High throughput sequencing for detection of foodborne pathogens

Frontiers in Microbiology

Volumn 8, Issue OCT, 2017, Pages

  Sekse, Camilla ^a   Holst Jensen, Arne ^a   Dobrindt, Ulrich ^b   Johannessen, Gro S ^a   Li, Weihua ^c   Spilsberg, Bjørn ^a   Shi, Jianxin ^c  

^a NORWEGIAN VETERINARY INSTITUTE   (Norway)

^b UNIVERSITY OF MÜNSTER   (Germany)

^c SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Bacteria and viruses; Fungi and parasites; Metagenomics; Metataxonomics; Microbial profiling; Outbreak investigation; Surveillance; Whole genome sequencing

Indexed keywords

BACTERIUM EXAMINATION; BIBLIOGRAPHIC DATABASE; BIOINFORMATICS; BIOLOGICAL ACCIDENT; COST EFFECTIVENESS ANALYSIS; FOOD ANALYSIS; FOOD POISONING; FOOD SAFETY; FUNGAL EXAMINATION; HEALTH SURVEY; HIGH THROUGHPUT SEQUENCING; HUMAN; LEGAL SERVICE; METAGENOMICS; MICROBIAL COMMUNITY; MICROORGANISM DETECTION; NONHUMAN; PARASITE EXAMINATION; QUALITY CONTROL; REVIEW; VIRUS EXAMINATION;

EID: 85031725864     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.02029     Document Type: Review

References (203)

1. Aarestrup, F. M., Brown, E. W., Detter, C., Gerner-Smidt, P., Gilmour, M. W., Harmsen, D., et al. (2012). Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg. Infect. Dis. 18:120453. doi: 10.3201/eid1811.120453
2. Adeolu, M., Alnajar, S., Naushad, S., and Gupta, R. S. (2016). Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int. J. Syst. Evol. Microbiol. 66, 5575-5599. doi: 10.1099/ijsem.0.001485
3. Ahrenfeldt, J., Skaarup, C., Hasman, H., Pedersen, A. G., Aarestrup, F. M., and Lund, O. (2017). Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods. BMC Genomics 18:19. doi: 10.1186/s12864-016-3407-6
4. Antonissen, G., Martel, A., Pasmans, F., Ducatelle, R., Verbrugghe, E., Vandenbroucke, V., et al. (2014). The impact of Fusarium mycotoxins on human and animal host susceptibility to infectious diseases. Toxins 6, 430-452. doi: 10.3390/toxins6020430
5. Arulandhu, A. J., Staats, M., Hagelaar, R., Voorhuijzen, M. M., Prins, T. W., Scholtens, I., et al. (2017). Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples. GigaScience 6:gix080. doi: 10.1093/gigascience/gix080
6. Arulandhu, A. J., van Dijk, J. P., Dobnik, D., Holst-Jensen, A., Shi, J., Zel, J., et al. (2016). DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs). Anal. Bioanal. Chem. 408, 4575-4593. doi: 10.1007/s00216-016-9513-0
7. Ashton, P. M., Nair, S., Peters, T. M., Bale, J. A., Powell, D. G., Painset, A., et al. (2016). Identification of Salmonella for public health surveillance using whole genome sequencing. Peerj 4:e1752. doi: 10.7717/peerj.1752
8. Ashton, P. M., Peters, T., Ameh, L., McAleer, R., Petrie, S., Nair, S., et al. (2015). Whole genome sequencing for the retrospective investigation of an outbreak of Salmonella Typhimurium DT 8. PLoS Curr. Outbreaks 2015:1. doi: 10.1371/currents.outbreaks.2c05a47d292f376afc5a6fcdd8a7a3b6
9. Astridge, K., Barker, M., Bell, R., Combs, B., Boyle, C., Fearnley, E., et al. (2015). Monitoring the incidence and causes of diseases potentially transmitted by food in Australia: Annual report of the OzFoodNet network, (2011). Commun. Dis. Intell. 39, E236-E264. Available online at: http://www.health.gov.au/internet/main/publishing.nsf/Content/cda-cdi3902-pdf-cnt.htm/$FILE/cdi3902g.pdf
10. Aw, T. G., Wengert, S., and Rose, J. B. (2016). Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses. Int. J. Food Microbiol. 223, 50-56. doi: 10.1016/j.ijfoodmicro.2016.02.008
11. Aziz, N., Zhao, Q., Bry, L., Driscoll, D. K., Funke, B., Gibson, J. S., et al. (2015). College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Arch. Pathol. Lab. Med. 139, 481-493. doi: 10.5858/arpa.2014-0250-CP
12. Barratt, J. L., Cao, M., Stark, D. J., and Ellis, J. T. (2015). The transcriptome sequence of Dientamoeba fragilis offers new biological insights on its metabolism, kinome, degradome and potential mechanisms of pathogenicity. Protist 166, 389-408. doi: 10.1016/j.protis.2015.06.002
13. Barzon, L., Lavezzo, E., Militello, V., Toppo, S., and Palù, G. (2011). Applications of next-generation sequencing technologies to diagnostic virology. Int. J. Mol. Sci. 12, 7861-7884. doi: 10.3390/ijms12117861
14. Benedict, K., Chiller, T. M., and Mody, R. K. (2016). Invasive fungal infections acquired from contaminated food or nutritional supplements: a review of the literature. Foodborne Pathog. Dis. 13, 343-349. doi: 10.1089/fpd.2015.2108
15. Bergholz, T. M., Switt, A. I., and Wiedmann, M. (2014). Omics approaches in food safety: fulfilling the promise? Trends Microbiol. 22, 275-281. doi: 10.1016/j.tim.2014.01.006
16. Billmyre, R. B., Croll, D., Li, W., Mieczkowski, P., Carter, D. A., Cuomo, C. A., et al. (2014). Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution. mBio 5:e01494-14. doi: 10.1128/mBio.01494-14
17. Bitar, D., Lortholary, O., Le Strat, Y., Nicolau, J., Coignard, B., Tattevin, P., et al. (2014). Population-based analysis of invasive fungal infections, France, 2001-2010. Emerging Infect. Dis. 20, 1149-1155. doi: 10.3201/eid2007.140087
