Recent developments and future prospects in subtyping of foodborne bacterial pathogens

Future Microbiology

Volumn 2, Issue 2, 2007, Pages 175-185

  Hyytiä Trees, Eija K ^a   Cooper, Kara ^b   Ribot, Efrain M ^b   Gerner Smidt, Peter ^b  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

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

Author keywords

Foodborne bacteria; MALDI TOF; Microarray; Multilocus sequence typing; Multiple locus variable number tandem repeat analysis; PulseNet; Single nucleotide polymorphism; Subtyping

Indexed keywords

AEROBIC RESPIRATION CONTROL PROTEIN A; BACTERIAL DNA; ENDOPEPTIDASE CLP; ESCHERICHIA COLI SECRETED PROTEIN A; FERRIC HYDROXAMATE UPTAKE PROTEIN COMPONENT A; FLAGELLIN; MALATE DEHYDROGENASE; OUTER MEMBRANE PROTEIN A; PHOSPHOGLUCOMUTASE; RNA 16S;

BACILLUS ANTHRACIS; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM CONTAMINATION; BACTERIUM IDENTIFICATION; CAMPYLOBACTER JEJUNI; DNA MICROARRAY; DNA SEQUENCE; ESCHERICHIA COLI; FOOD CONTAMINATION; HOUSEKEEPING GENE; HUMAN; INTERMETHOD COMPARISON; LISTERIA MONOCYTOGENES; MASS SPECTROMETRY; MICROARRAY ANALYSIS; MULTILOCUS SEQUENCE TYPING; NEISSERIA MENINGITIDIS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; REVIEW; SALMONELLA TYPHIMURIUM; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENTIATION; VARIABLE NUMBER OF TANDEM REPEAT;

BACTERIA; BACTERIAL TYPING TECHNIQUES; ELECTROPHORESIS, GEL, PULSED-FIELD; FOOD MICROBIOLOGY; MINISATELLITE REPEATS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS);

EID: 34248653460     PISSN: 17460913     EISSN: None     Source Type: Journal    
DOI: 10.2217/17460913.2.2.175     Document Type: Review

References (59)

