Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens

Annual Review of Food Science and Technology

Volumn 7, Issue , 2016, Pages 353-374

  Deng, Xiangyu ^a   Den Bakker, Henk C ^b   Hendriksen, Rene S ^c  

^a UNIVERSITY OF GEORGIA   (United States)

^b TEXAS TECH UNIVERSITY   (United States)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Bioinformatics; Epidemiology; Food safety; Genomics; Public health; Subtyping

Indexed keywords

BIOINFORMATICS; EPIDEMIOLOGY; FOOD SAFETY; FORMAL LANGUAGES; GENES; HEALTH; NEXT GENERATION NETWORKS; PUBLIC HEALTH;

BACTERIAL PATHOGENS; FOOD-BORNE ILLNESS; GENOMICS; NEXT-GENERATION SEQUENCING; REAL TIME; REGULATORY LABORATORIES; SUBTYPINGS; WHOLE GENOME SEQUENCING;

FOOD MICROBIOLOGY;

BACTERIAL GENOME; BACTERIUM; BIOLOGY; CLASSIFICATION; EPIDEMIC; EPIDEMIOLOGICAL MONITORING; EUROPE; FOOD CONTROL; FOODBORNE DISEASES; GENETICS; GENOMICS; HUMAN; MICROBIOLOGY; PHYLOGENY; PROCEDURES; PUBLIC HEALTH; SEQUENCE ANALYSIS; UNITED STATES; WORLD HEALTH ORGANIZATION;

BACTERIA; COMPUTATIONAL BIOLOGY; DISEASE OUTBREAKS; EPIDEMIOLOGICAL MONITORING; EUROPE; FOOD MICROBIOLOGY; FOODBORNE DISEASES; GENOME, BACTERIAL; GENOMICS; HUMANS; PHYLOGENY; PUBLIC HEALTH; SEQUENCE ANALYSIS; UNITED STATES; WORLD HEALTH ORGANIZATION;

EID: 84959932823     PISSN: 19411413     EISSN: 19411421     Source Type: Journal    
DOI: 10.1146/annurev-food-041715-033259     Document Type: Article

References (132)

