Salmonella source attribution based on microbial subtyping

International Journal of Food Microbiology

Volumn 163, Issue 2-3, 2013, Pages 193-203

  Barco, Lisa ^a   Barrucci, Federica ^a   Olsen, John Elmerdahl ^b   Ricci, Antonia ^a  

^a ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLE VENEZIE   (Italy)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Microbial subtyping source attribution models; Salmonella spp.; Subtyping methods

Indexed keywords

ANTIMICROBIAL RESISTANCE TYPING; BACTERIOPHAGE; BACTERIUM IDENTIFICATION; CAMPYLOBACTER JEJUNI; GENOTYPE; LISTERIA MONOCYTOGENES; MICROBIAL SUBTYPING; MICROBIOLOGICAL EXAMINATION; MOLECULAR TYPING; MULTILOCUS SEQUENCE TYPING; MULTIPLE LOCUS VARIABLE NUMBER TANDEM REPEAT ANALYSIS; NONHUMAN; PHENOTYPE; PLASMID PROFILE ANALYSIS; PULSED FIELD GEL ELECTROPHORESIS; REVIEW; RIBOTYPING; SALMONELLA; SALMONELLA ENTERITIDIS; SALMONELLA GALLINARUM; SALMONELLA INFANTIS; SALMONELLA TYPHI; SALMONELLA TYPHIMURIUM; SEROTYPE;

EID: 84876054517     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2013.03.005     Document Type: Review

References (118)

1. Achtman M., Wain J., Weill F.-X., Nair S., Zhou Z., Sangal V., Krauland M.G., Hale J.L., Harbottle H., Uesbeck A., Dougan G., Harrison L.H., Brisse S. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathogens 2012, 8(6):e1002776. the S. enterica MLST study group.
2. Adaska J.M., Silva A.J., Berge A.C.B., Sischo W.M. Genetic and phenotypic variability among Salmonella enterica serovar Typhimurium isolates from California dairy cattle and humans. Applied and Environmental Microbiology 2006, 72:6632-6637.
3. Alcaine S.D., Soyer Y., Warnick L.D., Su W.-L., Sukhnanand S., Richards J., Fortes E.D., McDonough P., Root T.P., Dumas N.B., Gröhn Y., Wiedmann M. Multilocus sequence typing supports the hypothesis that cow- and human-associated Salmonella isolates represent distinct and overlapping populations. Applied and Environmental Microbiology 2006, 72:7575-7585.
4. Baggesen D.L., Soresen G., Nielsen E.M., Wegener H.C. Phage typing of Salmonella typhimurium - is it still a useful tool for surveillance and outbreak investigation?. Eurosurveillance 2010, 15(4). (pii=19471).
5. Baker S., Holt K., van de Vosse E., Roumagnac P., Whitehead S., King E., Ewels P., Keniry A., Weill F.-X., Lightfoot D., van Dissel J.T., Sanderson K.E., Farrar J., Achtman M., Deloukas P., Dougan G. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban district of Jakarta, Indonesia. Journal of Clinical Microbiology 2008, 46:1741-1746.
6. Barco L., Lettini A.A., Ramon E., Longo A., Saccardin C., Dalla Pozza M.C., Ricci A. A rapid and sensitive method to identify and differenziate Salmonella enterica serotype Typhimurium and Salmonella enterica serotype 4,[5],12:i:- by combining traditional serotyping and multiplex polymerase chain reaction. Foodborne Pathogens and Disease 2011, 8:741-743.
7. Barco L., Mancin M., Ruffa M., Saccardin C., Minorello C., Zavagnin P., Lettini A.A., Olsen J.E., Ricci A. Application of the random forest method to analyse epidemiological and phenotypic characteristics of Salmonella 4,[5],12:i:- and Salmonella Typhimurium strains. Zoonoses and Public Health 2012, 59:505-512.
8. Barrett T.J., Gerner-Smidt P., Swaminathan B. Interpretation of pulsed-field gel electrophoresis patterns in foodborne disease investigations and surveillance. Foodborne Pathogens and Disease 2006, 3:20-31.
