What has molecular epidemiology ever done for wildlife disease research? Past contributions and future directions

European Journal of Wildlife Research

Volumn 61, Issue 1, 2015, Pages 1-16

  Benton, Clare H ^a   Delahay, Richard J ^a   Trewby, Hannah ^b   Hodgson, David J ^c  

^a VETERINARY LABORATORIES AGENCY   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Disease surveillance; Disease transmission; Host pathogen evolution; Next generation sequencing; Wildlife reservoirs; Wildlife vaccines

Indexed keywords

EID: 84925493059     PISSN: 16124642     EISSN: 14390574     Source Type: Journal    
DOI: 10.1007/s10344-014-0882-4     Document Type: Review

References (135)

1. Acevedo-Whitehouse K, Cunningham AA (2006) Is MHC enough for understanding wildlifeimmunogenetics? Trends Ecol Evol 21:433–438
2. Achtman M (2001) A phylogenetic perspective on molecular epidemiology. Molecul Med Microbiol 1–3:485–509
3. Angulo E, Juan B (2007) Towards a unique and transmissible vaccine against myxomatosis and rabbit haemorrhagic disease for rabbit populations. Wildl Res 34:567–577
4. Archie EA, Luikart G, Ezenwa VO (2009) Infecting epidemiology with genetics: a new frontier in disease ecology. Trends Ecol Evol 24:21–30
5. Artois M, Bengis R, Delahay RJ, Duchêne M-J, Duff JP, Ferroglio E, Gortazar C, Hutchings MR, Kock RA, Leighton FA (2009) Wildlife disease surveillance and monitoring. In: Management of disease in wild mammals. Springer, pp 187–213
6. Baker M (2010) Next-generation sequencing: adjusting to data overload. Nat Meth 7:495–499
7. Barker EN, Darby AC, Helps CR, Peters IR, Heesom KJ, Arthur CJ, Crossett B, Hughes MA, Radford AD, Tasker S (2011) Molecular characterization of the uncultivatable hemotropic bacterium Mycoplasma haemofelis. Vet Res 42:83
8. Baron S (1996) Medical microbiology, 4th edn. University of Texas Medical Branch, Galveston
9. Barros SC, Ramos F, Luis TM, Vaz A, Duarte M, Henriques M, Cruz B, Fevereiro M (2007) Molecular epidemiology of bluetongue virus in Portugal during 2004–2006 outbreak. Vet Microbiol 124:25–34
10. Biek R, Real LA (2010) The landscape genetics of infectious disease emergence and spread. Mol Ecol 19:3515–3531
11. Biek R, O’Hare A, Wright D, Mallon T, McCormick C, Orton RJ, McDowell S, Trewby H, Skuce RA, Kao RR (2012) Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathog 8:e1003008
12. Blaustein AR, Romansic JM, Scheessele EA, Han BA, Pessier AP, Longcore JE (2005) Interspecific variation in susceptibility of frog tadpoles to the pathogenic fungus Batrachochytrium dendrobatidi. Conserv Biol 19:1460–1468
13. Blehert DS (2011) Population genetics of geomyces destructans from whole genome sequences US geological survey
14. Boyce WM, Weisenberger ME, Penedo MCT, Johnson CK (2011) Wildlife translocation: the conservation implications of pathogen exposure and genetic heterozygosity. BMC Ecol 11(1):5
15. Boyd SD (2013) Diagnostic applications of high-throughput DNA sequencing. Annu Rev Pathol 8:381–410
16. Buckee CO, Recker M, Watkins ER, Gupta S (2011) Role of stochastic processes in maintaining discrete strain structure in antigenically diverse pathogen populations. Proc Natl Acad Sci U S A 108:15504–15509
17. Bull JJ (1994) Perspective: virulence. Evolution 48:1423–1437
18. Byrnes EJ III, Li W, Lewit Y, Ma H, Voelz K, Ren P, Carter DA, Chaturvedi V, Bildfell RJ, May RC, Heitman J (2010) Emergence and pathogenicity of highly virulent Cryptococcus gattii genotypes in the Northwest United States. PLoS Pathog 6:e1000850
19. Carey AJ, Timms P, Rawlinson G, Brumm J, Nilsson K, Harris JM, Beagley KW (2010) A multi-subunit chlamydial vaccine induces antibody and cell-mediated immunity in immunized koalas (Phascolarctos cinereus): comparison of three different adjuvants. Am J Reprod Immunol 63:161–172
