Chapter 15 : Genomic and Metagenomic Approaches for Predicting Pathogen Evolution

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Genomic and Metagenomic Approaches for Predicting Pathogen Evolution, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818432/9781555818425_Chap15-1.gif /docserver/preview/fulltext/10.1128/9781555818432/9781555818425_Chap15-2.gif


Emerging infectious diseases have been defined as microbial infections “whose incidence in humans has increased in the past 2 decades or threatens to increase in the near future” ( ). Microbial causes of emerging infectious diseases generally fall into two groups: (i) new pathogens that arise following environmental disturbance or acquisition of novel virulence traits and (ii) existing and known pathogens that have spread to new geographic areas or populations. In both cases, human activities play a key role in the evolution and transmission of these diseases. Human disruption of the natural environment alters not only the physical landscape but also the invisible microbial landscape. This process can facilitate transfer of virulence genes to new hosts or exposure of naïve hosts to previously unidentified pathogens. Due to the tremendous impact of emerging diseases on human and animal populations, we need a better understanding of how new diseases evolve and how to detect emerging diseases in order to develop more effective ways to predict outbreaks before they happen.

Citation: Casas V, Maloy S. 2014. Genomic and Metagenomic Approaches for Predicting Pathogen Evolution, p 227-235. In Atlas R, Maloy S (ed), One Health. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.OH-0019-2013
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Centers for Disease Control and Prevention . 2010. Emerging Infectious Diseases journal background and goals. Centers for Disease Control and Prevention, Atlanta, GA. http://wwwnc.cdc.gov/eid/pages/background-goals.htm (last accessed April 2, 2013).
2. Parmesan C . 2006. Ecological and evolutionary responses to recent climate change. Annu Rev Ecol Evol Syst 37 : 637 669.
3. Cione JJ,, Uhlhorn EW . 2003. Sea surface temperature variability in hurricanes: implications with respect to intensity change. Mon Weather Rev 131 : 1783 1796.
4. Rohwer F,, Youle M,, Vosten D . 2010. Coral Reefs in the Microbial Seas. Plaid Press, Basalt, CO.
5. Casas V,, Sobrepeña G,, Rodriguez-Mueller B,, Ahtye J,, Maloy SR . 2011. Bacteriophage-encoded shiga toxin gene in atypical bacterial host. Gut Pathog 3 : 10. doi:10.1186/1757-4749-3-10. [PubMed] [CrossRef]
6. Casas V,, Magbanua J,, Sobrepeña G,, Kelley ST,, Maloy SR . 2010. Reservoir of bacterial exotoxin genes in the environment. Int J Microbiol 2010 : 754368. doi:10.1155/2010/754368. [PubMed] [CrossRef]
7. Casas V,, Miyake J,, Balsley H,, Roark J,, Telles S,, Leeds S,, Zurita I,, Breitbart M,, Azam F,, Bartlett D,, Rohwer F . 2006. Widespread occurrence of phage-encoded exotoxin genes in terrestrial and aquatic environments in Southern California. FEMS Microbiol Lett 261 : 141 149. [PubMed] [CrossRef]
8. Harvell CD,, Mitchell CE,, Ward JR,, Altizer S,, Dobson AP,, Ostfeld RS,, Samuel MD . 2002. Climate warming and disease risks for terrestrial and marine biota. Science 296 : 2158 2162. [PubMed] [CrossRef]
9. Harvell CD,, Kim K,, Burkholder JM,, Colwell RR,, Epstein PR,, Grimes DJ,, Hofmann EE,, Lipp EK,, Osterhaus AD,, Overstreet RM,, Porter JW,, Smith GW,, Vasta GR . 1999. Emerging marine diseases—climate links and anthropogenic factors. Science 285 : 1505 1510. [PubMed]
10. Dearing MD,, Dizney L . 2010. Ecology of hantavirus in a changing world. Ann N Y Acad Sci 1195 : 99 112. [PubMed] [CrossRef]
11. Le Guenno B . 1997. Haemorrhagic fevers and ecological perturbations. Arch Virol Suppl 13 : 191 199. [PubMed]
12. Weil AA,, Ivers LC,, Harris JB . 2012. Cholera: lessons from Haiti and beyond. Curr Infect Dis Rep 14 : 1 8. [PubMed] [CrossRef]