9. Bauchet V., Huot H., Goldstein R. Molecular genetic basis of ribotyping. Clinical Microbiology Reviews 2008, 21:262-273.
10. Beranek A., Mikula C., Rabold P., Arnhold D., Berghold C., Lederer I., Allerberger F., Kornschober C. Multiple-locus variable-number tandem repeat analysis for subtyping of Salmonella enterica subsp. enterica serovar Enteritidis. International Journal of Medical Microbiology 2009, 299:43-51.
11. Bergamini F., Iori A., Massi P., Pongolini S. Multilocus variable-number of tandem-repeats analysis of Salmonella enterica serotype Gallinarum and comparison with pulsed-field gel electrophoresis genotyping. Veterinary Microbiology 2011, 149:430-436.
12. Best E.L., Lindstedt B.-A., Cook A., Clifton Hadley F.A., Threlfall E.J., Liebana E. Multiple-locus variable-number tandem repeat analysis of Salmonella enterica subsp. enterica serovar Typhimurium: comparison of isolates from pigs, poultry, and cases of human gastroenteritidis. Journal of Applied Microbiology 2007, 103:565-572.
13. Boxrud D. Advances in subtyping methods of foodborne disease pathogens. Current Opinion in Biotechnology 2010, 21:137-141.
14. Boxrud D., Pederson-Gulrud K., Wotton J., Medus C., Lyszkowicz E., Besser J., Bartkus J.M. Comparison of multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and phage typing for subtype analysis of Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology 2007, 45:536-543.
15. Broschat S.L., Call D.R., Davis M.A., Meng D., Lockwood S., Ahmed R., Besser T.E. Improved identification of epidemiologically related strains of Salmonella enterica by use of a fusion algorithm based on pulsed-field gel electrophoresis and multiple-locus variable-number tandem-repeat analysis. Journal of Clinical Microbiology 2010, 48:4072-4082.
16. Call D.R., Orfe L., Davis M.A., Lafrentz S., Kang M.-S. Impact of compounding error on strategies for subtyping pathogenic bacteria. Foodborne Pathogens and Disease 2008, 5:505-516.
17. Capita R., Alonso-Calleja C., Prieto M. Prevalence of Salmonella enterica serovars and genovars from chicken carcasses in slaughterhouses in Spain. Journal of Applied Microbiology 2007, 103:1366-1375.
18. Carattoli A. Plasmid in Gram negatives: molecular typing of resistance plasmids. International Journal of Medical Microbiology 2011, 301:654-658.
19. Carrique-Mas J.J., Papadopoulou C., Evans S.J., Wales A., Teale C.J., Davies R.H. Trends in phage types and antimicrobial resistance of Salmonella enterica serovar Enteritidis isolated from animals in Great Britain from 1990 to 2005. Veterinary Record 2008, 162:541-546.
20. Chiou C.-S., Hung C.-S., Torpdahl M., Watanabe H., Tung S.K., Terajima J., Liang S.-Y., Wang Y.-W. Development and evaluation of multilocus variable number repeat analysis for fine typing and phylogenic analysis of Salmonella enterica serovar Typhimurium. International Journal of Food Microbiology 2010, 142:67-73.
21. 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 Microbiology Letters 2007, 275:16-23.
22. Cho S., Whittam T.S., Boxrud D.J., Bartkus J.M., Saeed A.M. Allele distribution and genetic diversity of VNTR loci in Salmonella enterica serotype Enteritidis isolates from different sources. BMC Microbiology 2008, 8:146-156.
23. Cho S., Whittam T.S., Boxrud D.J., Bartkus J.M., Wilkins M.J., Somsel P., Downes F.P., Musser K.A., Root T.P., Warnick L.D., Wiedmann M., Saeed A.M. Use of multiple-locus variable number tandem repeat analysis and phage typing for subtyping of Salmonella enteritidis from sporadic human cases in the United Stated. Journal of Applied Microbiology 2010, 108(859):867.