20. Carter SP, Chambers MA, Rushton SP, Shirley MDF, Schuchert P, Pietravalle S, Murray A, Rogers F, Gettinby G, Smith GC, Delahay RJ, Hewinson RG, McDonald RA (2012) BCG vaccination reduces risk of tuberculosis infection in vaccinated badgers and unvaccinated badger cubs. PloS one 7:e49833
21. Castro-Prieto A, Wachter B, Melzheimer J, Thalwitzer S, Hofer H, Sommer S (2012) Immunogenetic variation and differential pathogen exposure in free-ranging cheetahs across namibian farmlands. PLoS One 7:e49129
22. Chambers MA, Rogers F, Delahay RJ, Lesellier S, Ashford R, Dalley D, Gowtage S, Davé D, Palmer S, Brewer J, Crawshaw T, Clifton-Hadley R, Carter S, Cheeseman C, Hanks C, Murray A, Palphramand K, Pietravalle S, Smith GC, Tomlinson A, Walker NJ, Wilson GJ, Corner LA, Rushton SP, Shirley MD, Gettinby G, McDonald RA, Hewinson RG (2010) Bacillus Calmette-Guérin vaccination reduces the severity and progression of tuberculosis in badgers. Proc Biol Sci 278(1713):1913–1920
23. Chapman DA, Darby AC, Da Silva M, Upton C, Radford AD, Dixon LK (2011) Genomic analysis of highly virulent Georgia 2007/1 isolate of African swine fever virus. Emerg Infect Dis 17:599–605
24. Cheng X, Tan Y, He M, Lam TT-Y, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, H-f K, Holmes EC, Cheng J (2012) Epidemiological dynamics and phylogeography of influenza virus in Southern China. J Infect Dis 207(1):106–114
25. Chibucos MC, Crabtree J, Nagaraj S, Chaturvedi S, Chaturvedi V (2013) Draft genome sequences of human pathogenic fungus geomyces pannorum sensu lato and bat white nose syndrome pathogen Geomyces (Pseudogymnoascus) destructans. Genome Announce 1(6):e01045–13
26. Cook VJ, Sun SJ, Tapia J, Muth SQ, Argüello DF, Lewis BL, Rothenberg RB, McElroy PD (2007) Transmission network analysis in tuberculosis contact investigations. J Infect Dis 196:1517–1527
27. Cortey M, Bertran K, Toskano J, Majo N, Dolz R (2012) Phylogeographic distribution of very virulent infectious bursal disease virus isolates in the Iberian Peninsula. Avian Pathol 41:277–284
28. Cottam EM, Haydon DT, Paton DJ, Gloster J, Wilesmith JW, Ferris NP, Hutchings GH, King DP (2006) Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001. J Virol 80:11274–11282
29. Cowled BD, Ward MP (2012) Integrating survey and molecular approaches to better understand wildlife disease ecology. PLoS One 7:1–8
30. Cross PC, Lloyd-Smith JO, Johnson PLF, Getz WM (2005) Duelling timescales of host movement and disease recovery determine invasion of disease in structured populations. Ecol Lett 8:587–595
31. Daboussi MJ (1997) Fungal transposable elements and genome evolution. In: Capy P (ed) Evolution and impact of transposable elements. Springer, Netherlands, pp 253–260
32. Daszak P, Cunningham AA, Hyatt AD (2000) Emerging infectious diseases of wildlife - threats to biodiversity and human health. Science 287:443–449
33. Daszak P, Tabor GM, Kilpatrick AM, Epstein J, Plowright R (2004) Conservation medicine and a new agenda for emerging diseases. Ann N Y Acad Sci 1026:1–11
34. de Carvalho LM, Santos LB, Faria NR, de Castro SW (2013) Phylogeography of foot-and-mouth disease virus serotype O in Ecuador. Infect Genet Evol 13:76–88
35. Delahay RJ, Langton S, Smith GC, Clifton-Hadley RS, Cheeseman CL (2000) The spatio-temporal distribution of Mycobacterium bovis (bovine tuberculosis) infection in a high-density badger population. J Anim Ecol 69:428–441
36. Delahay RJ, Smith GC, Hutchings MR (2008) The science of wildlife disease management. In: Delahay RJ, Smith GC, Hutchings MR (eds) Management of disease in wild mammals. Springer, pp 1–8
37. Doolittle WF, Zhaxybayeva O (2010) Metagenomics and the units of biological organization. BioSci 60:102–112
38. Drewe JA (2010) Who infects whom? Social networks and tuberculosis transmission in wild meerkats. Proc Biol Sci 277:633–642
39. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973
40. Duffield B, Young D (1985) Survival of Mycobacterium bovis in defined environmental conditions. Vet Microbiol 10:193–197