18. Blagden, T., Schneider, W., Melcher, U., Daniels, J., and Fletcher, J. (2016). Adaptation and validation of e-probe diagnostic nucleic acid analysis for detection of Escherichia coli O157:H7 in metagenomic data from complex food matrices. J. Food Prot. 79, 574-581. doi: 10.4315/0362-028X.JFP-15-440
19. Brown, G. D., Denning, D. W., and Levitz, S. M. (2012). Tackling human fungal infections. Science 336, 647-647. doi: 10.1126/science.1222236
20. Brüssow, H., Canchaya, C., and Hardt, W. D. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68, 560-602. doi: 10.1128/MMBR.68.3.560-602.2004
21. Brzuszkiewicz, E., Thürmer, A., Schuldes, J., Leimbach, A., Liesegang, H., Meyer, F. D., et al. (2011). Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch. Microbiol. 193, 883-891. doi: 10.1007/s00203-011-0725-6
22. Byrnes, E. J. III, Li, W., Lewit, Y., Ma, H., Voelz, K., Ren, P., et al. (2010). Emergence and pathogenicity of highly virulent Cryptococcus gattii genotypes in the northwest United States. PLoS Pathog. 6:e1000850. doi: 10.1371/journal.ppat.1000850
23. Cacho, R. A., Tang, Y., and Chooi, Y.-H. (2015). Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. Front. Microbiol. 5:774. doi: 10.3389/fmicb.2014.00774
24. Ceuppens, S., Delbeke, S., De Coninck, D., Boussemaere, J., Boon, N., and Uyttendaele, M. (2015). Characterization of the bacterial community naturally present on commercially grown basil leaves: evaluation of sample preparation prior to culture-independent techniques. Int. J. Environ. Res. Public Health 12, 10171-10197. doi: 10.3390/ijerph120810171
25. Ceuppens, S., Li, D., Uyttendaele, M., Renault, P., Ross, P., Van Ranst, M., et al. (2014). Molecular methods in food safety microbiology: interpretation and implications of nucleic acid detection. Comprehen. Rev. Food Science Food Safety 13, 551-577. doi: 10.1111/1541-4337.12072
26. Chattaway, M. A., Dallman, T. J., Gentle, A., Wright, M. J., Long, S. E., Ashton, P. M., et al. (2016). Whole genome sequencing for public health surveillance of Shiga toxin-producing Escherichia coli other than serogroup O157. Front. Microbiol. 7:258. doi: 10.3389/fmicb.2016.00258
27. Chiapponi, C., Pavoni, E., Bertasi, B., Baioni, L., Scaltriti, E., Chiesa, E., et al. (2014). Isolation and genomic sequence of hepatitis A virus from mixed frozen berries in Italy. Food Environ. Virol. 6, 202-206. doi: 10.1007/s12560-014-9149-1
28. Clemons, K. V., Salonen, J. H., Issakainen, J., Nikoskelainen, J., McCullough, M. J., Jorge, J. J., et al. (2010). Molecular epidemiology of Saccharomyces cerevisiae in an immunocompromised host unit. Diagn. Microbiol. Infect. Dis. 68, 220-227. doi: 10.1016/j.diagmicrobio.2010.06.010
29. Collier, M. G., Khudyakov, Y. E., Selvage, D., Adams-Cameron, M., Epson, E., Cronquist, A., et al. (2014). Outbreak of hepatitis A in the USA associated with frozen pomegranate arils imported from Turkey: an epidemiological case study. Lancet Infect. Dis. 14, 976-981. doi: 10.1016/S1473-3099(14)70883-7
30. Cook, N. (2013). Viruses in Food and Water: Risks, Surveillance and Control. Cambridge, UK: Woodhead Publishing.
31. Crim, S. M., Iwamoto, M., Huang, J. Y., Griffin, P. M., Gilliss, D., Cronquist, A. B., et al. (2014). Incidence and trends of infection with pathogens transmitted commonly through food-Foodborne Diseases Active Surveillance Network: 10 US Sites, 2006-2013. MMWR 63, 328-332. Available online at: https://www.cdc.gov/mmwr/pdf/wk/mm6315.pdf
32. Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., et al. (2014). Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics 30, 1928-1929. doi: 10.1093/bioinformatics/btu135
33. Davis, S., Pettengill, J., Luo, Y., Payne, J., Shpuntoff, A., Rand, H., et al. (2015). CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Comput. Sci. 1:11. doi: 10.7717/peerj-cs.20
34. Davis, T. K., Van De Kar, N. C. A. J., and Tarr, P. I. (2014). Shiga toxin/Verocytotoxin-producing Escherichia coli infections: practical clinical perspectives. Microbiol. Spect. 2:EHEC-0025-2014. doi: 10.1128/microbiolspec.EHEC-0025-2014
35. de Wit, M. A., Koopmans, M. P. G., and van Duynhoven, Y. (2003). Risk factors for norovirus, Sapporo-like virus, and group A rotavirus gastroenteritis. Emerging Infect. Dis. 9, 1563-1570. doi: 10.3201/eid0912.020076
36. Deagle, B. E., Jarman, S. N., Coissac, E., Pompanon, F., and Taberlet, P. (2014). DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biol. Lett. 10:20140562. doi: 10.1098/rsbl.2014.0562
37. Desnos-Ollivier, M., Patel, S., Raoux-Barbot, D., Heitman, J., Dromer, F., and Group, F. C. S. (2015). Cryptococcosis serotypes impact outcome and provide evidence of Cryptococcus neoformans speciation. mBio 6:e00311-15. doi: 10.1128/mBio.00311-15
38. Desselberger, U. (2014). Rotaviruses. Virus Res. 190, 75-96. doi: 10.1016/j.virusres.2014.06.016
39. ECDC (2015a). Annual Epidemiological Reports [Online]. European Centre for Disease Prevention and Control,. Available online at: http://ecdc.europa.eu/EN/PUBLICATIONS/SURVEILLANCE_REPORTS/annual_epidemiological_report/Pages/epi_index.aspx [Accessed 4th November 2015].
40. ECDC (2015b). Expert Opinion on the Introduction of Next-Generation Typing Methods for Food- and Waterborne Diseases in the EU and EEA. Stockholm: Sweden: European Centre for Disease Prevention and Control.