24. Clark C.G., Kruk T.M.A.C., Bryden L., Hirvi Y., Ahmed R., Rodgers F.G. Subtyping of Salmonella enterica serotype Enteritidis strains by manual and automated PstI-SphI ribotyping. Journal of Clinical Microbiology 2003, 41:27-33.
25. David J.M., Guillemot D., Bemrah N., Thébault A., Brisabois A., Chemaly M., Weill F., Sanders P., Watier L. The Bayesian microbial subtyping attribution model: robustness to prior information and a proposition. Risk Analysis 2012, 10.1111/j.1539-6924.2012.01877.x.
26. Davis M.A., Baker K.N.K., Call D.R., Warnick L.D., Soyer Y., Wiedmann M., Gröhn Y., McDonough P.L., Hancock D.D., Besser T.E. Multilocus variable-number tandem-repeat method for typing Salmonella enterica serovar Newport. Journal of Clinical Microbiology 2009, 47:1934-1938.
27. Dione M.M., Ikumapayi U.N., Saha D., Mohammed N.I., Geerts S., Ieven M., Adegbola R.A., Antonio M. Clonal differences between non-typhoidal Salmonella (NTS) recovered from children and animals living in close contact in the Gambia. PLoS Neglected Tropical Diseases 2011, 5:e1148.
28. Dunbar S.A. Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clinica Chimica Acta 2006, 363:71-82.
29. Dunner W.M., Westblade L.F., Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. European Journal of Clinical Microbiology and Infectious Disease 2012, 31:1719-1726.
30. EFSA Scientific opinion of the panel on biological hazards on a request from EFSA on overview of methods for source attribution for human illness from food-borne microbiological hazards. EFSA Journal 2008, 764:1-43.
31. EFSA Report on the availability of molecular typing methods for Salmonella, Campylobacter, verotoxigenic Escherichia coli, Listeria monocytogenes and Staphylococcus aureus isolates from food, animals and feedingstuffs in European Union Member States (and in some other reporting countries). EFSA Journal 2009, 272:1-52.
32. EFSA The European Union Summary Report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2010. EFSA Journal 2012, 2597:1-442.
33. Eriksson J., Löfström C., Aspán A., Gunnarsson A., Karlsson I., Borch E., de Jong B., Rådström P. Comparison of genotyping methods by application to Salmonella livingstone strains associated with an outbreak of human salmonellosis. International Journal of Food Microbiology 2005, 104:93-103.
34. Fabre L., Zhang J., Guigon G., Le Hello S., Guibert V., Accou-Demartin M., de Romans S., Lim C., Roux C., Passet V., Diancourt L., Guibourdenche M., Issenhuth-Jeanjean S., Achtman M., Brisse S., Sola C., Weill F.-X. CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS One 2012, 7(5):e36995. 10.1371/journal.pone.0036995.
35. Fang N.-X., Huang B., Hiley L., Bates J., Savill J. A rapid multiplex DNA suspension array method for Salmonella typhimurium subtyping using prophage-related markers. Journal of Microbiological Methods 2012, 88:19-27.
36. Fitzgerald C., Collins M., van Duyne S., Mikoleit M., Brown T., Fields P. Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups. Journal of Clinical Microbiology 2007, 45:3323-3334.
37. Foley S.L., White D.G., McDermott P.F., Walker R.D., Rhodes B., Fedorka-Cray P.J., Simjee S., Zhao S. Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. Journal of Clinical Microbiology 2006, 44:3569-3577.
38. Foley S.L., Lynne A.M., Nayak R. Molecular typing methodologies for microbial source tracking and epidemiological investigations of Gram-negative bacterial foodborne pathogens. Infection, Genetics and Evolution 2009, 9:430-440.
39. Fontana J., Stout A., Bolstorff B., Timperi R. Automated ribotyping and pulsed-field gel electrophoresis for rapid identification of multidrug-resistant Salmonella serotype Newport. Emerging Infectious Diseases 2003, 9:496-499.