41. El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran A-N, Wortman JR, Alsmark UCM, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N (2005) Comparative genomics of trypanosomatid parasitic protozoa. Science 309:404–409
42. Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O’Connor L, Ip CLC, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TEA, Walker AS (2013) Diverse sources of C. difficile infection identified on whole-genome sequencing. New Engl J Med 369:1195–1205
43. Feng Y, Xiao L (2011) Zoonotic potential and molecular epidemiology of Giardia species and giardiasis. Clin Microbiol Rev 24:110–140
44. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066
45. Fisher MC, Garner TW, Walker SF (2009) Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. Annu Rev Microbiol 63:291–310
46. Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PSG, Roberto FF, Hnath J, Brettin T, Keim P (2009) Whole-genome-based phylogeny and divergence of the genus brucella. J Bacteriol 191:2864–2870
47. Frothingham R (1995) Differentiation of strains in Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG. J Clin Microbiol 33:840–844
48. Gardy JL, Johnston JC, Sui SJH, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJM, Brinkman FSL, Brunham RC, Tang P (2011) Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. New Engl J Med 364:730–739
49. Geue L, Schares S, Schnick C, Kliemt J, Beckert A, Freuling C, Conraths FJ, Hoffmann B, Zanoni R, Marston D, McElhinney L, Johnson N, Fooks AR, Tordo N, Müller T (2008) Genetic characterisation of attenuated SAD rabies virus strains used for oral vaccination of wildlife. Vaccine 26:3227–3235
50. Goodchild AV, Watkins GH, Sayers AR, Jones JR, Clifton-Hadley RS (2012) Geographical association between the genotype of bovine tuberculosis in found dead badgers and in cattle herds. Vet Rec 170:259
51. Gould AR, Kattenbelt JA, Selleck P, Hansson E, Della-Porta A, Westbury HA (2001) Virulent Newcastle disease in Australia: molecular epidemiological analysis of viruses isolated prior to and during the outbreaks of 1998–2000. Virus Res 77:51–60
52. Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, FitzGerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, DeSmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill F-X, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP (2012) Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci 109:3065–3070
53. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, Mumford JA, Holmes EC (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303:327–332
54. Griffin AS, West SA, Buckling A (2004) Cooperation and competition in pathogenic bacteria. Nature 430:1024–1027
55. Hacker J, Carniel E (2001) Ecological fitness, genomic islands and bacterial pathogenicity. EMBO Rep 2:376–381
56. Hamede RK, Bashford J, McCallum H, Jones M (2009) Contact networks in a wild Tasmanian devil (Sarcophilus harrisii) population: using social network analysis to reveal seasonal variability in social behaviour and its implications for transmission of devil facial tumour disease. Ecol Lett 12:1147–1157
57. Hamede R, Lachish S, Belov K, Woods G, Kreiss A, Pearse AM, Lazenby B, Jones M, McCallum H (2012) Reduced effect of Tasmanian devil facial tumor disease at the disease front. Conserv Biol 26:124–134
58. Harris SR, Cartwright EJP, Török ME, Holden MTG, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ (2013) Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 13:130–136
59. Harwood VJ, Whitlock J, Withington V (2000) Classification of antibiotic resistance patterns of indicator bacteria by discriminant analysis: use in predicting the source of fecal contamination in subtropical waters. Appl Environ Microbiol 66:3698–3704
60. Haydon DT, Cleaveland S, Taylor LH, Laurenson MK (2002) Identifying reservoirs of infection: a conceptual and practical challenge. Emerg Infect Dis 8:1468–1473