1. Fisher IS, Threlfall EJ: 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, 1-7 (2005).
2. Lynch M, Painter J, Woodruff R, Braden C: Surveillance for foodborne-disease outbreaks - United States. MMWR Surveill. Summ. 55, 1-42 (2006).
3. Struelens MJ: Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clin. Microbiol. Infect. 2, 2-11 (1996).
4. Batz MB, Doyle MP, Morris G Jr et al.: Attributing illness to food. Emerg. Infect. Dis. 11, 993-999 (2005).
5. Swaminathan B, Gerner-Smidt P, Ng LK et al.: 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 (2006).
6. Maiden MC, Bygraves JA, Feil E et al.: Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl Acad. Sci. USA 95, 3140-3145 (1998).
7. Wick LM, Qi W, Lacher DW, Whittam TS: Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7. J. Bacteriol. 187, 1783-1791 (2005).
8. Noller AC, McEllistrem MC, Stine OC et al.: Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis. J. Clin. Mirobiol. 41, 675-679 (2003).
9. Foley SL, White DG, McDermott PF et al.: Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurim isolates obtained from food animal sources. J. Clin. Microbiol. 44, 3569-3577 (2006).
10. Ross I, Heuzenroeder MW: 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 (2005).
11. Zhang W, Jayarao BM, Knabel SJ: Multi-virulence-locus sequence typing of Listeria monocytogenes. Appl. Environ. Microbiol. 70, 913-920 (2004).
12. Dingle KE, Colles FM, Wareing DRA et al.: Multilocus sequence typing system for Campylobacter jejuni. J. Clin. Microbiol. 39, 14-23 (2001).
13. Sails AD, Swaminathan B, Fields PI: Utility of multilocus sequence typing as an epidemiological tool for investigation of outbreaks of gastroenteritis caused by Campylobacter jejuni. J. Clin. Microbil. 41, 4733-4739 (2003).
14. Clark CG, Bryden L, Cuff WR et al.: 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 Caropylobacter sp. strains in Walkerton, Ontario, Canada. J. Clin. Microbiol. 43, 2080-2091 (2005).
15. Miller WG, On SLW, Wang G, Fontanoz S, Lastovica AJ, Mandrell RE: Extended multilocus sequence typing system for Campylobacter coli, C. lari, C. upsaliensis, and C. helveticus. J. Clin. Microbiol. 43, 2315-2329 (2005).
16. van Belkum A, Scherer S, Van Alphen L, Verbrugh H: Short-sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62, 275-293 (1998).
17. Nakamura Y, Leppert M, O'Connell P et al.: Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235, 1616-1622 (1987).
18. Hoffmaster AR, Fitzgerald CC, Ribot E, Mayer LW, Popovic T: Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States. Emerg. Infect. Dis. 8, 1111-1116 (2002).
19. Lindstedt BA, Heir E, Vardund T, Kapperud G: DNA fingerprinting of Shigatoxin producing Eschirichia coli O157 based on multiple-locus variable-number tandem-repeats analysis (MLVA). Ann. Clin. Microbiol. Antimicrob. 2, 12 (2003).
20. Noller AC, McEllistrem MC, Pacheco AGF, Boxrud DJ, Harrison LH: Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates. J. Clin. Microbiol. 41, 5389-5397 (2003).
21. Keys C, Kemper S, Keim P: 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, 928-940 (2005).
22. Hyytia-Trees E, Smole SC, Fields PA, Swaminathan B, Ribot EM: Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157). Foodborne Pathog. Dis. 3, 118-131 (2006).
23. Lindstedt BA, Vardund T, Aas L, Kapperud G: 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 (2004).
24. Ramisse V, Houssu P, Hernendez E et al.: Variable number of tandem repeats in Salmonella enterica subsp. enterica for typing purposes. J. Clin. Microbiol. 42, 5722-5730 (2004).
25. Torpdahl M, Sorensen G, Ethelberg S, Sando G, Gammelgard K, Porsbo, LJ: A regional outbreak of Salmonella Typhimurium in Denmark and identification of the source using MLVA typing. Eurosurveillance 11, 134-136 (2006).
26. Noller AC, McEllistrem MC, Shutt KA, Harrison LH: Locus-specific mutational events in a multilocus variable-number tandem repeat analysis of Escherichia coli O157:H7. J. Clin. Microbiol. 44, 374-377 (2006).
27. Vogler AJ, Keys C, Nemoto Y, Colman RE, Jay Z, Keim P: Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7. J. Bacteriol. 188, 4253-4263 (2006).
28. Cebula TA, Jackson SA, Brown EW, Goswami B, LeClerc JE: Chips and SNPs, bugs and thugs: a molecular sleuthing perspective. J. Food Prot. 68, 1271-1284 (2005).
29. Best EL, Fox AJ, Frost JA, Bolton FJ: Real-time single nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes. J. Med. Microbiol. 54, 919-925 (2005).
30. Hommais F, Pereira S, Acquaviva C, Escobar-Paramo P, Denamur E: Single-nucleotide polymorphism phylotyping of Escherichia coli. Appl. Environ. Microbiol. 71, 4784-4792 (2005).