40. Giraud E., Cloeckaert A., Baucheron S., Mouline C., Chaslus-Dancia E. Fitness cost of fluoroquinolone resistance in Salmonella enterica serovar Typhimurium. Journal of Medical Microbiology 2003, 52:697-703.
41. Grimont P.A.D., Weill F.X. P. 166 in Antigenic Formulae of Salmonella Serovars 2007, WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur website, Paris, France, (Available at: http://www.pasteur.fr/ip/portal/action/WebdriveActionEvent/oid/01s-000036-089). 9th ed.
42. Guo C., Hoekstra R.M., Schroeder C.M., Pires S.M., Ong K.L., Hartnett E., Naugle A., Harman J., Bennett P., Cieslak P., Scallan E., Rose B., Holt K.G., Kissler B., Mbandi E., Roodsari R., Angulo F.J., Cole D. Application of Bayesian techniques to model the burden of human salmonellosis attributable to U.S. food commodities at the point of processing: adaptation of a Danish model. Foodborne Pathogens and Disease 2011, 8:509-516.
43. Hald T., Vose D., Wegener H.C., Koupeev T. A Bayesian approach to quantify the contribution of animal-food sources to human salmonellosis. Risk Analysis 2004, 24:255-269.
44. Hald T., Lo Fo Wong D.M.A., Aarestrup F.M. The attribution of human infections with antimicrobial resistant Salmonella bacteria in Denmark to sources of animal origin. Foodborne Pathogens and Disease 2007, 4:313-324.
45. Hald T., Pires S.M., de Knegt L. External Scientific Report - Development of a Salmonella Source-attribution Model for Evaluating Targets in the Turkey Meat Production 2012.
46. Harada T., Sakata J., Kanki M., Seto K., Taguchi M., Kumeda Y. Molecular epidemiological investigation of a diffuse out break caused by Salmonella enterica serotype Montevideo isolates in Osaka prefecture, Japan. Foodborne Pathogens and Disease 2011, 8:1083-1088.
47. Harbottle H., White D.G., McDermott P.F., Walker R.D., Zhao S. Comparison of multilocus sequence typing, pulsed-field gel electrophoresis, and antimicrobial susceptibility typing for characterization of Salmonella enterica serotype Newport isolates. Journal of Clinical Microbiology 2006, 44:2449-2457.
48. Hauser E., Hebner F., Titze E., Helmuth R., Junker E., Prager R., Schroeter A., Rabsch W., Fruth A., Malorny B. Diversity of Salmonella enterica serovar Derby isolated from pig, pork and humans in Germany. International Journal of Food Microbiology 2011, 151:141-149.
49. Hauser E., Tietze E., Helmuth R., Junker E., Prager R., Schroeter A., Rabsch W., Fruth A., Toboldt A., Malorny B. Clonal dissemination of Salmonella enterica serovar Infantis in Germany. Foodborne Pathogens and Disease 2012, 9:352-360.
50. Hopkins K.L., Maguire C., Best E., Liebana E., Threlfall E.J. Stability of multiple-locus variable-number tandem repeats in Salmonella enterica serovar Typhimurium. Journal of Clinical Microbiology 2007, 45:3058-3061.
51. Hopkins K.L., Kirchner M., Guerra B., Granier S.A., Lucarelli C., Porrero M.C., Jakubczak A., Threlfall E.J., Mevius D.J. Multiresistant Salmonella enterica serovar 4,[5],12:i:- in Europe: a new pandemic strain?. Eurosurveillance 2010, 15(22). (pii=19580).
52. Hopkins K.L., Peters T.M., de Pinna E., Wain J. Standardisation of multilocus variable-number tandem-repeat analysis (MLVA) for subtyping of Salmonella enterica serovar Enteritidis. Eurosurveillance 2011, 16(32). (pii=19942).
53. Huehn S., Malorny B. DNA microarray for molecular epidemiology of Salmonella. Methods in Molecular Biology 2009, 51:249-285.
54. Hunter P.R., Gaston M.A. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. Journal of Clinical Microbiology 1988, 26:2465-2466.
