. Environ. Microbiol. 76: 5269– 5277.

95. Southern, E. M. 1979. Analysis of restriction-fragment patterns from complex deoxyribonucleic acid species. Biochem. Soc. Symp. 44: 37– 41.

96. Sperry, K. E.,, S. Kathariou,, J. S. Edwards,, and L. A. Wolf. 2008. Multiple-locus variable-number tandem-repeat analysis as a tool for subtyping Listeria monocytogenes strains. J. Clin. Microbiol. 46: 1435– 1450.

97. Suzuki, Y.,, M. Ishihara,, M. Saito,, N. Ishikawa,, and T. Yokochi. 1994. Discrimination by means of pulsed-field gel electrophoresis between strains of Campylobacter jejuni Lior type 4 derived from sporadic cases and from outbreaks of infection. J. Infect. 29: 183– 187.

98. Swaminathan, B.,, T. J. Barrett,, S. B. Hunter,, R. V. Tauxe, and the CDC PulseNet Task Force. 2001. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg. Infect. Dis. 7: 382– 389.

99. Swaminathan, B.,, P. Gerner-Smidt,, L. K. Ng,, S. Lukinmaa,, K. M. Kam,, S. Rolando,, E. P. Gutierrez,, and N. Binsztein. 2006. Building PulseNet International: an interconnected system of laboratory networks to facilitate timely public health recognition and response to foodborne disease outbreaks and emerging foodborne diseases. Foodborne Pathog. Dis. 3: 36– 50.

100. Taylor, D. N.,, I. K. Wachsmuth,, Y. H. Shangkuan,, E. V. Schmidt,, T. J. Barrett,, J. S. Schrader,, C. S. Scherach,, H. B. McGee,, R. A. Feldman,, and D. J. Brenner. 1982. Salmonellosis associated with marijuana: a multistate outbreak traced by plasmid fingerprinting. N. Engl. J. Med. 306: 1249– 1253.

101. Tomkinson, A. E.,, S. Vijayakumar,, J. M. Pascal,, and T. Ellenberger. 2006. DNA ligases: structure, reaction mechanism, and function. Chem. Rev. 106: 687– 699.

102. Torres-Cruz, J.,, and M. W. van der Woude. 2003. Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli. J. Bacteriol. 185: 6990– 6994.

103. Valouev, A.,, J. Ichikawa,, T. Tonthat,, J. Stuart,, S. Ranade,, H. Peckham,, K. Zeng,, J. A. Malek,, G. Costa,, K. McKernan,, A. Sidow,, A. Fire,, and S. M. Johnson. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18: 1051– 1063.

104. van Belkum, A. 1999. Short sequence repeats in microbial pathogenesis and evolution. Cell. Mol. Life Sci. 56: 729– 734.

105. Versalovic, J.,, T. Koeuth,, and J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19: 6823– 6831.

106. Vos, P.,, R. Hogers,, M. Bleeker,, M. Reijans,, T. van de Lee,, M. Hornes,, A. Frijters,, J. Pot,, J. Peleman,, M. Kuiper, et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407– 4414.

107. Wachsmuth, I. K.,, J. A. Kiehlbauch,, C. A. Bopp,, D. N. Cameron,, N. A. Strockbine,, J. G. Wells,, and P. A. Blake. 1991. The use of plasmid profiles and nucleic acid probes in epidemiologic investigations of foodborne, diarrheal diseases. Int. J. Food Microbiol. 12: 77– 89.

108. Ward, T. J.,, T. F. Ducey,, T. Usgaard,, K. A. Dunn,, and J. P. Bielawski. 2008. Multilocus genotyping assays for single nucleotide polymorphism-based subtyping of Listeria monocytogenes isolates. Appl. Environ. Microbiol. 74: 7629– 7642.