1. Allard MW, Luo Y, Strain E, Pettengill J, Timme R, et al. 2013. On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01. 0004. PLOS ONE 8(1):e55254
2. Allos BM, Moore MR, Griffin PM, Tauxe RV. 2004. Surveillance for sporadic foodborne disease in the 21st century: the FoodNet perspective. Clin. Infect. Dis. 38(Suppl. 3):S115-20
3. Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, et al. 2015. College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Arch. Pathol. Lab. Med. 139(4):481-93
4. Baez-Ortega A, Lorenzo-Diaz F, Hernandez M, Gonzalez-Vila CI, Roda-Garcia JL, et al. 2015. IonGAP: Integrative bacterial genome analysis for Ion Torrent sequence data. Bioinformatics 31:2870-73
5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5):455-77
6. Barco L, Barrucci F, Olsen JE, Ricci A. 2013. Salmonella source attribution based on microbial subtyping. Int. J. Food Microbiol. 163(2-3):193-203
7. Bazinet AL, Zwickl DJ, CummingsMP. 2014. A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2. 0. Syst. Biol. 63(5):812-18
8. Bolton DJ. 2015. Campylobacter virulence and survival factors. Food Microbiol. 48:99-108
9. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, et al. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58(7):3895-903
10. Cent. Dis. Control Prev. 2008. Salmonella Annual Summary 2006. Atlanta, GA: CDC
11. Chevreux B. 2005. MIRA: an automated genome and EST assembler. PhD Thesis, Ruprecht-Karls-Univ., Heidelberg, Ger.
12. Clark TA, Murray IA, Morgan RD, Kislyuk AO, Spittle KE, et al. 2012. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res. 40(4):e29
13. Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, et al. 2013. Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J. Clin. Microbiol. 51(8):2526-34
14. Collins FS, Hamburg MA. 2013. First FDA authorization for next-generation sequencer. N. Engl. J. Med. 369(25):2369-71
15. Compeau PEC, Pevzner PA, Tesler G. 2011. How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol. 29(11):987-91
16. Counc. Eur. Union. 1990. On expenditure in the veterinary field. Counc. Decis. 90/424/EEC, Counc. Eur. Union., Brussels, Belg.
17. Counc. Eur. Union. 1992. Concerning measures for protection against specified zoonoses and specified zoonotic agents in animals and products of animal origin in order to prevent outbreaks of food-borne infections and intoxications. Counc. Dir. 92/117/EEC, Counc. Eur. Union., Brussels, Belg.
18. Counc. Eur. Union. 2003a. On the control of Salmonella and other specified food-borne zoonotic agents. Counc. Dir. 2160/2003, Counc. Eur. Union., Brussels, Belg.
19. Counc. Eur. Union. 2003b. On the monitoring of zoonoses and zoonotic agents. Counc. Dir. 2003/99/EC, Counc. Eur. Union., Brussels, Belg.
20. Crim SM, Iwamoto M, Huang JY, Griffin PM, Gilliss D, et al. 2014. Incidence and trends of infection with pathogens transmitted commonly through food: Foodborne Diseases Active Surveillance Network, 10 U. S. sites, 2006-2013. Morb. Mortal. Wkly. Rep. 63(15):328-32
21. Cronquist AB, Mody RK, Atkinson R, Besser J, Tobin-D'Angelo M, et al. 2012. Impacts of cultureindependent diagnostic practices on public health surveillance for bacterial enteric pathogens. Clin. Infect. Dis. 54(Suppl. 5):S432-39
22. den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, et al. 2014. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar Enteritidis. Emerg. Infect. Dis. 20(8):1306-14
23. den Bakker HC, Switt AIM, Cummings CA, Hoelzer K, Degoricija L, et al. 2011. A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. Enterica serovar Montevideo pulsed-field gel electrophoresis type. Appl. Environ. Microbiol. 77(24):8648-55
24. Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, et al. 2014. Genomic epidemiology of Salmonella enterica erotype Enteritidis based on population structure of prevalent lineages. Emerg. Infect. Dis. 20(9):1481-89
25. Deng X, Shariat N, Driebe EM, Roe CC, Tolar B, et al. 2015. Comparative analysis of subtyping methods against awhole-genome-sequencing standard for Salmonella enterica serotype Enteritidis. J. Clin. Microbiol. 53(1):212-18
26. Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. 2012. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13:601-12
27. Didelot X, Wilson DJ. 2015. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLOS Comput. Biol. 11(2):e1004041
28. Doyle MP, Erickson MC, Alali W, Cannon J, Deng X, et al. 2015. The food industry's current and future role in preventing microbial foodborne illness within the United States. Clin. Infect. Dis. 61(2):252-59
29. Drummond AJ, SuchardMA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1. 7. Mol. Biol. Evol. 29(8):1969-73
30. Earl DA, Bradnam K, St. John J, Darling A, Lin D, et al. 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 21(12):2224-41
31. Eur. Cent. Dis. Prev. Control. 2013. Surveillance of communicable diseases in Europe - A concept to integrate molecular typing data into EU-level surveillance. Stockholm, Sweden: Eur. Cent. Dis. Prev. Control. http://ecdc. Europa. Eu/en/publications/Publications/surveillance-concept-molecular%20typing-sept2011. Pdf