55. Hyytiä-Trees E.K., Cooper K., Ribot E.M., Gerner-Smidt P. Recent developments and future prospects in subtyping of foodborne bacteria pathogens. Future Microbiology 2007, 2:175-185.
56. Kang M.S., Kwon Y.K., Oh J.Y., Call D.R., An B.K., Song E.A., Kim J.Y., Shin E.G., Kim M.J., Kwon J.H., Chung G.S. Multilocus variable-number tandem-repeat analysis for subtyping Salmonella enterica serovar Gallinarum. Avian Pathology 2011, 40:559-564.
57. Kotetishvili M., Stine O.C., Kreger A., Morris J.G., Sulakvelidze A. Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. Journal of Clinical Microbiology 2002, 40:1626-1635.
58. Larsson J.T., Torpdahl M., Petersen R.F., Sorensen G., Lindstedt B.A., Nielsen E.M. Development of a new nomenclature for Salmonella typhimurium multilocus variable number of tandem repeats analysis (MLVA). Eurosurveillance 2009, 14(15). (pii=19174).
59. Lawson A.J., Desai M., O'Brien S.J., Davies R.H., Ward L.H., Threlfall E.J. Molecular characterization of an outbreak strain of multiresistant Salmonella enterica serovar Typhimurium DT104 in the UK. Clinical Microbiology and Infection 2004, 10:143-147.
60. Le Minor L. Typing of Salmonella species. European Journal of Clinical Microbioly & Infectious Disease 1988, 7:214-218.
61. Leader B.T., Frye J.G., Hu J., Fedorka-Cray P.J., Boyle D.S. High-Throughput molecular determination of Salmonella enterica serovars by use of multiplex PCR and capillary electrophoresis analysis. Journal of Clinical Microbiology 2009, 47:1290-1299.
62. Li W., Raoult D., Fournier P.-E. Bacterial strain typing in the genomic era. FEMS Microbiology Reviews 2009, 33:892-916.
63. Liebana E., Garcia-Migura L., Breslin M.F., Davies R.H., Woodward M.J. Diversity of strains of Salmonella enterica serotype Enteritidis from English poultry farms assessed by multiple genetic fingerprinting. Journal of Clinical Microbiology 2001, 39:154-161.
64. Liebana E., Garcia-Migura L., Clouting C., Cessar C.A., Clifton-Hadley F.A., Lindsay E.A., Threlfall E.J., Chappell S.A., Davies R.H. Investigation of the genetic diversity among isolates of Salmonella enterica serovar Dublin from animals and humans from England, Wales and Ireland. Journal of Applied Microbiology 2002, 93:732-744.
65. Liebana E., Garcia-Migura L., Clouting C., Clifton-Hadley F.A., Lindsay E., Threlfall E.J., McDowell S.W., Davies R.H. Multiple genetic typing of Salmonella enterica serotype Typhimurium isolates of different phage types (DT104, U302, DT204b, and DT49) from animals and humans in England, Wales and Northern Ireland. Journal of Clinical Microbiology 2002, 40:4450-4456.
66. Liebana E., Clouting C., Garcia-Migura L., Clifton-Hadley F.A., Lindsay E., Threlfall E.J., Davies R.H. Multiple genetic typing of Salmonella Enteritidis phage types 4, 6, 7, 8 and 13a from animals and humans in the UK. Veterinary Microbiology 2004, 100:189-195.
67. Lindqvist N., Heinikainen S., Siitonen A., Pelkonen S. Molecular characterization of Salmonella enterica subsp. enterica serovar Typhimurium DT1 isolates. Epidemiology and Infection 2004, 132:263-272.
68. Lindstedt B.-A. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005, 26:2567-2582.
69. 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. Journal of Clinical Microbiology 2003, 41:1469-1479.
70. Lindstedt B.-A., 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. Journal of Microbiological Methods 2004, 59:163-172.