41. Edgar, R. C., and Flyvbjerg, H. (2015). Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics 31, 3476-3482. doi: 10.1093/bioinformatics/btv401
42. EFSA (2011). Scientific Opinion on an update on the present knowledge on the occurrence and control of foodborne viruses. EFSA J. 9, 2190-2285. doi: 10.2903/j.efsa.2011.2190
43. EFSA (2013). Scientific opinion on VTEC-seropathotype and scientific criteria regarding pathogenicity assessment. EFSA J. 11, 3138-3243. doi: 10.2903/j.efsa.2013.3138
44. EFSA (2014). Use of Whole Genome Sequencing (WGS) of Food-Borne Pathogens for Public Health Protection. EFSA.
45. EFSA (2015a). The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in (2013). EFSA J. 13, 165. doi: 10.2903/j.efsa.2015.3991
46. EFSA (2015b). The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in (2014). EFSA J. 13, 191. doi: 10.2903/j.efsa.2015.4329
47. EMAN (2015). European Mycotoxin Awareness Network: Basic Factsheet Trichothecenes. European Mycotoxin Awareness Network. Available online at: http://eman.leatherheadfood.com/node/45
48. Emond-Rheault, J.-G., Jeukens, J., Freschi, L., Kukavica-Ibrulj, I., Boyle, B., Dupont, M.-J., et al. (2017). A syst-OMICS approach to ensuring food safety and reducing the economic burden of salmonellosis. Front. Microbiol. 8:996. doi: 10.3389/fmicb.2017.00996
49. European Commission (2005). Commission Regulation (EC) No 2073/2005 of 15 November 2005 on microbiological criteria for foodstuffs. Official J. Eur. Union 2005, 1-26. Available online at: http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2005:338:0001:0026:EN:PDF
50. FDA (2011). FDA Food Safety Modernization Act, Public Law 111-353-January 4th 2011, 124 Stat. (3885). Washington, DC: United States Government Printing Office; Government of the United States of America.
51. FDA (2013). Establishment Inspection Report, Chobani Idaho, FEEI: 3009726115. U.S. Food and Drug Administration. Available online at: http://www.fda.gov/ucm/groups/fdagov-public/@fdagov-afda-orgs/documents/document/ucm376634.pdf.
52. Fernandez-Cassi, X., Timoneda, N., Gonzales-Gustavson, E., Abril, J. F., Bofill-Mas, S., and Girones, R. (2017). A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. Int. J. Food Microbiol. 257, 80-90. doi: 10.1016/j.ijfoodmicro.2017.06.001
53. Ferri, E., Galimberti, A., Casiraghi, M., Airoldi, C., Ciaramelli, C., Palmioli, A., et al. (2015). Towards a universal approach based on omics technologies for the quality control of food. BioMed Res. Int. 2015, 14. doi: 10.1155/2015/365794
54. Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J. A., et al. (2013). Topographic diversity of fungal and bacterial communities in human skin. Nature 498, 367-370. doi: 10.1038/nature12171
55. Finkbeiner, S. R., Li, Y., Ruone, S., Conrardy, C., Gregoricus, N., Toney, D., et al. (2009). Identification of a novel astrovirus (Astrovirus VA1) associated with an outbreak of acute gastroenteritis. J. Virol. 83, 10836-10839. doi: 10.1128/JVI.00998-09
56. Fiore, A. E. (2004). Hepatitis A transmitted by food. Clin. Infect. Dis. 38, 705-715. doi: 10.1086/381671
57. Forbes, J. D., Knox, N. C., Ronholm, J., Pagotto, F., and Reimer, A. (2017). Metagenomics: the next culture-independent game changer. Front. Microbiol. 8:1069. doi: 10.3389/fmicb.2017.01069
58. Foth, B. J., Tsai, I. J., Reid, A. J., Bancroft, A. J., Nichol, S., Tracey, A., et al. (2014). Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nat. Genet. 46, 693-700. doi: 10.1038/ng.3010
59. Franz, E., Gras, L., and Dallman, T. (2016). Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens. Curr. Opin. Food Sci. 8, 74-79. doi: 10.1016/j.cofs.2016.04.004
60. Galbraith, E. A., Antonopoulos, D. A., and White, B. A. (2004). Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ. Microbiol., 6, 928-937. doi: 10.1111/j.1462-2920.2004.00575.x
61. Ganova-Raeva, L., Punkova, L., Campo, D. S., Dimitrova, Z., Skums, P., Vu, N. H., et al. (2015). Cryptic hepatitis B and E in patients with acute hepatitis of unknown etiology. J. Infect. Dis. 212, 1962-1969. doi: 10.1093/infdis/jiv315
62. Gargis, A. S., Kalman, L., Berry, M. W., Bick, D. P., Dimmock, D. P., Hambuch, T., et al. (2012). Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat. Biotechnol. 30, 1033-1036. doi: 10.1038/nbt.2403
63. Gargis, A. S., Kalman, L., Bick, D. P., da Silva, C., Dimmock, D. P., Funke, B. H., et al. (2015). Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nat. Biotechnol. 33, 689-693. doi: 10.1038/nbt.3237
64. Gillings, M. R., Paulsen, I. T., and Tetu, S. G. (2015). Ecology and evolution of the human microbiota: fire, farming and antibiotics. Genes 6, 841-857. doi: 10.3390/genes6030841
65. Gilmour, M. W., Graham, M., Van Domselaar, G., Tyler, S., Kent, H., Trout-Yakel, K. M., et al. (2010). High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 11:120. doi: 10.1186/1471-2164-11-120
66. GMI (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: Global Microbial Identifier website.
67. GMI (2015). Protocol for GMI Proficiency Test, 2015 (Global Microbial Identifier). Available online at: http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/Work-groups/GMI_PT_Protocol_v2_Incl_Appendices_2015_final_24082015.ashx?la=da.
