Abstract
Tracking sources of microbial contaminants has been a concern since the early days of commercial food processing; however, recent advances in the development of molecular subtyping methods have provided tools that allow more rapid and highly accurate determinations of these sources. Only individuals with an understanding of the molecular subtyping methods, and the epidemiological techniques used, can evaluate the reliability of a link between a food-manufacturing plant, a food, and a foodborne disease outbreak.
In principle, the goal of molecular subtyping methods is to compare the genetic material of two or more bacterial isolates to determine whether they have shared a recent common ancestor. The chapter addresses some of more commonly applied subtyping methods including pulsed field gel electrophoresis (PFGE), ribotyping, PCR methods applied to fragment length polymorphisms (RAPD and REP-PCR), DNA sequencing-based subtyping, and other characterization methods. This chapter also includes case studies. In preparing for potential emergencies, food companies may consider adding an outside expert in molecular subtyping to their emergency response team.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Ackers ML, Schoenfeld S, Markman J, et al. (2000) An outbreak of Yersinia enterocolitica O:8 infections associated with pasteurized milk. J Infect Dis 181:1834–1837
Braden CR, Templeton GL, Stead WW, Bates JH, Cave MD, Valway SE (1997) Retrospective detection of laboratory cross-contamination of Mycobacterium tuberculosis cultures with use of DNA fingerprint analysis. Clin Infect Dis 24:35–40
Brosch R, Chen J, Luchansky JB (1994) Pulsed-field fingerprinting of listeria: Identification of genomic divisions for Listeria monocytogenes and their correlation with serovar. Appl Environ Microbiol 60:2584–2592
Breuer T, Benkel D, Shapiro R, et al. (2001) A multistate outbreak of Escherichia coli O157:H7 infections linked to alfalfa sprouts grown from contaminated seeds. Emerg Infect Dis 7:977–982
Bruce J (1996) Automated system rapidly identifies and characterizes microorganisms in food. Food Technol 50:77–81
CDC 2009. Salmonella Strains Tables for Outbreak Related to Peanut Butter and Peanut Containing Products. January, 29. http://www.cdc.gov/salmonella/typhimurium/strains_table.html
Farber JM, Gendel SM, Tyler KD, Boerlin P, Landry WL, Fritschel SC, Barrett TJ (2001) Molecular typing and differentiation, Chapter 11. In: Compendium of Methods for the Microbiological Examination of Foods, 4th edn. American Public Health Association, Washington, DC
Graves LM, Swaminathan B, Hunter SB (1999) Subtyping Listeria monocytogenes. In: Ryser E, Marth E (eds) Listeria, listeriosis, and Food Safety. Marcel Dekker, New York, pp. 279–297
Grimont F, Grimont PAD (1986) Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann Inst Pasteur/Microbiol (Paris) 137B:165–175
Jay MT, Garrett V, Mohle-Boetani JC, et al. (2004) A multistate outbreak of Escherichia coli O157:H7 infection linked to consumption of beef tacos at a fast-food restaurant chain. Clin Infect Dis 39(1):1–7
Kerr KG (1994) The rap on REP-PCR-based typing systems. Rev Med Microbiol 5(4):233–244
Keys C, Kemper S, Keim P (2005) Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing. J Appl Microbiol 98(4):928–940
Kimura AC, Johnson K, Palumbo MS, et al. (2004) Multistate shigellosis outbreak and commercially prepared food, United States. Emerg Infect Dis 10(6):1147–1149
Lappi VR, Thimothe J, Nightingale KK, Gall K, Scott VN, Wiedmann M (2004) Longitudinal studies on Listeria in smoked fish plants: Impact of intervention strategies on contamination patterns. J Food Prot 67:2500–2514
Lai E, Birren B, Clark S, et al. (1989) Pulsed field gel electrophoresis. BioTechniques 7:34–42
MacDonald PD, Whitman RE, Boggs JD, et al. (2005) Outbreak of listeriosis among Mexican immigrants as a result of illicitly produced Mexican-style cheese. Clin Infect Dis 40(5):677–682
Olsen SJ, Patrick M, Hunter SB, et al. (2005) Multistate outbreak of Listeria monocytogenes infection linked to delicatessen turkey meat. Clin Infect Dis 40(7):962–967
Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669
Randazzo CL, Torriani S, Akkermans AD, de Vos WM, Vaughan EE (2002) Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16 S rRNA analysis. Appl Environ Microbiol 68:1882–1892
Ralyea RD, Wiedmann M, Boor KJ (1998) Bacterial tracking in a dairy production system using phenotypic and ribotyping methods. J Food Prot 61:1336–1340
Read TD, Salzberg SL, Pop M, et al. (2002) Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296(5575):2028–2033
Spratt BG (1999) Multilocus sequence typing: Molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the Internet. Curr Opin Microbiol 2:312–316
Strockbine NA, Wells JG, Bopp CA, et al. (1998) Overview of detection and subtyping methods. In: Kaper JB, O’Brien AD (eds) Escherichia coli O157:H7 and other Shiga-toxin producing E. coli strains. ASM Press, Washington, DC, pp. 331–356.
Swaminathan B, Barrett T, Hunter S, et al. (2001) PulseNet: The molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7:382–389
Tenover FC, Arbeit RD, Goering RV, 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
Threlfall E, Frost J (1990) The identification, typing and fingerprinting of Salmonella: Laboratory aspects and epidemiological applications. J Appl Bacteriol 68:5–16
Top J, Schouls LM, Bonten MJ, Willems RJ (2004) Multiple-locus variable-number tandem repeat analysis, a novel typing scheme to study the genetic relatedness and epidemiology of Enterococcus faecium isolates. J Clin Microbiol 42:4503–4511
Van Belkum A, Struelens M, de Visser A, et al. (2001) Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin Microbiol Rev 14:547–560
Wassenaar TM, Newell DG (2000) Genotyping of Campylobacter spp. Appl Environ Microbiol 66:1–9
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Wiedmann M (2002a) Subtyping of bacterial foodborne pathogens. Nutr Rev 60:201–208
Wiedmann M (2002b) Molecular subtyping methods for Listeria monocytogenes. J AOAC Int 85:524–531
Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Woodford N, Johnson AP (2004) Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews. Humana Press, Totowa, NJ
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag New York
About this chapter
Cite this chapter
Moorman, M., Pruett, P., Weidman, M. (2010). Value and Methods for Molecular Subtyping of Bacteria. In: Kornacki, J. (eds) Principles of Microbiological Troubleshooting in the Industrial Food Processing Environment. Food Microbiology and Food Safety. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5518-0_10
Download citation
DOI: https://doi.org/10.1007/978-1-4419-5518-0_10
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4419-5517-3
Online ISBN: 978-1-4419-5518-0
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)