71. Little C.L., Pires S.M., Gillespie I.A., Grant K., Nichols G.L. Attribution of human Listeria monocytogenes infections in England and Wales to ready-to-eat food sources placed on the market: adaptation of the Hald Salmonella source attribution model. Foodborne Pathogens and Disease 2010, 7:749-756.
72. Liu Y., Lee M.-A., Ooi E.-E., Mavis Y., Tan A.-L., 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. Journal of Clinical Microbiology 2003, 41:4388-4394.
73. Malorny B., Junker E., Helmuth R. Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis. BMC Microbiology 2008, 8:84-92.
74. Malorny B., Huehn S., Dieckmann R., Krämer N., Helmuth R. Polymerase chain reaction for the rapid detection and serovar identification of Salmonella in food and feeding stuff. Food Analytical Methods 2009, 2:81-95.
75. McQuiston J.R., Waters R.J., Dinsmore B.A., Mikoleit M.L., Fields P.I. Molecular determination of H antigens of Salmonella by use of a microsphere-based liquid array. Journal of Clinical Microbiology 2011, 49:565-573.
76. Miriagou V., Carattoli A., Fanning S. Antimicrobial resistance islands: resistance gene clusters in Salmonella chromosome and plasmids. Microbes and Infection 2006, 8:1923-1930.
77. Mullner P., Jones G., Noble A., Spencer S.E.F., Hathaway S., French N.P. Source attribution of food-borne zoonoses in New Zealand: a modified Hald model. Risk Analysis 2009, 29:970-984.
78. Mullner P., Spencer S.E.F., Wilson D.J., Jones G., Noble A.D., Midwinter A.C., Collins-Emerson J.M., Carter P., Hathaway S., French N.P. Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach. Infection, Genetics and Evolution 2009, 9:1311-1319.
79. Murase T., Nagato M., Shirota K., Katoh H., Otsuki K. Pulsed-field gel electrophoresis-based subtyping of DNA degradation-sensitive Salmonella enterica subsp. enterica serovar Livingstone and serovar Cerro isolates obtained from chicken layer farm. Veterinary Microbiology 2004, 99:139-143.
80. Octavia S., Lan R. Multiple-locus variable-number tandem-repeat analysis of Salmonella enterica serovar Typhi. Journal of Clinical Microbiology 2009, 47:2369-2376.
81. Octavia S., Lan R. Single nucleotide polymorphism typing of global Salmonella enterica serovar typhi isolates by use of a hairpin primer real-time PCR assay. Journal of Clinical Microbiology 2010, 48:3504-3509.
82. Oloya J., Doetkott D., Khaitsa M.L. Antimicrobial drug resistance and molecular characterization of Salmonella isolates from domestic animals, humans, and meat products. Foodborne Pathogens and Disease 2009, 6:273-284.
83. Olsen J.E., Brown D.J., Skov M.N., Christensen J.P. Bacterial typing methods suitable for epidemiological analysis. Applications in investigations of salmonellosis among livestock. Veterinary Quarterly 1993, 15:125-135.
84. Pang S., Octavia S., Reeves P.R., Wang Q., Gilbert G.L., Sintchenko V., Lan R. Genetic relationship of phage types and single nucleotide polymorphism typing of Salmonella enterica serovar Typhimurium. Journal of Clinical Microbiology 2012, 50:727-734.
85. Pavlic M., Griffiths M.W. Principles, applications and limitations of automated ribotyping as a rapid method in food safety. Foodborne Pathogens and Disease 2009, 6:1047-1055.
86. Pires S.M., Hald T. Assessing the differences in public health impact of Salmonella subtypes using a Bayesian microbial subtyping approach for source attribution. Foodborne Pathogens and Disease 2010, 7:143-151.
87. Pires S.M., Evers E.G., van Pelt W., Ayers T., Scallan E., Angulo F.J., Havelaar A., Hald T. Attributing the human disease burden of foodborne infections to specific sources. Foodborne Pathogens and Disease 2009, 6:417-424. the Med-Vet-Net Workpackage 28 Working Group.