61. Hemelaar J, Gouws E, Ghys PD, Osmanov S (2011) Global trends in molecular epidemiology of HIV-1 during 2000–2007. AIDS 25:679–689
62. Henderson M, Okamura B (2004) The phylogeography of salmonid proliferative kidney disease in Europe and North America. Proc Roy Soc Biol Sci 271:1729–1736
63. Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S (2012) Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8:e1002529
64. Hernandez SM, Keel K, Sanchez S, Trees E, Gerner-Smidt P, Adams JK, Cheng Y, Ray A III, Martin G, Presotto A, Ruder MG, Brown J, Blehert DS, Cottrell W, Maurer JJ (2012) Epidemiology of a Salmonella enterica subsp enterica serovar typhimurium strain associated with a songbird outbreak. Appl Environ Microbiol 78:7290–7298
65. Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, Bushman FD (2007) DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 35:e91
66. Holman PJ, Carroll JE, Pugh R, Davis DS (2011) Molecular detection of Babesia bovis and Babseia bigemina in white-tailed deer (Odocoileus virginianus) from Tom Green County in central Texas. Vet Parasitol 177:298–304
67. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3:e300
68. Hostnik P, Picard-Meyer E, Rihtaric D, Toplak I, Cliquet F (2014) Vaccine-induced rabies in a red fox (Vulpes vulpes): isolation of vaccine virus in brain tissue and salivary glands. J Wildl Dis 50(2):397–401
69. Hoye BJ, Munster VJ, Nishiura H, Klaassen M, Fouchier RAM (2010) Surveillance of wild birds for avian influenza virus. Emerg Infect Dis 16:1827–1834
70. Hu B, Xie G, Lo C-C, Starkenburg SR, Chain PSG (2011) Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Brief Funct Genomics 10:322–333
71. Hudson PJ, Rizzoli A, Grenfell BT, Heesterbeek J, Dobson AP (2002) Ecology of wildlife diseases. Oxford University Press
72. Hyndman RJ, Khandakar Y (2007) Automatic time series for forecasting: the forecast package for R. (No. 6/07). Monash University, Department of Econometrics and Business Statistics
73. Ip HS, Wiley MR, Long R, Palacios G, Shearn-Bochsler V, Whitehouse CA (2014) Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing. J Virol Methods 206:42–45
74. James TY, Litvintseva AP, Vilgalys R, Morgan JAT, Taylor JW, Fisher MC, Berger L, Weldon C, du Preez L, Longcore JE (2009) Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations. PLoS Pathog 5:e1000458
75. Jenkins HE, Woodroffe R, Donnelly CA, Cox DR, Johnston WT, Bourne FJ, Cheeseman CL, Clifton-Hadley RS, Gettinby G, Gilks P, Hewinson RG, McInerney JP, Morrison WI (2007) Effects of culling on spatial associations of Mycobacterium bovis infections in badgers and cattle. J Appl Ecol 44:897–908
76. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N (2014) Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Comput Biol 10:e1003457
77. Joshi D, Harris NB, Waters R, Thacker T, Mathema B, Krieswirth B, Sreevatsan S (2012) Single nucleotide polymorphisms in the Mycobacterium bovis genome resolve phylogenetic relationships. J Clin Microbiol 50:3853–3861
78. Kao RR, Haydon DT, Lycett SJ, Murcia PR (2014) Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol 22:282–291
79. Keim P, Smith KL, Keys C, Takahashi H, Kurata T, Kaufmann A (2001) Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan. J Clin Microbiol 39:4566–4567
80. Köndgen S, Kühl H, N’Goran PK, Walsh PD, Schenk S, Ernst N, Biek R, Formenty P, Mätz-Rensing K, Schweiger B, Junglen S, Ellerbrok H, Nitsche A, Briese T, Lipkin WI, Pauli G, Boesch C, Leendertz FH (2008) Pandemic human viruses cause decline of endangered great apes. Curr Biol 18:260–264
81. Koopmans M, Vinjé J, de Wit M, Leenen I, van der Poel W, van Duynhoven Y (2000) Molecular epidemiology of human enteric caliciviruses in The Netherlands. J Infect Dis 181:S262–S269
82. Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, Holden MTG, Dougan G, Bentley SD, Parkhill J, Peacock SJ (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8:e1002824