68. Gomi, R., Matsuda, T., Matsui, Y., and Yoneda, M. (2014). Fecal source tracking in water by next-generation sequencing technologies using host-specific Escherichia coli genetic markers. Environ. Sci. Technol. 48, 9616-9623. doi: 10.1021/es501944c
69. Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M. C., and McCombie, W. R. (2015). Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res. 25, 1750-1756. doi: 10.1101/gr.191395.115
70. Goodwin, S., McPherson, J. D., and McCombie, W. R. (2016). Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333-351. doi: 10.1038/nrg.2016.49
71. Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., et al. (2015). Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 7:99. doi: 10.1186/s13073-015-0220-9
72. Gurgui, M., Sanchez, F., March, F., Lopez-Contreras, J., Martino, R., Cotura, A., et al. (2011). Nosocomial outbreak of Blastoschizomyces capitatus associated with contaminated milk in a haematological unit. J. Hosp. Infect. 78, 274-278. doi: 10.1016/j.jhin.2011.01.027
73. Gweon, H. S., Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., et al. (2015). PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol. Evol. 6, 973-980. doi: 10.1111/2041-210X.12399
74. Hadfield, S. J., Pachebat, J. A., Swain, M. T., Robinson, G., Cameron, S. J. S., Alexander, J., et al. (2015). Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples. BMC Genomics 16:650. doi: 10.1186/s12864-015-1805-9
75. Hall, A. J. (2012). Noroviruses: the Perfect Human Pathogens? J. Infect. Dis. 205, 1622-1624. doi: 10.1093/infdis/jis251
76. Halliday, M. L., Kang, L. Y., Zhou, T. K., Hu, M. D., Pan, Q. C., Fu, T. Y., et al. (1991). An epidemic of hepatitis-A attributable to the ingestion of raw clams in Shanghai, China. J. Infect. Dis. 164, 852-859. doi: 10.1093/infdis/164.5.852
77. Hartmann, E. M., and Halden, R. U. (2012). Analytical methods for the detection of viruses in food by example of CCL-3 bioagents. Anal. Bioanal. Chem. 404, 2527-2537. doi: 10.1007/s00216-012-5974-y
78. Hasman, H., Saputra, D., Sicheritz-Ponten, T., Lund, O., Svendsen, C. A., Frimodt-Möller, N., et al. (2014). Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J. Clin. Microbiol. 52, 139-146. doi: 10.1128/JCM.02452-13
79. Hayes, S., Mahony, J., Nauta, A., and van Sinderen, D. (2017). Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9:127. doi: 10.3390/v9060127
80. Hedberg, C. W., and Osterholm, M. T. (1993). Outbreaks of food-borne and waterborne viral gastroenteritis. Clin. Microbiol. Rev. 6, 199-210. doi: 10.1128/CMR.6.3.199
81. Henao, O. L., Jones, T. F., Vugia, D. J., Griffin, P. M., and Network, F. D. A. S. (2015). Foodborne diseases active surveillance network-2 decades of achievements, 1996-2015. Emerging Infect. Dis. 21, 1529-1536. doi: 10.3201/eid2109.150581
82. Holland, J., Spindler, K., Horodyski, F., Grabau, E., Nichol, S., and VandePol, S. (1982). Rapid evolution of RNA genomes. Science 215, 1577-1585. doi: 10.1126/science.7041255
83. Holmes, A., Allison, L., Ward, M., Dallman, T. J., Clark, R., Fawkes, A., et al. (2015). Utility of whole-genome sequencing of Escherichia coli O157 for outbreak detection and epidemiological surveillance. J. Clin. Microbiol. 53, 3565-3573. doi: 10.1128/JCM.01066-15
84. Holst-Jensen, A., Johannessen, G., Sekse, C., Spilsberg, B., Dobnik, D., Dreo, T., et al. (2016). Minimum Performance Parameters for Molecular Analytical Methods-Deliverable 6.6 of the Decathlon Project. Available online at: http://www.decathlon-project.eu/reports-and-deliverables
85. Holst-Jensen, A., Rønning, S. B., Løvseth, A., and Berdal, K. G. (2003). PCR technology for screening and quantification of genetically modified organisms (GMOs). Anal. Bioanal. Chem. 375, 985-993. doi: 10.1007/s00216-003-1767-7
86. Imamura, S., Haruna, M., Goshima, T., Kanezashi, H., Okada, T., and Akimoto, K. (2016a). Application of next-generation sequencing to evaluate the profile of noroviruses in pre- and post-depurated oysters. Foodborne Pathog. Dis. 13, 559-565. doi: 10.1089/fpd.2016.2150
87. Imamura, S., Haruna, M., Goshima, T., Kanezashi, H., Okada, T., and Akimoto, K. (2016b). Application of next-generation sequencing to investigation of norovirus diversity in shellfish collected from two coastal sites in Japan from 2013 to (2014). Japan. J. Veterin. Res. 64, 113-122. doi: 10.14943/jjvr.64.2.113
88. Iriart, X., Fior, A., Blanchet, D., Berry, A., Neron, P., and Aznar, C. (2010). Monascus ruber: invasive gastric infection caused by dried and salted fish consumption. J. Clin. Microbiol. 48, 3800-3802. doi: 10.1128/JCM.01000-10
89. Jarvis, K. G., White, J. R., Grim, C. J., Ewing, L., Ottesen, A. R., Beaubrun, J. J.-G., et al. (2015). Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing. BMC Microbiol. 15:160. doi: 10.1186/s12866-015-0497-2
90. Jenkins, C., Dallman, T. J., Launders, N., Willis, C., Byrne, L., Jorgensen, F., et al. (2015). Public health investigation of two outbreaks of Shiga toxin-producing Escherichia coli O157 associated with consumption of watercress. Appl. Environ. Microbiol. 81, 3946-3952. doi: 10.1128/AEM.04188-14
91. Joensen, K. G., Scheutz, F., Lund, O., Hasman, H., Kaas, R. S., Nielsen, E. M., et al. (2014). Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52, 1501-1510. doi: 10.1128/JCM.03617-13
92. Jones, Y. L., Peters, S. M., Weland, C., Ivanova, N. V., and Yancy, H. F. (2013). Potential use of DNA barcodes in regulatory science: identification of the US food and drug administration's "Dirty 22," contributors to the spread of foodborne pathogens. J. Food Prot. 76, 144-149. doi: 10.4315/0362-028X.JFP-12-168
93. Junemann, S., Sedlazeck, F. J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., et al. (2013). Updating benchtop sequencing performance comparison. Nat. Biotechnol. 31, 294-296. doi: 10.1038/nbt.2522
94. Kawai, T., Sekizuka, T., Yahata, Y., Kuroda, M., Kumeda, Y., Iijima, Y., et al. (2012). Identification of Kudoa septempunctata as the causative agent of novel food poisoning outbreaks in Japan by consumption of Paralichthys olivaceus in raw fish. Clin. Infect. Dis. 54, 1046-1052. doi: 10.1093/cid/cir1040