88. Pires S.M., de Knegt L., Hald T. Scientific/Technical Report Submitted to EFSA - Estimation of relative contribution of different food and animal sources to human Salmonella infection in the European Union 2011.
89. Ramazanzadeh R., Mc Nerney R. Variable number of tandem repeats (VNTR) and its application in bacterial epidemiology. Pakistan Journal of Biological Sciences 2007, 10:2612-2621.
90. Ramisse V., Houssu P., Hernandez E., Denoeud F., Hilaire V., Lisanti O., Ramisse F., Cavallo J.-D., Vergnaud G. Variable number of tandem repeats in Salmonella enterica subsp. enterica for typing purposes. Journal of Clinical Microbiology 2004, 42:5722-5730.
91. Ribot E.M., Fair M.A., Gautom R., Cameron D.N., Hunter S.B., Swaminathan B., Barrett T.J. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella and Shigella for PulseNet. Foodborne Pathogens and Disease 2006, 3:59-67.
92. Ross I.L., Heuzenroeder M.W. Discrimination within phenotypically closely related definitive types of Salmonella enterica serovar Typhimurium by the multiple amplification of phage locus typing technique. Journal of Clinical Microbiology 2005, 43:1604-1611.
93. Ross I.L., Heuzenroeder M.W. A comparison of three molecular typing methods for the discrimination of Salmonella enterica serovar Infantis. FEMS Immunology and Medical Microbiology 2008, 53:375-384.
94. Ross I.L., Parkinson I.H., Heuzenroeder M.W. The use of MAPLT and MLVA analyses of phenotypically closely related isolates of Salmonella enterica serovar Typhimurium. International Journal of Medical Microbiology 2009, 299:37-41.
95. Ross I.L., Davos D.E., Mwanri L., Raupach J., Heuzenroeder M.W. MLVA and phage typing as complementary tools in the epidemiological investigation of Salmonella enterica serovar Typhimurium clusters. Current Microbiology 2011, 62:1034-1038.
96. Scaria J., Palaniappan R.U.M., Chiu D., Phan J.A., Ponnala L., McDonough P., Grohn Y.T., Porwollik S., McClelland M., Chiou C.-S., Chu C., Chang Y.-F. Microarray for molecular typing of Salmonella enterica serovars. Molecular and Cellular Probes 2008, 22:238-243.
97. Silbert S., Boyken L., Hollis R.J., Pfaller M.A. Improving typeability of multiple bacterial species using pulsed-field gel electrophoresis and thiourea. Diagnostic Microbiology and Infectious Disease 2003, 47:619-621.
98. Silley P., de Jong A., Simjee S., Thomas V. Harmonisation of resistance monitoring programmes in veterinary medicine: an urgent need in the EU?. International Journal of Antimicrobial Agents 2011, 37:504-512.
99. Sintchenko V., Wang Q., Howard P., Ha C.W.Y., Kardamanidis K., Musto J., Gilbert G.L. Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA). BMC Infectious Diseases 2012, 12:78-88.
100. Soyer Y., Alcaine S.D., Schoonmaker-Bopp D.J., Root T.P., Warnick L.D., McDonough P.L., Dumas N.B., Gröhn Y.T., Wiedmann M. Pulsed-field gel electrophoresis diversity of human and bovine clinical Salmonella isolates. Foodborne Pathogens and Disease 2010, 7:707-717.
101. Swaminathan B., Gerner-Smidt P., Ng L.-K., Lukinmaa S., Kam K.-M., Rolando S., Gutierrez E.P., Binsztein N. Building PulseNet international: an interconnected system for laboratory networks to facilitate timely public health recognition and response to foodborne disease outbreaks and emerging foodborne diseases. Foodborne Pathogens and Disease 2006, 3:36-50.
102. Tankouo-Sandjong B., Sessitsch A., Liebana E., Kornschober C., Allerberger F., Hachler H., Bodrossy L. MLST-v, multilocus sequence typing based on virulence genes, for molecular typing of Salmonella enterica subsp. enterica serovars. Journal of Microbiological Methods 2007, 69:23-36.