83. Kumarasamy KK, Toleman MA, Walsh TR, Bagaria J, Butt F, Balakrishnan R, Chaudhary U, Doumith M, Giske CG, Irfan S, Krishnan P, Kumar AV, Maharjan S, Mushtaq S, Noorie T, Paterson DL, Pearson A, Perry C, Pike R, Rao B, Ray U, Sarma JB, Sharma M, Sheridan E, Thirunarayan MA, Turton J, Upadhyay S, Warner M, Welfare W, Livermore DM, Woodford N (2010) Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect Dis 10:597–602
84. Liu C, Graber CJ, Karr M, Diep BA, Basuino L, Schwartz BS, Enright MC, O’Hanlon SJ, Thomas JC, Perdreau-Remington F, Gordon S, Gunthorpe H, Jacobs R, Jensen P, Leoung G, Rumack JS, Chambers HF (2008) A population-based study of the incidence and molecular epidemiology of methicillin-resistant Staphylococcus aureus disease in San Francisco, 2004–2005. Clin Infect Dis 46:1637–1646
85. Lloyd-Smith JO, Cross PC, Briggs CJ, Daugherty M, Getz WM, Latto J, Sanchez MS, Smith AB, Swei A (2005) Should we expect population thresholds for wildlife disease? Trends Ecol Evol 20:511–519
86. Maan S, Samuel AR, Maan NS, Attoui H, Rao S, Mertens PP (2004) Molecular epidemiology of bluetongue viruses from disease outbreaks in the Mediterranean Basin. Vet Ital 40:489–496
87. Maan S, Belaganahalli M, Maan N, Mertens PC (2013) Whole genome sequencing strategies and development of orbivirus sequence database: implications for novel dsRNA virus detection. In: Salar RK, Gahlawat SK, Siwach P, Duhan JS (eds) Biotechnology: prospects and applications. Springer, India, pp 237–255
88. Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R (2008) Microbiology in the post-genomic era. Nat Rev Microbiol 6:419–430
89. Meli ML, Cattori V, Martínez F, López G, Vargas A, Simón MA, Zorrilla I, Muñoz A, Palomares F, López-Bao JV, Pastor J, Tandon R, Willi B, Hofmann-Lehmann R, Lutz H (2009) Feline leukemia virus and other pathogens as important threats to the survival of the critically endangered Iberian Lynx (Lynx pardinus). PLoS One 4:e4744
90. Metzker ML (2010) Sequencing technologies -the next generation. Nat Rev Genet 11:31–46
91. Millan J, Blasco-Costa I (2012) Molecular evidence of shared hookworm Ancylostoma tubaeforme haplotypes between the critically endangered Iberian lynx and sympatric domestic cats. Vet Parasitol 186:518–522
92. Monot M, Honore N, Garnier T, Zidane N, Sherafi D, Paniz-Mondolfi A, Matsuoka M, Taylor GM, Donoghue HD, Bouwman A, Mays S, Watson C, Lockwood D, Khamispour A, Dowlati Y, Jianping S, Rea TH, Vera-Cabrera L, Stefani MM, Banu S, Macdonald M, Sapkota BR, Spencer JS, Thomas J, Harshman K, Singh P, Busso P, Gattiker A, Rougemont J, Brennan PJ, Cole ST (2009) Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 41:1282–1289
93. Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL, Wong W, Aken B, White S, Alsop A, Becq J, Bignell GR, Cheetham RK, Cheng W, Connor TR, Cox AJ, Feng ZP, Gu Y, Grocock RJ, Harris SR, Khrebtukova I, Kingsbury Z, Kowarsky M, Kreiss A, Luo S, Marshall J, McBride DJ, Murray L, Pearse AM, Raine K, Rasolonjatovo I, Shaw R, Tedder P, Tregidgo C, Vilella AJ, Wedge DC, Woods GM, Gormley N, Humphray S, Schroth G, Smith G, Hall K, Searle SM, Carter NP, Papenfuss AT, Futreal PA, Campbell PJ, Yang F, Bentley DR, Evers DJ, Stratton MR (2012) Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell 148:780–791
94. Neel C (2010) Molecular epidemiology of simian immunodeficiency virus infection in wild-living gorillas. J Virol 84:1464–1476
95. Nielsen L, Arctander P, Jensen TH, Dietz H-H, Hammer AS, Banyard AC, Barrett T, Blixenkrone-Moller M (2009) Genetic diversity and phylogenetic analysis of the attachment glycoprotein of phocine distemper viruses of the 2002 and 1988 epizootics. Virus Res 144:323–328
96. Nunes MR, Faria NR, Vasconcelos HB, Medeiros DB, Silva de Lima CP, Carvalho VL, Pinto da Silva EV, Cardoso JF, Sousa EC, Nunes KN, Rodrigues SG, Abecasis AB, Suchard MA, Lemey P, Vasconcelos PF (2012) Phylogeography of dengue virus serotype 4, Brazil, 2010–2011. Emerg Infect Dis 18:1858–1864