95. Kazan, E., Maertens, J., Herbrecht, R., Weisser, M., Gachot, B., Vekhoff, A., et al. (2011). A retrospective series of gut aspergillosis in haematology patients. Clin. Microbiol. Infect. 17, 588-594. doi: 10.1111/j.1469-0691.2010.03310.x
96. Kergourlay, G., Taminiau, B., Daube, G., and Champomier Verges, M.-C. (2015). Metagenomic insights into the dynamics of microbial communities in food. Int. J. Food Microbiol. 213, 31-39. doi: 10.1016/j.ijfoodmicro.2015.09.010
97. Kundu, S., Lockwood, J., Depledge, D. P., Chaudhry, Y., Aston, A., Rao, K., et al. (2013). Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin. Infect. Dis. 57, 407-414. doi: 10.1093/cid/cit287
98. Kupferschmidt, K. (2011). Scientists rush to study genome of lethal E. coli. Science 332, 1249-1250. doi: 10.1126/science.332.6035.1249
99. Kwon, T., Yoo, W. G., Lee, W.-J., Kim, W., and Kim, D.-W. (2015). Next-generation sequencing data analysis on cloud computing. Genes Genomics 37, 489-501. doi: 10.1007/s13258-015-0280-7
100. Lambert, D., Pightling, A., Griffiths, E., Van Domselaar, G., Evans, P., Berthelet, S., et al. (2017). Baseline practices for the application of genomic data supporting regulatory food safety. J. AOAC Int. 100, 721-731. doi: 10.5740/jaoacint.16-0269
101. Lammers, Y., Peelen, T., Vos, R. A., and Gravendeel, B. (2014). The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics 15:44. doi: 10.1186/1471-2105-15-44
102. Lassen, S. G., Ethelberg, S., Bjorkman, J. T., Jensen, T., Sorensen, G., Jensen, A. K., et al. (2016). Two listeria outbreaks caused by smoked fish consumption-using whole-genome sequencing for outbreak investigations. Clin. Microbiol. Infect. 21, 620-624. doi: 10.1016/j.cmi.2016.04.017
103. Lassmann, T. (2015). TagDust2: a generic method to extract reads from sequencing data. BMC Bioinformatics 16:24. doi: 10.1186/s12859-015-0454-y
104. Lee, H. B., Patriarca, A., and Magan, N. (2015). Alternaria in food: ecophysiology, mycotoxin production and toxicology. Mycobiology 43, 93-106. doi: 10.5941/MYCO.2015.43.2.93
105. Lee, S. C., Billmyre, R. B., Li, A., Carson, S., Sykes, S. M., Huh, E. Y., et al. (2014). Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. mBio 5:e01390-14. doi: 10.1128/mBio.01390-14
106. Leekitcharoenphon, P., Nielsen, E. M., Kaas, R. S., Lund, O., and Aarestrup, F. M. (2014). Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS ONE 9:e87991. doi: 10.1371/journal.pone.0087991
107. Leichty, A. R., and Brisson, D. (2014). Selective whole genome amplification for resequencing target microbial species from complex natural samples. Genetics 198, 473-481. doi: 10.1534/genetics.114.165498
108. Leonard, S. R., Mammel, M. K., Lacher, D. W., and Elkins, C. A. (2015). Application of metagenomic sequencing to food safety: detection of Shiga toxin-producing Escherichia coli on fresh bagged spinach. Appl. Environ. Microbiol. 81, 8183-8191. doi: 10.1128/AEM.02601-15
109. Leonard, S. R., Mammel, M. K., Lacher, D. W., and Elkins, C. A. (2016). Strain-level discrimination of Shiga toxin-producing Escherichia coli in spinach using metagenomic sequencing. PLoS ONE 11:e0167870. doi: 10.1371/journal.pone.0167870
110. Leray, M., and Knowlton, N. (2015). DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc. Natl. Acad. Sci. U.S.A. 112, 2076-2081. doi: 10.1073/pnas.1424997112
111. Li, J.-W., Schmieder, R., Ward, R. M., Delenick, J., Olivares, E. C., and Mittelman, D. (2012). SEQanswers: an open access community for collaboratively decoding genomes. Bioinformatics 28, 1272-1273. doi: 10.1093/bioinformatics/bts128
112. Lindsey, R. L., Pouseele, H., Chen, J. C., Strockbine, N. A., and Carleton, H. A. (2016). Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coil (STEC) in the United States. Front. Microbiol. 7:766. doi: 10.3389/fmicb.2016.00766
113. Litvintseva, A. P., Hurst, S., Gade, L., Frace, M. A., Hilsabeck, R., Schupp, J. M., et al. (2014). Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections. J. Clin. Microbiol. 52, 3216-3222. doi: 10.1128/JCM.00936-14
114. Litvintseva, A. P., Marsden-Haug, N., Hurst, S., Hill, H., Gade, L., Driebe, E. M., et al. (2015). Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection. Clin. Infect. Dis. 60, E1-E3. doi: 10.1093/cid/ciu681
115. Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., et al. (2012). Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012:251364. doi: 10.1155/2012/251364
116. Livezey, K., Kaplan, S., Wisniewski, M., and Becker, M. M. (2013). A new generation of food-borne pathogen detection based on ribosomal RNA. Annu. Rev. Food. Sci. Technol. 4, 313-325. doi: 10.1146/annurev-food-050412-104448
117. Loman, N. J., Constantinidou, C., Christner, M., Rohde, H., Chan, J. Z. M., Quick, J., et al. (2013). A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309, 1502-1510. doi: 10.1001/jama.2013.3231
118. Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J., et al. (2012). Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30:434. doi: 10.1038/nbt0612-562f
119. Loman, N. J., and Pallen, M. J. (2015). Twenty years of bacterial genome sequencing. Nat. Rev. Microbiol. 13, 787-794. doi: 10.1038/nrmicro3565
120. Loman, N. J., Quick, J., and Simpson, J. T. (2015). A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12, 733-U51. doi: 10.1038/nmeth.3444
121. Loose, M., Malla, S., and Stout, M. (2016). Real-time selective sequencing using nanopore technology. Nat. Methods 13, 751-754. doi: 10.1038/nmeth.3930
122. Lukes, J., Stensvold, C. R., Jirku-Pomajbikova, K., and Parfrey, L. W. (2015). Are human intestinal eukaryotes beneficial or commensals? PLoS Pathog. 11:e1005039. doi: 10.1371/journal.ppat.1005039
123. Luo, C. W., Tsementzi, D., Kyrpides, N., Read, T., and Konstantinidis, K. T. (2012). Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7:e30087. doi: 10.1371/journal.pone.0030087
124. Marchesi, J. R., and Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome 3:3. doi: 10.1186/s40168-015-0094-5
125. Martin, J., Rosa, B. A., Ozersky, P., Hallsworth-Pepin, K., Zhang, X., Bhonagiri-Palsikar, V., et al. (2015). Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. Nucleic Acids Res. 43, D698-D706. doi: 10.1093/nar/gku1128
126. Martinovic, T., Andjelkovic, U., Gajdosik, M. S., Resetar, D., and Josic, D. (2016). Foodborne pathogens and their toxins. J. Proteomics 147, 226-235. doi: 10.1016/j.jprot.2016.04.029