103. Tankouo-Sandjong B., Sessitsch A., Stralis-Pavese N., Liebana E., Kornschober C., Allerberger F., Hachler H., Bodrossy L. Development of an oligonucleotide microarray method for Salmonella serotyping. Microbial Biotechnology 2008, 1:513-522.
104. Tenover F.C., Arbeit R.D., Goering R.V., Mickelsen P.A., Murray B.E., Persing D.H., Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. Journal of Clinical Microbiology 1995, 33:2233-2239.
105. Tien Y.-Y., Wang Y.-W., Tung S.-K., Liang S.-Y., Chiou C.-S. Comparison of multilocus variable-number tandem repeat analysis and pulsed-field gel electrophoresis in molecular subtyping of Salmonella enterica serovars Paratyphi A. Diagnostic Microbiology and Infectious Disease 2011, 69:1-6.
106. Tien Y.-Y., Ushijima H., Mizuguchi M., Liang S.-Y., Chiou C.-S. Use of multilocus variable-number tandem repeat analysis in molecular subtyping of Salmonella enterica serovar Typhi isolates. Journal of Medical Microbiology 2012, 61:223-232.
107. Török M.E., Peacock S.J. Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory - pipe dream or reality?. Journal of Antimicrobial Chemotherapy 2012, 67:2307-2308.
108. Torpdahl M., Skow M.N., Sandvang D., Baggesen D.L. Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism. Journal of Microbiological Methods 2005, 63:173-184.
109. Torpdahl M., Sorensen G., Lindstedt B.A., Nielsen E.M. Tandem repeat analysis for surveillance of human Salmonella typhimurium infections. Emerging Infectious Diseases 2007, 13:388-395.
110. Tracz D.M., Tabor H., Jerome M., Ng L.-K., Gilmour M.W. Genetic determinants and polymorphisms specific for human-adapted serovars of Salmonella enterica that cause enteric fever. Journal of Clinical Microbiology 2006, 44:2007-2018.
111. van Belkum A., Tassios P.T., Dijkshoorn L., Haeggman S., Cookson B., Fry N.K., Fussing V., Green J., Feil E., Gerner-Smidt P., Brisse S., Struelens M. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clinical Microbiology and Infection 2007, 13:1-46.
112. van Cuyck H., Farbos-Granger A., Leroy P., Yith V., Guillard B., Sarthou J.L., Koeck J.L., Kruy S.L. MLVA polymorphism of Salmonella enterica subspecies isolated from humans, animals and food in Cambodia. BMC Research Notes 2011, 4:306-404.
113. Van Pelt W., Van De Giessen A.W., Leeuwen W.J., Wannet W., Henken A.M., Evers E.G. Oorsprong, omvang en kosten van humane salmonellose. Deel 1. Oorsprong van humane salmonellose met betrekking tot varken, rund, kip, ei en overige bronnen. Infectieziekten Bulletin 1999, 10:240-243.
114. Wahlström H., Andersson Y., Plym-Forshell L., Pires S.M. Source attribution of human Salmonella cases in Sweden. Epidemiology and Infection 2011, 139:1246-1253.
115. Wattiau P., Boland C., Bertrand S. Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives. Applied and Environmental Microbiology 2011, 77:7877-7885.
116. Witonski D., Stefanova R., Ranganathan A., Schultze G.E., Eisenach K.D., Cave M.D. Variable-number tandem repeats that are useful in genotyping isolates of Salmonella enterica subsp. enterica serovars Typhimurium and Newport. Journal of Clinical Microbiology 2006, 44:3849-3854.
117. Zheng J., Keys C.E., Zhao S., Ahmed R., Meng J., Brown E.W. Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationship among homogeneous Salmonella strains. Journal of Clinical Microbiology 2011, 49:85-91.
118. Zou W., Lin W.-J., Hise K.B., Chen H.C., Keys C., Chen J.J. Prediction system for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis fingerprints. Journal of Clinical Microbiology 2012, 50:1524-1532.