32. Eur. Food Saf. Auth. 2010. Community Summary Report on Trends and Sources of Zoonoses, Zoonotic Agents and Food-borne Outbreaks in the European Union in 2008. Parma, Italy: EFSA. http://www. Efsa. Europa. Eu/en/efsajournal/pub/1496
33. Eur. Food Saf. Auth. 2014. Technical specifications for the pilot on the collection of data on molecular testing of food-borne pathogens from food, feed and animal samples. Parma, Italy: EFSA. http://www. Efsa. Europa. Eu/it/supporting/pub/712e
34. Farber JM, Peterkin PI. 1991. Listeria monocytogenes, a food-borne pathogen. Microbiol. Rev. 55(3):476-511
35. Fisher IST, Threlfall EJ, Enter-net, Salm-gene. 2005. 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):1-7
36. Foxman B, Zhang L, Koopman JS, Manning SD, Marrs CF. 2005. Choosing an appropriate bacterial typing technique for epidemiologic studies. Epidemiol. Perspect. Innov. 2:10
37. Gardner SN, Hall BG. 2013. When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLOS ONE 8(12):e81760
38. Gardner SN, Slezak T, Hall BG. 2015. kSNP3. 0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31:2877-78
39. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, et al. 2012. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat. Biotechnol. 30(11):1033-36
40. Garrison E, Marth G. 2012. Haplotype-based variant detection from short-read sequencing. ArXiv:1207. 3907v2
41. Gerner-Smidt P, Hise K, Kincaid J, Hunter S, Rolando S, et al. 2006. PulseNet USA: a five-year update. Foodborne Pathog. Dis. 3(1):9-19
42. Gilbert JM, White DG, McDermott PF. 2007. The US national antimicrobial resistance monitoring system. Future Microbiol. 2(5):493-500
43. Gilmour MW, Graham M, van Domselaar G, Tyler S, Kent H, et al. 2010. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 11:120
44. Glob. Microb. Identif. 2011. Perspectives of a Global, Real-Time Microbiological Genomic Identification System-Implications for National and Global Detection and Control of Infectious Diseases. Consensus Report of an Expert Meeting 1-2 September 2011, Bruxelles, Belgium. Lyngby, Den. : Natl. Food Inst. Tech. Univ. Den. http://www. globalmicrobialidentifier. org/-/media/Sites/gmi/News-and-events/2011/1-meeting-2011-report. Ashx?la=da
45. Gordon NC, Price JR, Cole K, Everitt R, Morgan M, et al. 2014. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J. Clin. Microbiol. 52(4):1182-91
46. Grad YH, Lipsitch M. 2014. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 15(11):538
47. Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, et al. 2012. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. PNAS 109(8):3065-70
48. Grimont PAD, Weill F. 2007. Antigenic formulae of the Salmonella serovars. WHO Collab. Cent. Ref. Res. Salmonella, Paris, Fr.
49. Hald T, Vose D, Wegener HC, Koupeev T. 2004. A Bayesian approach to quantify the contribution of animal-food sources to human salmonellosis. Risk Anal. 24(1):255-69
50. Hedge J, Wilson DJ. 2014. Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not. mBio 5(6):e02158-14
51. Hendriksen RS, Vieira AR, Karlsmose S, Lo Fo Wong DM, Jensen AB, et al. 2011. Global monitoring of Salmonella serovar distribution from the WorldHealthOrganization global foodborne infections network country data bank: results of quality assured laboratories from 2001 to 2007. Foodborne Pathog. Dis. 8:887-900
52. Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18(5):802-9
53. Hoffmann M, Luo Y, Monday SR, Gonzales-Escalona N, Ottesen AR, Muruvanda T, et al. 2016. Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States. J. Infect Dis. 213(4):502-8
54. Hohmann EL. 2001. Nontyphoidal salmonellosis. Clin. Infect. Dis. 32(2):263-69
55. Holmes EC, Urwin R, Maiden MC. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol. Biol. Evol. 16(6):741-49
56. InouyeM, Dashnow H, Raven L-A, Schultz MB, Pope BJ, et al. 2014. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6(11):90
57. Inst. Med. 2012. Improving Food Safety Through a One Health Approach:Workshop Summary. Washington, DC: Natl. Acad. Press
58. Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G. 2012. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet. 44(2):226-32
59. Iqbal Z, Turner I, McVean G. 2013. High-throughput microbial population genomics using the Cortex variation assembler. Bioinformatics 29(2):275-76
60. Jamison DT, Bremen JG, Measham AR, Alleyne G, Claeson M, et al., eds. 2006. Disease Control Priorities in Developing Countries. Washington, DC:World Bank. 2nd ed.
61. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, et al. 2014. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52(5):1501-10
62. Joensen KG, Tetzschner AMM, Iguchi A, Aarestrup FM, Scheutz F. 2015. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J. Clin. Microbiol. 53(8):2410-26
63. Jones TF, Scallan E, Angulo FJ. 2007. FoodNet: overview of a decade of achievement. Foodborne Pathog. Dis. 4(1):60-66
64. Kaakoush NO, Castaño-Rodríguez N, Mitchell HM, Man SM. 2015. Global epidemiology of Campylobacter infection. Clin. Microbiol. Rev. 28(3):687-720
65. Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, et al. 2013. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio 4(4):e00398-13
66. Keim P, van Ert MN, Pearson T, Vogler AJ, Huynh LY, Wagner DM. 2004. Anthraxmolecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect. Genet. Evol. 4(3):205-13
67. Klumpp J, Fouts DE, Sozhamannan S. 2012. Next generation sequencing technologies and the changing landscape of phage genomics. Bacteriophage 2(3):190-99
68. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, et al. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22(3):568-76
69. Koren S, Phillippy A. 2015. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23:110-20
70. Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, et al. 2012. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLOS Pathog. 8(8):e1002824
71. Kupferschmidt K. 2011. Epidemiology. Outbreak detectives embrace the genome era. Science 30:1818-19
72. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Meth. 9(4):357-59
73. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, et al. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol. 50(4):1355-61
74. Leekitcharoenphon P, Kaas RS, ThomsenMCF, Friis C, Rasmussen S, Aarestrup FM. 2012. snpTree: a webserver to identify and construct SNP trees from whole genome sequence data. BMC Genomics 13(Suppl. 7):S6
75. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-60
76. Lienau EK, Strain E, Wang C, Zheng J, Ottesen AR, et al. 2011. Identification of a salmonellosis outbreak by means of molecular sequencing. N. Engl. J. Med. 364(10):981-82
77. Liljebjelke KA, Hofacre CL, Liu T, White DG, Ayers S, et al. 2005. Vertical and horizontal transmission of Salmonella within integrated broiler production system. Foodborne Pathog. Dis. 2(1):90-102
78. Lindstedt B-A, Heir E, Gjernes E, KapperudG. 2003. DNAfingerprinting of Salmonella enterica subsp. Enterica serovar Typhimurium with emphasis on phage type DT104 based on variable number of tandem repeat loci. J. Clin. Microbiol. 41(4):1469-79
79. Lipkin WI. 2013. The changing face of pathogen discovery and surveillance. Nat. Rev. Microbiol. 11(2):133-41
80. Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ-M, et al. 2013. A culture-independent sequence-basedmetagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309(14):1502-10
81. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, et al. 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30:434-39
82. Maiden MCJ, Bygraves JA, Feil EJ, Morelli G, Russell JE, et al. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. PNAS 95(6):3140-45
83. Majowicz SE, Scallan E, Jones-Bitton A, Sargeant JM, Stapleton J, et al. 2014. Global incidence of human Shiga toxin-producing Escherichia coli infections and deaths: a systematic review and knowledge synthesis. Foodborne Pathog. Dis. 11(6):447-55
84. Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764-70
85. Martin SM, Bean NH. 1995. Data management issues for emerging diseases and new tools for managing surveillance and laboratory data. Emerg. Infect. Dis. 1(4):124-28
86. Mather AE, Reid SWJ, Maskell DJ, Parkhill J, FookesMC, et al. 2013. Distinguishable epidemics of multidrugresistant Salmonella Typhimurium DT104 in different hosts. Science 341(6153):1514-17
87. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20(9):1297-303
88. Meacham F, Boffelli D, Dhahbi J, Martin DIK, Singer M, Pachter L. 2011. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinform. 12:451
89. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. 2011. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLOS ONE 6(7):e22751
90. Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95(6):315-27
91. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. 2000. Awhole-genome assembly of Drosophila. Science 287(5461):2196-204
92. Neuman JA, Isakov O, Shomron N. 2013. Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Brief. Bioinform. 14(1):46-55
93. O'Brien SJ, Gillespie IA, Adak GK. 2005. Foodborne disease surveillance as a basis for policy-making. In Food Safety Assurance and Veterinary Public Health: Risk Management Strategies, Monitoring and Surveillance, ed. FJM Smulders, JD Collins, pp. 33-52. Wageningen, Neth. : Wageningen Acad. Publ.
94. Octavia S, Wang Q, Tanaka MM, Kaur S, Sintchenko V, Lan R. 2015. Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak. J. Clin. Microbiol. 53(4):1063-71
95. Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, et al. 2012. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat. Genet. 44:1215-21
96. Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW, et al. 2015. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. Front. Genet. 6:235
97. Orsi RH, Borowsky ML, Lauer P, Young SK, Nusbaum C, et al. 2008. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics 9:539
98. Pettengill JB, Luo Y, Davis S, Chen Y, González-Escalona N, et al. 2014. An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella. PeerJ 2:e620