127. Mayo, B., Rachid, C. T. C. C., Alegria, A., Leite, A. M. O., Peixoto, R. S., and Delgado, S. (2014). Impact of next generation sequencing techniques in food microbiology. Curr. Genomics 15, 293-309. doi: 10.2174/1389202915666140616233211
128. Mellmann, A., Harmsen, D., Cummings, C. A., Zentz, E. B., Leopold, S. R., Rico, A., et al. (2011). Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE 6:e22751. doi: 10.1371/journal.pone.0022751
129. Menke, S., Gillingham, M. A. F., Wilhelm, K., and Sommer, S. (2017). Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research. Front. Microbiol. 8:102. doi: 10.3389/fmicb.2017.00102
130. Mikheyev, A. S., and Tin, M. M. (2014). A first look at the Oxford Nanopore MinION sequencer. Mol. Ecol. Resour. 14, 1097-1102. doi: 10.1111/1755-0998.12324
131. Mizukoshi, F., Kuroda, M., Tsukagoshi, H., Sekizuka, T., Funatogawa, K., Morita, Y., et al. (2014). A food-borne outbreak of gastroenteritis due to genotype G1P[8] rotavirus among adolescents in Japan. Microbiol. Immunol. 58, 536-539. doi: 10.1111/1348-0421.12176
132. Moore, M. D., Goulter, R. M., and Jaykus, L.-A. (2015). Human norovirus as a foodborne pathogen: challenges and developments. Annu. Rev. Food. Sci. Technol. 6, 411-433. doi: 10.1146/annurev-food-022814-015643
133. Moran-Gilad, J., Sintchenko, V., Pedersen, S. K., Wolfgang, W. J., Pettengill, J., Strain, E., et al. (2015). Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities. BMC Infect. Dis. 15:174. doi: 10.1186/s12879-015-0902-3
134. Moreira, D., and López-García, P. (2009). Ten reasons to exclude viruses from the tree of life. Nat. Rev. Microbiol. 7, 306-311. doi: 10.1038/nrmicro2108
135. Moura, A., Criscuolo, A., Pouseele, H., Maury, M., Leclercq, A., Tarr, C., et al. (2016). Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 10:16185. doi: 10.1038/nmicrobiol.2016.185
136. Müenz, M., Ruark, E., Renwick, A., Ramsay, E., Clarke, M., Mahamdallie, S., et al. (2015). CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting. Genome Med. 7:76. doi: 10.1186/s13073-015-0195-6
137. Newell, D. G., Koopmans, M., Verhoef, L., Duizer, E., Aidara-Kane, A., Sprong, H., et al. (2010). Food-borne diseases-The challenges of 20 years ago still persist while new ones continue to emerge. Int. J. Food Microbiol. 139, S3-S15. doi: 10.1016/j.ijfoodmicro.2010.01.021
138. Nieuwenhuijse, D. F., and Koopmans, M. P. G. (2017). Metagenomic sequencing for surveillance of food- and waterborne viral diseases. Front. Microbiol. 8:230. doi: 10.3389/fmicb.2017.00230
139. Octavia, S., Wang, Q., Tanaka, M. M., Kaur, S., Sintchenko, V., and 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, 1063-1071. doi: 10.1128/JCM.03235-14
140. OIE (2017). Manual of Diagnostic Tests and Vaccines for Terrestrial Animals. Paris: World Organisation for Animal Health.
141. Olsen, A. R., Gecan, J. S., Ziobro, G. C., and Bryce, J. R. (2001). Regulatory action criteria for filth and other extraneous materials V. Strategy for evaluating hazardous and nonhazardous filth. Regul. Toxicol. Pharmacol. 33, 363-392. doi: 10.1006/rtph.2001.1472
142. Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S., et al. (2016). Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17:132. doi: 10.1186/s13059-016-0997-x
143. Orlandi, P. A., Chu, D. M. T., Bier, J. W., and Jackson, G. J. (2002). Parasites and the food supply. Food Technol. 56, 72-81. Available online at: http://www.ift.org/~/media/Knowledge%20Center/Science%20Reports/Scientific%20Status%20Summaries/parasitesfoodsupply_0402.pdf
144. Ottesen, A., Ramachandran, P., Reed, E., White, J. R., Hasan, N., Subramanian, P., et al. (2016). Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak. BMC Microbiol. 16:275. doi: 10.1186/s12866-016-0894-1
145. Ottesen, A. R., Gonzalez, A., Bell, R., Arce, C., Rideout, S., Allard, M., et al. (2013). Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere. PLoS ONE 8:e73079. doi: 10.1371/journal.pone.0073079
146. Petersen, T. N., Rasmussen, S., Hasman, H., Caroe, C., Baelum, J., Schultz, A. C., et al. (2015). Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance. Sci. Rep. 5:11444. doi: 10.1038/srep11444
147. Pipan, V., and Kunaj, T. (2015). Initiative for standardization of the format of the next generation sequencing (NGS) results. Discoveries 3:4. doi: 10.15190/d.2015.36
148. Pires, S. M., Fischer-Walker, C. L., Lanata, C. F., Devleesschauwer, B., Hall, A. J., Kirk, M. D., et al. (2015). Aetiology-specific estimates of the global and regional incidence and mortality of diarrhoeal diseases commonly transmitted through food. PLoS ONE 10:e0142927. doi: 10.1371/journal.pone.0142927
149. Pires, S. M., Vieira, A. R., Perez, E., Wong, D. L. F., and Hald, T. (2012). Attributing human foodborne illness to food sources and water in Latin America and the Caribbean using data from outbreak investigations. Int. J. Food Microbiol. 152, 129-138. doi: 10.1016/j.ijfoodmicro.2011.04.018
150. Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J., et al. (2015). Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16:114. doi: 10.1186/s13059-015-0677-2
151. Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., et al. (2017). Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc. 12, 1261-1276. doi: 10.1038/nprot.2017.066
152. Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Ettore, S., Cowley, L., et al. (2016). Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228-+. doi: 10.1038/nature16996
153. Ranjan, R., Rani, A., Metwally, A., McGee, H. S., and Perkins, D. L. (2016). Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem. Biophys. Res. Commun. 469, 967-977. doi: 10.1016/j.bbrc.2015.12.083
154. Rasko, D. A., Webster, D. R., Sahl, J. W., Bashir, A., Boisen, N., Scheutz, F., et al. (2011). Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. New Engl. J. Med. 365, 709-717. doi: 10.1056/NEJMoa1106920
155. Ratan, A., Olson, T. L., Loughran, T. P. Jr., and Miller, W. (2015). Identification of indels in next-generation sequencing data. BMC Bioinformatics 16:42. doi: 10.1186/s12859-015-0483-6
156. Reuter, S., Ellington, M. J., Cartwright, E. J. P., Köser, C. U., Török, M. E., Gouliouris, T., et al. (2013). Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern. Med. 173, 1397-1404. doi: 10.1001/jamainternmed.2013.7734