97. Paillot R, Darby AC, Robinson C, Wright NL, Steward KF, Anderson E, Webb K, Holden MT, Efstratiou A, Broughton K, Jolley KA, Priestnall SL, Marotti Campi MC, Hughes MA, Radford A, Erles K, Waller AS (2010) Identification of three novel superantigen-encoding genes in Streptococcus equi subsp. zooepidemicus, szeF, szeN, and szeP. Infect Immun 78:4817–4827
98. Pandit A, Sinha S (2010) Using genomic signatures for HIV-1 sub-typing. BMC Bioinformat 11:S26
99. Perez de Rosas AR, Segura EL, Garcia BA (2011) Molecular phylogeography of the Chagas’ disease vector Triatoma infestans in Argentina. Heredity 107:71–79
100. Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24:142–149
101. Price LB, Stegger M, Hasman H, Aziz M, Larsen J, Andersen PS, Pearson T, Waters AE, Foster JT, Schupp J, Gillece J, Driebe E, Liu CM, Springer B, Zdovc I, Battisti A, Franco A, Żmudzki J, Schwarz S, Butaye P, Jouy E, Pomba C, Porrero MC, Ruimy R, Smith TC, Robinson DA, Weese JS, Arriola CS, Yu F, Laurent F, Keim P, Skov R, Aarestrup FM (2012) Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio 3(1):e00305–e00311
102. Rankin DJ, Bargum K, Kokko H (2007) The tragedy of the commons in evolutionary biology. Trends Ecol Evol 22:643–651
103. Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, Keim PS, Fraser-Liggett CM, Ravel J (2011) Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A 108:5027–5032
104. Recker M, Pybus OG, Nee S, Gupta S (2007) The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types. Proc Natl Acad Sci 104:7711–7716
105. Relman DA (2011) Microbial genomics and infectious diseases. N Engl J Med 365:347–357
106. Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S (2013) Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10:e1001387
107. Romero B, Aranaz A, Sandoval A, Alvarez J, de Juan L, Bezos J, Sanchez C, Galka M, Fernandez P, Mateos A, Dominguez L (2008) Persistence and molecular evolution of Mycobacterium bovis population from cattle and wildlife in Donana National Park revealed by genotype variation. Vet Microbiol 132:87–95
108. Sainsbury AW, Nettleton P, Gilray J, Gurnell J (2000) Grey squirrels have high seroprevalence to a parapoxvirus associated with deaths in red squirrels. Anim Conservat 3:229–233
109. Salyer SJ, Gillespie TR, Rwego IB, Chapman CA, Goldberg TL (2012) Epidemiology and molecular relationships of cryptosporidium spp. in people, primates, and livestock from Western Uganda. PLoS Negl Trop Dis 6(4):e1597
110. Santolaya ME, O’Ryan ML, Valenzuela MT, Prado V, Vergara R, Munoz A, Toneatto D, Grana G, Wang H, Clemens R, Dull PM (2012) Immunogenicity and tolerability of a multicomponent meningococcal serogroup B (4CMenB) vaccine in healthy adolescents in Chile: a phase 2b/3 randomised, observer-blind, placebo-controlled study. Lancet 379:617–624
111. Seib KL, Dougan G, Rappuoli R (2009) The key role of genomics in modern vaccine and drug design for emerging infectious diseases. PLoS Genet 5:e1000612
112. Serruto D, Serino L, Masignani V, Pizza M (2009) Genome-based approaches to develop vaccines against bacterial pathogens. Vaccine 27:3245–3250
113. Siddle HV, Kreiss A, Eldridge MDB, Noonan E, Clarke CJ, Pyecroft S, Woods GM, Belov K (2007) Transmission of a fatal clonal tumor by biting occurs due to depleted MHC diversity in a threatened carnivorous marsupial. Proc Natl Acad Sci 104:16221–16226
114. Siddle HV, Marzec J, Cheng Y, Jones M, Belov K (2010) MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer. Proc Biol Sci 277:2001–2006
115. Smith NH, Dale J, Inwald J, Palmer S, Gordon SV, Hewinson RG, Smith JM (2003) The population structure of Mycobacterium bovis in Great Britain: clonal expansion. Proc Natl Acad Sci U S A 100:15271–15275
116. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Segre JA (2012) Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4:148ra116