109. Ward, T. J.,, P. Evans,, M. Wiedmann,, T. Usgaard,, S. E. Roof,, S. G. Stroika,, and K. Hise. 2010. Molecular and phenotypic characterization of Listeria monocytogenes from U.S. Department of Agriculture Food Safety and Inspection Service surveillance of ready-to-eat foods and processing facilities. J. Food Prot. 73: 861– 869.

110. Ward, T. J.,, T. Usgaard,, and P. Evans. 2010. A targeted multilocus genotyping assay for lineage, serogroup, and epidemic clone typing of Listeria monocytogenes. Appl. Environ. Microbiol. 76: 6680– 6684.

111. Wassenaar, T. M.,, B. Geilhausen,, and D. G. Newell. 1998. Evidence of genomic instability in Campylobacter jejuni isolated from poultry. Appl. Environ. Microbiol. 64: 1816– 1821.

112. Wise, M. G.,, G. R. Siragusa,, J. Plumblee,, M. Healy,, P. J. Cray,, and B. S. Seal. 2009. Predicting Salmonella enterica serotypes by repetitive sequence-based PCR. J. Microbiol. Methods 76: 18– 24.

113. Yan, W.,, N. Chang,, and D. E. Taylor. 1991. Pulsed-field gel electrophoresis of Campylobacter jejuni and Campylobacter coli genomic DNA and its epidemiologic application. J. Infect. Dis. 163: 1068– 1072.

114. Yeramian, E.,, and H. Buc. 1999. Tandem repeats in complete bacterial genome sequences: sequence and structural analyses for comparative studies. Res. Microbiol. 150: 745– 754.

115. Yoshida, C.,, K. Franklin,, P. Konczy,, J. R. McQuiston,, P. I. Fields,, J. H. Nash,, E. N. Taboada,, and K. Rahn. 2007. Methodologies towards the development of an oligonucleotide microarray for determination of Salmonella serotypes. J. Microbiol. Methods 70: 261– 271.

116. Zhang, W.,, B. M. Jayarao,, and S. J. Knabel. 2004. Multi-virulence-locus sequence typing of Listeria monocytogenes. Appl. Environ. Microbiol. 70: 913– 920.

117. Zhang, W.,, and S. J. Knabel. 2005. Multiplex PCR assay simplifies serotyping and sequence typing of Listeria monocytogenes associated with human outbreaks. J. Food Prot. 68: 1907– 1910.

118. Zhang, W.,, W. Qi,, T. J. Albert,, A. S. Motiwala,, D. Alland,, E. K. Hyytia-Trees,, E. M. Ribot,, P. I. Fields,, T. S. Whittam,, and B. Swaminathan. 2006. Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Res. 16: 757– 767.

119. Zhao, S. H.,, S. E. Mitchell,, J. H. Meng,, S. Kresovich,, M. P. Doyle,, R. E. Dean,, A. M. Casa,, and J. W. Weller. 2000. Genomic typing of Escherichia coli O157:H7 by semi-automated fluorescent AFLP analysis. Microbes Infect. 2: 107– 113.

120. Zou, W.,, J. G. Frye,, C. W. Chang,, J. Liu,, C. E. Cerniglia,, and R. Nayak. 2009. Microarray analysis of antimicrobial resistance genes in Salmonella enterica from preharvest poultry environment. J. Appl. Microbiol. 107: 906– 914.

121. Zou, W.,, W. J. Lin,, S. L. Foley,, C. H. Chen,, R. Nayak,, and J. J. Chen. 2010. Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes. J. Clin. Microbiol. 48: 3122– 3126.

Tables

Molecular Source Tracking and Molecular Subtyping

/content/10.1128/9781555818463.chap43.tab43-1

Table 43.1

Properties of methods commonly used for molecular subtyping of foodborne pathogens

10.1128/9781555818463/tab43-1_thmb.gif

10.1128/9781555818463/tab43-1.gif

Table 43.1

Properties of methods commonly used for molecular subtyping of foodborne pathogens