31. Read TD, Salzberg SL, Pop M et al.: Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296, 2028-1033 (2002).
32. Zhang W, Qi W, Albert TJ et al.: Probing genomic diversity and evolution of Escherichia coli O157 by single-nucleotide polymorphisms. Gen. Res. 16, 757-767 (2006).
33. Hu H, Lan R, Reeves PR: Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium. Genetics 172, 743-750 (2006).
34. Ducey TF, Page B, Usgaard T, Borucki MK, Pupedis K, Ward TJ: A single-nucleotide-polymorphism-based multilocus genotyping assay for subtyping lineage I isolates of Listeria monocytogenes. Appl. Environ. Microbiol. 73, 133-147 (2007).
35. Garaizar J, Rementeria A, Porwollik S: DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? FEMS Immunol. Med. Microbiol. 47, 178-189 (2006).
36. Boruckl MK, Reynolds J, Call DR, Ward TJ, Page B, Kadushin J: Suspension microarray with dendrimer signal amplification allows direct and high-throughput subtyping of Listeria monocytogenes from genomic DNA. J. Clin. Microbiol. 43, 3255-3259 (2005).
37. Dunbar SA: Applications of Luminex xMAP technology for rapid, high-throughput multiplex nucleic acid detection. Clin. Chim. Acta. 363, 71-82 (2006).
38. Dziejman M, Balon E, Boyd D, Fraser CM, Heidelberg JF, Mekalanos JJ: Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc. Natl Acad. Sci. USA 99, 1556-1561 (2002).
39. Fukiya S, Mizoguchi H, Tobe T, Mori H: Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J. Bacteriol. 186, 3911-3921 (2004).
40. Leonard EE, Takata T, Blaser MJ, Falkow S, Tompkins LS, Gaynor EC: Use of an open-reading frame-specific Campylobacter jejuni microarray as a new genotyping tool for studying epidemiologically related isolates. J. Infect. Dis. 187, 691-694 (2003).
41. Call DR, Borucki MK, Loge FJ: Detection of bacterial pathogens in environmental samples using DNA microarrays. J. Microbiol. Methods 53, 235-243 (2003).
42. Borucki MK, Kim SH, Call DR, Smole SC, Pagotto F: 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 (2004).
43. Nelson KE, Fouts DE, Mongodin EF et al.: Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res. 32, 2386-2395 (2004).
44. Fux CA, Shirtliff M, Stoodley P, Costerton JW: Can laboratory reference strains mirror 'real-world' pathogenesis? Trends Microbiol. 13, 58-63 (2005).
45. Reen FJ, Boyd EF, Porwollik S et al.: Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray. Appl. Environ. Microbiol. 71, 1616-1625 (2005).
46. Dunbar SA, Vander Zee CA, Oliver KG, Karem KL, Jacobsen JW: Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J. Microbiol. Methods 53, 245-252 (2003).
47. Margulies M, Egholm M, Altman WE et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 326-327 (2005).
48. Zhou S, Kile A, Bechner M et al.: Single-molecule approach to bacterial genomic comparisons via optical mapping. J. Bacteriol. 186, 7773-7782 (2004).
49. Clarke SC: Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications. Expert Rev. Mol. Diagn. 5, 947-953 (2005).
50. Valicer GJ, Raddatz G, Keller H et al..: Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc. Natl Acad. Sci. USA 103, 8107-8112 (2006).
51. Siuzdak G: The emergence of mass spectrometry in biochemical research. Proc. Natl Acad. Sci. USA 91, 11290-11297 (1994).
52. Fenselau C, Demirev P: Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 20, 157-171 (2001).
53. Madonna AJ, Basile F, Ferrer I, Metanni MA, Rees JC, Voorhees KJ: On-probe sample preparation for the detection of proteins above 15 kDa for whole cell bacteria by MALDI/TOF. Mass Spectrom. 14, 2220 (2000).
54. Bright JJ, Claydon MA, Soufian M, Gordon DB: Rapid typing of bacteria using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry and pattern recognition software. J. Microbiol. Methods 48, 127-138 (2002).
55. Jarman KH, Cebula ST, Saenz AJ et al.: An algorithm for automated bacterial Identification using matrix-assisted desorption/ionization mass spectrometry. Anal. Chem. 72, 1217-1223 (2000).
56. Mazzeo MF, Sorrentino A, Gaita M et al.: Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the discrimination of food-borne microorganisms. Appl. Environ. Microbiol. 72, 1180-1189 (2006).
57. Honisch C, Raghunathan A, Cantor CR, Palsson BO, van den Boom D: High-throughput mutation detection underlying adaptive evolution of Escherichia cali-K12. Gen. Res. 14, 2495-2502 (2004).
58. Mandrell RE, Harden LA, Bates A, Miller WG, Haddon WF, Fagerquist CK: Speciation of Campylobacter coli, C. jejuni, C. helveticus, C. lari, C. sputorum, and C. upsaliensis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 71, 6292-6307 (2005).
59. von Wintzingerode F, Bocker S, Schlotelburg C et al.: Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc. Natl Acad. Sci. USA 99, 7039-7044 (2002).