117. Snow M (2011) The contribution of molecular epidemiology to the understanding and control of viral diseases of salmonid aquaculture. Vet Res 42:56
118. Spibey N, McCabe VJ, Greenwood NM, Jack SC, Sutton D, van der Waart L (2012) Novel bivalent vectored vaccine for control of myxomatosis and rabbit haemorrhagic disease. Vet Rec. doi:10.1136/vr.100366
119. Starkman SE, MacDonald DM, Lewis JCM, Holmes EC, Simmonds P (2003) Geographic and species association of hepatitis B virus genotypes in non-human primates. Virology 314:381–393
120. Streicker DG, Lemey P, Velasco-Villa A, Rupprecht CE (2012) Rates of viral evolution are linked to host geography in bat rabies. PLoS Pathog 8:e1002720
121. Szentiks CA, Tsangaras K, Abendroth B, Scheuch M, Stenglein MD, Wohlsein P, Heeger F, Höveler R, Chen W, Sun W, Damiani A, Nikolin V, Gruber AD, Grobbel M, Kalthoff D, Höper D, Czirják GÁ, DeRisi J, Mazzoni CJ, Schüle A, Aue A, East ML, Hofer H, Beer M, Osterrieder N, Greenwood AD (2014) Polar bear encephalitis: establishment of a comprehensive next-generation pathogen analysis pipeline for captive and free-living wildlife. J Comp Pathol 150:474–488
122. Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11:472–477
123. Tibayrenc M (1998) Beyond strain typing and molecular epidemiology: integrated genetic epidemiology of infectious diseases. Parasitol Today 14:323–329
124. Tonellato PJ, Crawford JM, Boguski MS, Saffitz JE (2011) A national agenda for the future of pathology in personalized medicine: report of the proceedings of a meeting at the Banbury conference center on genome-era pathology, precision diagnostics, and preemptive care: a stakeholder summit. Am J Clin Pathol 135:668–672
125. Vineis P, Perera F (2007) Molecular epidemiology and biomarkers in etiologic cancer research: the new in light of the old. Cancer Epidemiol Biomarkers Prev 16:1954–1965
126. Vogler AJ, Chan F, Wagner DM, Roumagnac P, Lee J, Nera R, Eppinger M, Ravel J, Rahalison L, Rasoamanana BW, Beckstrom-Sternberg SM, Achtman M, Chanteau S, Keim P (2011) Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS Negl Trop Dis 5:e1319
127. Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TEA (2013) Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 13:137–146
128. Wedlock DN, Denis M, Vordermeier HM, Hewinson RG, Buddle BM (2007) Vaccination of cattle with Danish and Pasteur strains of Mycobacterium bovis BCG induce different levels of IFNgamma post-vaccination, but induce similar levels of protection against bovine tuberculosis. Vet Immunol Immunopathol 118:50–58
129. Williams ES, Miller MW, Kreeger TJ, Kahn RH, Thorne ET (2002) Chronic wasting disease of Deer and Elk: a review with recommendations for management. J Wildlife Manag 66:551–563
130. Woodroffe R, Donnelly CA, Johnston WT, Bourne FJ, Cheeseman CL, Clifton-Hadley RS, Cox DR, Gettinby G, Hewinson RG, Le Fevre AM, McInerney JP, Morrison WI (2005) Spatial association of Mycobacterium bovis infection in cattle and badgers (Meles meles). J Appl Ecol 42:852–862
131. Woodroffe R, Prager KC, Munson L, Conrad PA, Dubovi EJ, Mazet JAK (2012) Contact with domestic dogs increases pathogen exposure in endangered African wild dogs (Lycaon pictus). PLoS One 7:e30099
132. Woolhouse ME, Dye C, Etard J-F, Smith T, Charlwood J, Garnett G, Hagan P, Hii J, Ndhlovu P, Quinnell R (1997) Heterogeneities in the transmission of infectious agents: implications for the design of control programs. Proc Natl Acad Sci 94:338–342
133. Wylie JL, Cabral T, Jolly AM (2005) Identification of networks of sexually transmitted infection: a molecular, geographic, and social network analysis. J Infect Dis 191:899–906
134. Xiao L, Ryan UM (2004) Cryptosporidiosis: an update in molecular epidemiology. Curr Opin Infect Dis 17:483–490
135. Yoshimura A, Koketsu M, Bando H, Saiki E, Suzuki M, Watanabe Y, Kanuka H, Fukumoto S (2014) Phylogenetic comparison of avian Haemosporidian parasites from resident and migratory birds in northern Japan. J Wildl Dis 50(2):235–242