99. Pires SM, Vieira AR, Hald T, Cole D. 2014. Source attribution of human salmonellosis: an overview of methods and estimates. Foodborne Pathog. Dis. 11(9):667-76
100. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2: approximately maximum-likelihood trees for large alignments. PLOS ONE 5(3):e9490
101. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, et al. 2012. A tale of three next generation sequencing platforms: comparison of IonTorrent, Pacific Biosciences and Illumina MiSeq sequencers. BMCGenomics 13(1):341
102. Quick J, Ashton P, Calus S, Chatt C, Gossain S, et al. 2015. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16(1):114
103. Ribot EM, Fair MA, Gautom R, Cameron DN, Hunter SB, et al. 2006. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog. Dis. 3(1):59-67
104. Robinson ER, Walker TM, Pallen MJ. 2013. Genomics and outbreak investigation: from sequence to consequence. Genome Med. 5(4):36
105. RohdeH, Qin J, Cui Y, LiD, Loman NJ, et al. 2011. Open-source genomic analysis of Shiga-toxin-producing E. Coli O104:H4. N. Engl. J. Med. 365(8):718-24
106. Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, et al. 2013. Characterizing and measuring bias in sequence data. Genome Biol. 14(5):R51
107. Rump B, Cornelis C, Woonink F, Verweij M. 2013. The need for ethical reflection on the use of molecular microbial characterisation in outbreak management. Eur. Surveill. 18(4):20384
108. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, et al. 2015. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes. J. Clin. Microbiol. 53(9):2869-76
109. Sabat AJ, Budimir A, Nashev D, Sa-Leao R, van Dijl JM, et al. 2013. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Eur. Surveill. 18(4):20380
110. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, et al. 2011. Foodborne illness acquired in the United States: major pathogens. Emerg. Infect. Dis. 17(1):7-15
111. SmithHW. 1951. The typing of Salmonella Thompson by means of bacteriophage. J. Gen. Microbiol. 5(3):472-79
112. Smith JM, Smith NH, O'Rourke M, Spratt BG. 1993. How clonal are bacteria? PNAS 90(10):4384-88
113. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-90
114. Stasiewicz MJ, Oliver HF, Wiedmann M, den Bakker HC. 2015. Whole genome sequencing allows for improved identification of persistent Listeria monocytogenes in food associated environments. Appl. Environ. Microbiol. In Press
115. Swaminathan B, Barrett TJ, Fields P. 2006a. Surveillance for human Salmonella infections in theUnited States. J. AOAC Int. 89(2):553-59
116. Swaminathan B, Gerner-Smidt P, Ng L-K, Lukinmaa S, Kam K-M, et al. 2006b. 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(1):36-50
117. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6. 0. Mol. Biol. Evol. 30(12):2725-29
118. Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, et al. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33(9):2233-39
119. Timme RE, Pettengill JB, AllardMW, Strain E, Barrangou R, et al. 2013. Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. Enterica inferred from genome-wide reference-free SNP characters. Genome. Biol. Evol. 5(11):2109-23
120. Treangen TJ, Ondov BD, Koren S, Phillippy A. 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 15(11):524
121. Tyson GH, McDermott PF, Li C, Chen Y, Tadesse DA, et al. 2015. WGS accurately predicts antimicrobial resistance in Escherichia coli. J. Antimicrob. Chemother. 70:2763-69
122. van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, et al. 2007. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 13(Suppl. 3):1-46
123. van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, et al. 2013. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinform. 11(1110):11. 10. 1-11. 10. 33
124. vanDijk EL, AugerH, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet. 30(9):418-26
125. Vergnaud G, Pourcel C. 2009. Multiple locus variable number of tandem repeats analysis. Methods Mol. Biol. 551:141-58
126. Ward LR, de Sa JD, Rowe B. 1987. A phage-typing scheme for Salmonella enteritidis. Epidemiol. Infect. 99(2):291-94
127. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, et al. 2014. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. 370(25):2408-17
128. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, et al. 2012. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67(11):2640-44
129. Zerbino DR. 2010. Using the Velvet de novo assembler for short-read sequencing technologies. Curr. Protoc. Bioinform. Chapter 11:Unit 11. 5
130. Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, et al. 2015. Salmonella serotype determination utilizing high-throughput genome sequencing data. J. Clin. Microbiol. 53(5):1685-92
131. Zheng J, Pettengill J, Strain E, AllardMW, Ahmed R, et al. 2014. Genetic diversity and evolution of Salmonella enterica serovar Enteritidis strains with different phage types. J. Clin. Microbiol. 52(5):1490-500
132. Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, et al. 2013. Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. PLOS Genet. 9(4):e1003471