157. Rhoads, A., and Au, K. F. (2015). PacBio sequencing and its applications. Genom. Proteom. Bioinform. 13, 278-289. doi: 10.1016/j.gpb.2015.08.002
158. Robertson, L. J., Sprong, H., Ortega, Y. R., van der Giessen, J. W. B., and Fayer, R. (2014). Impacts of globalisation on foodborne parasites. Trends Parasitol. 30, 37-52. doi: 10.1016/j.pt.2013.09.005
159. Roden, M. M., Zaoutis, T. E., Buchanan, W. L., Knudsen, T. A., Sarkisova, T. A., Schaufele, R. L., et al. (2005). Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clin. Infect. Dis. 41, 634-653. doi: 10.1086/432579
160. Rodríguez-Lazaro, D., Cook, N., Ruggeri, F. M., Sellwood, J., Nasser, A., Nascimento, M. S. J., et al. (2012). Virus hazards from food, water and other contaminated environments. FEMS Microbiol. Rev. 36, 786-814. doi: 10.1111/j.1574-6976.2011.00306.x
161. Salmond, G. P. C., and Fineran, P. C. (2015). A century of the phage: past, present and future. Nat. Rev. Microbiol. 13, 777-786. doi: 10.1038/nrmicro3564
162. Sboner, A., Mu, X. J., Greenbaum, D., Auerbach, R. K., and Gerstein, M. B. (2011). The real cost of sequencing: higher than you think! Genome Biol. 12:125. doi: 10.1186/gb-2011-12-8-125
163. Scallan, E., Hoekstra, R. M., Angulo, F. J., Tauxe, R. V., Widdowson, M.-A., Roy, S. L., et al. (2011). Foodborne illness acquired in the United States-major pathogens. Emerging Infect. Dis. 17, 7-15. doi: 10.3201/eid1701.P11101
164. Scheutz, F., Nielsen, E. M., Frimodt-Möller, J., Boisen, N., Morabito, S., Tozzoli, R., et al. (2011). Characteristics of the enteroaggregative Shiga toxin/verotoxin-producing Escherichia coli O104:H4 strain causing the outbreak of haemolytic uraemic syndrome in Germany, May to June (2011). Eurosurveillance 16, 5-10. doi: 10.2807/ese.16.24.19889-en
165. Schmid, D., Allerberger, F., Huhulescu, S., Pietzka, A., Amar, C., Kleta, S., et al. (2014). Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011-2013. Clin. Microbiol. Infect. 20, 431-436. doi: 10.1111/1469-0691.12638
166. Schmitz-Esser, S., and Wagner, M. (2014). Genome sequencing of Listeria monocytogenes. Methods Mol. Biol. 1157, 223-232. doi: 10.1007/978-1-4939-0703-8_19
167. Severi, E., Verhoef, L., Thornton, L., Guzman-Herrador, B. R., Faber, M., Sundqvist, L., et al. (2015). Large and prolonged food-borne multistate hepatitis A outbreak in Europe associated with consumption of frozen berries, 2013 to (2014). Eurosurveillance 20, 11-19. doi: 10.2807/1560-7917.ES2015.20.29.21192
168. Singer, E., Bushnell, B., Coleman-Derr, D., Bowman, B., Bowers, R. M., Levy, A., et al. (2016). High-resolution phylogenetic microbial community profiling. ISME J. 10, 2020-2032. doi: 10.1038/ismej.2015.249
169. Smits, S. L., Schapendonk, C. M. E., van Beek, J., Vennema, H., Schürch, A. C., Schipper, D., et al. (2014). New viruses in idiopathic human diarrhea cases, the Netherlands. Emerging Infect. Dis. 20, 1218-1222. doi: 10.3201/eid2007.140190
170. Spellberg, B. (2012). Gastrointestinal mucormycosis: an evolving disease. Gastroenterol. Hepatol. 8, 140-142.
171. Spilsberg, B., Lagesen, K., Kristoffersen, A. B., and Holst-Jensen, A. (2017). "Identification and quantification of genetically modified organisms (GMO) from high throughput sequencing data," in qPCR dPCR & NGS (2017). eds S. Bustin and M. W. Pfaffl (Freising: Biomolecular Detection and Quantification), 11, S33.
172. Staats, M., Arulandhu, A. J., Gravendeel, B., Holst-Jensen, A., Scholtens, I., Peelen, T., et al. (2016). Advances in DNA metabarcoding for food and wildlife forensic species identification. Anal. Bioanal. Chem. 408, 4615-4630. doi: 10.1007/s00216-016-9595-8
173. Stapleton, A. E. (2014). A biologist, a statistician, and a bioinformatician walk into a conference room...and walk out with a great metagenonnics project plan. Front. Plant Sci. 5:250. doi: 10.3389/fpls.2014.00250
174. Stasiewicz, M. J., Oliver, H. F., Wiedmann, M., and den Bakker, H. C. (2015). Whole-genome sequencing allows for improved identification of persistent Listeria monocytogenes in food-associated environments. Appl. Environ. Microbiol. 81, 6024-6037. doi: 10.1128/AEM.01049-15
175. Stoev, S. D. (2015). Foodborne mycotoxicoses, risk assessment and underestimated hazard of masked mycotoxins and joint mycotoxin effects or interaction. Environ. Toxicol. Pharmacol. 39, 794-809. doi: 10.1016/j.etap.2015.01.022
176. Struelens, M. J., Palm, D., and Takkinen, J. (2011). Enteroaggregative, Shiga toxin-producing Escherichia coli O104:H4 outbreak: new microbiological findings boost coordinated investigations by European public health laboratories. Eurosurveillance 16, 2-4. doi: 10.2807/ese.16.24.19890-en
177. Taboada, E. N., Graham, M. R., Carriço, J. A., and Van Domselaar, G. (2017). Food safety in the age of next generation sequencing, bioinformatics, and open data access. Front. Microbiol. 8:909. doi: 10.3389/fmicb.2017.00909
178. Tallon, L. J., Liu, X., Bennuru, S., Chibucos, M. C., Godinez, A., Ott, S., et al. (2014). Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis. BMC Genomics 15:788. doi: 10.1186/1471-2164-15-788
179. Tan, B., Ng, C., Nshimyimana, J. P., Loh, L. L., Gin, K. Y. H., and Thompson, J. R. (2015). Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front. Microbiol. 6:1027. doi: 10.3389/fmicb.2015.01027
180. Taylor, A. J., Lappi, V., Wolfgang, W. J., Lapierre, P., Palumbo, M. J., Medus, C., et al. (2015). Characterization of foodborne outbreaks of Salmonella enterica serovar Enteritidis with whole-genome sequencing single nucleotide polymorphism-based analysis for surveillance and outbreak detection. J. Clin. Microbiol. 53, 3334-3340. doi: 10.1128/JCM.01280-15
181. Tilden, J., Young, W., McNamara, A. M., Custer, C., Boesel, B., LambertFair, M., et al. (1996). A new route of transmission for Escherichia coli: infection from dry fermented salami. Am. J. Public Health 86, 1142-1145. doi: 10.2105/AJPH.86.8_Pt_1.1142
182. Timme, R., Rand, H., Trees, E., Agarwala, R., David, S., Shumway, M., et al. (2015). "Benchmark datasets for validating foodborne outbreak investigations: integrating WGS and phylogenomic analyses," in 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens (Washington, DC).
183. Timme, R. E., Allard, M. W., Luo, Y., Strain, E., Pettengill, J., Wang, C., et al. (2012). Draft genome sequences of 21 Salmonella enterica serovar Enteritidis strains. J. Bacteriol. 194, 5994-5995. doi: 10.1128/JB.01289-12
184. Tsai, I. J., Zarowiecki, M., Holroyd, N., Garciarrubio, A., Sanchez-Flores, A., Brooks, K. L., et al. (2013). The genomes of four tapeworm species reveal adaptations to parasitism. Nature 496, 57-63. doi: 10.1038/nature12031
185. Turabelidze, G., Lawrence, S. J., Gao, H., Sodergren, E., Weinstock, G. M., Abubucker, S., et al. (2013). Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. J. Clin. Microbiol. 51, 3950-3954. doi: 10.1128/JCM.01930-13
186. Tuttle, J., Gomez, T., Doyle, M. P., Wells, J. G., Zhao, T., Tauxe, R. V., et al. (1999). Lessons from a large outbreak of Escherichia coli O157: H7 infections: insights into the infectious dose and method of widespread contamination of hamburger patties. Epidemiol. Infect. 122, 185-192. doi: 10.1017/S0950268898001976
187. Underwood, A. P., Dallman, T., Thomson, N. R., Williams, M., Harker, K., Perry, N., et al. (2013). Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. J. Clin. Microbiol. 51, 232-237. doi: 10.1128/JCM.01696-12
188. van Dijk, E. L., Auger, H., Jaszczyszyn, Y., and Thermes, C. (2014). Ten years of next-generation sequencing technology. Trends Genet. 30, 418-426. doi: 10.1016/j.tig.2014.07.001
189. Vaux, S., Criscuolo, A., Desnos-Ollivier, M., Diancourt, L., Tarnaud, C., Vandenbogaert, M., et al. (2014). Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen. mBio 5:e02309-14. doi: 10.1128/mBio.02309-14
190. Wang, B., Cunningham, J. M., and Yang, X. (2015a). Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics 31, 3043-3045. doi: 10.1093/bioinformatics/btv289
191. Wang, C., and Zhang, D. (2011). A novel compression tool for efficient storage of genome resequencing data. Nucleic Acids Res. 39, E45-U74. doi: 10.1093/nar/gkr009
192. Wang, Q., Holmes, N., Martinez, E., Howard, P., Hill-Cawthorne, G., and Sintchenko, V. (2015b). It is not all about single nucleotide polymorphisms: comparison of mobile genetic elements and deletions in Listeria monocytogenes genomes links cases of hospital-acquired listeriosis to the environmental source. J. Clin. Microbiol. 53, 3492-3500. doi: 10.1128/JCM.00202-15
193. Wang, S.-H., Shen, M., Lin, H.-C., Sun, P.-L., Lo, H.-J., and Lu, J.-J. (2015c). Molecular epidemiology of invasive Candida albicans at a tertiary hospital in northern Taiwan from 2003 to (2011). Med. Mycol. 53, 828-836. doi: 10.1093/mmy/myv065
194. Wang, Y., Ye, Z., and Ying, Y. (2012). New trends in impedimetric biosensors for the detection of foodborne pathogenic bacteria. Sensors 12, 3449-3471. doi: 10.3390/s120303449
195. Weinmaier, T., Probst, A. J., La Duc, M. T., Ciobanu, D., Cheng, J. F., Ivanova, N., et al. (2015). A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. Microbiome 3:62. doi: 10.1186/s40168-015-0129-y
196. Weiss, M. M., Van der Zwaag, B., Jongbloed, J. D. H., Vogel, M. J., Brüggenwirth, H. T., Deprez, R. H. L., et al. (2013). Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories. Hum. Mutat. 34, 1313-1321. doi: 10.1002/humu.22368
197. Withlow, L., and Hagler, W. Jr. (2016). Mold and Mycotoxin Issues in Dairy Cattle: Effects, Prevention and Treatment. EXTENSION [Online]. Available online at: http://articles.extension.org/pages/11768/mold-and-mycotoxin-issues-in-dairy-cattle:-effects-prevention-and-treatment
198. Wong, T. H. N., Dearlove, B. L., Hedge, J., Giess, A. P., Piazza, P., Trebes, A., et al. (2013). Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Virol. J. 10:335. doi: 10.1186/1743-422X-10-335
199. Wu, Y., Zheng, J., Wang, Y., Li, S., Jin, H., Li, Z., et al. (2015). Draft genome sequence of Listeria monocytogenes LM201, isolated from foodstuff. Genome Announce. 3:e01417-14. doi: 10.1128/genomeA.01417-14
200. Wuyts, V., Denayer, S., Roosens, N. H. C., Mattheus, W., Bertrand, S., Marchal, K., et al. (2015). Whole genome sequence analysis of Salmonella Enteritidis PT4 outbreaks from a national reference laboratory's viewpoint. PLoS Curr. Outbreaks 2015:1. doi: 10.1371/currents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc
201. Xia, J., Wang, Q., Jia, P., Wang, B., Pao, W., and Zhao, Z. (2012). NGS Catalog: a database of next generation sequencing studies in humans. Hum. Mutat. 33, E2341-E2355. doi: 10.1002/humu.22096
202. Young, N. D., Nagarajan, N., Lin, S. J., Korhonen, P. K., Jex, A. R., Hall, R. S., et al. (2014). The Opisthorchis viverrini genome provides insights into life in the bile duct. Nat. Commun. 5:4378. doi: 10.1038/ncomms5378
203. Zhang, S. K., Yin, Y. L., Jones, M. B., Zhang, Z. Z., Kaiser, B. L. D., Dinsmore, B. A., et al. (2015). Salmonella serotype determination utilizing high-throughput genome sequencing data. J. Clin. Microbiol. 53, 1685-1692. doi: 10.1128/JCM.00323-15