13. Jutla AS,, Akanda AS,, Islam S . 2010. Tracking cholera in coastal regions using satellite observations. J Am Water Resour Assoc 46 : 651 662. [PubMed] [CrossRef]
14. Khasnis AA,, Nettleman MD . 2005. Global warming and infectious disease. Arch Med Res 36 : 689 696. [PubMed] [CrossRef]
15. Shuman EK . 2010. Global climate change and infectious diseases. N Engl J Med 362 : 1061 1063. [PubMed] [CrossRef]
16. Neerinckx S,, Bertherat E,, Leirs H . 2010. Human plague occurrences in Africa: an overview from 1877 to 2008. Trans R Soc Trop Med Hyg 104 : 97 103. [PubMed] [CrossRef]
17. Riesenfeld CS,, Schloss PD,, Handelsman J . 2004. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38 : 525 552. [PubMed] [CrossRef]
18. Handelsman J,, Rondon MR,, Brady SF,, Clardy J,, Goodman RM . 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5 : R245 R249. [PubMed]
19. Casas V,, Rohwer F . 2007. Phage metagenomics. Methods Enzymol 421 : 259 268. [PubMed] [CrossRef]
20. Gilbert JA,, Dupont CL . 2011. Microbial metagenomics: beyond the genome. Annu Rev Mar Sci 3 : 347 371. [PubMed]
21. Conlan S,, Kong HH,, Segre JA . 2012. Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PLoS One 7 : e47075. doi:10.1371/journal.pone.0047075. [PubMed] [CrossRef]
22. Gevers D,, Knight R,, Petrosino JF,, Huang K,, McGuire AL,, Birren BW,, Nelson KE,, White O,, Methé BA,, Huttenhower C . 2012. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol 10 : e1001377. doi:10.1371/journal.pbio.1001377. [PubMed] [CrossRef]
23. Ursell LK,, Metcalf JL,, Parfrey LW,, Knight R . 2012. Defining the human microbiome. Nutr Rev 70( Suppl 1) : S38 S44. [PubMed] [CrossRef]
24. Wylie KM,, Truty RM,, Sharpton TJ,, Mihindukulasuriya KA,, Zhou Y,, Gao H,, Sodergren E,, Weinstock GM,, Pollard KS . 2012. Novel bacterial taxa in the human microbiome. PLoS One 7 : e35294. doi:10.1371/journal.pone.0035294. [PubMed] [CrossRef]
25. Wooley JC,, Godzik A,, Friedberg I . 2010. A primer on metagenomics. PLoS Comput Biol 6 : e1000667. doi:10.1371/journal.pcbi.1000667. [PubMed] [CrossRef]
26. Breitbart M,, Salamon P,, Andresen B,, Mahaffy JM,, Segall AM,, Mead D,, Azam F,, Rohwer F . 2002. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99 : 14250 14255. [PubMed] [CrossRef]
27. Breitbart M,, Felts B,, Kelley S,, Mahaffy JM,, Nulton J,, Salamon P,, Rohwer F . 2004. Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci 271 : 565 574. [PubMed] [CrossRef]
28. Breitbart M,, Hewson I,, Felts B,, Mahaffy JM,, Nulton J,, Salamon P,, Rohwer F . 2003. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 85 : 6220 6223. [PubMed]
29. Cann AJ,, Fandrich SE,, Heaphy S . 2005. Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30 : 151 156. [PubMed] [CrossRef]
30. Culley AI,, Lang AS,, Suttle CA . 2006. Metagenomic analysis of coastal RNA virus communities. Science 312 : 1795 1798. [PubMed] [CrossRef]
31. Zhang T,, Breitbart M,, Lee WH,, Run JQ,, Wei CL,, Soh SW,, Hibberd ML,, Liu ET,, Rohwer F,, Ruan Y . 2006. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 4 : e3. doi:10.1371/journal.pbio.0040003. [PubMed] [CrossRef]
32. Willner D,, Furlan M,, Haynes M,, Schmieder R,, Angly FE,, Silva J,, Tammadoni S,, Nosrat B,, Conrad D,, Rohwer F . 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 4 : e7370. doi:10.1371/journal.pone.0007370. [PubMed] [CrossRef]
33. Edwards RA,, Rohwer F . 2005. Viral metagenomics. Nat Rev Microbiol 3 : 504 510. [PubMed] [CrossRef]
34. Deng Q,, Barbieri JT . 2008. Molecular mechanisms of the cytotoxicity of ADP-ribosylating toxins. Annu Rev Microbiol 62 : 271 288. [PubMed] [CrossRef]
35. Dayhoff MO,, Schwartz RM,, Orcutt BC, . 1978. A model of evolutionary change in proteins, p 345 352. In Dayhoff MO (ed), Atlas of Protein Sequence and Structure, vol. 5. National Biomedical Research Foundation, Washington, DC.
36. Murphy JR, . 1996. Chapter 32, Corynebacterium diphtheriae . In Baron S (ed), Medical Microbiology, 4th ed. University of Texas Medical Branch at Galveston, Galveston, TX. Available from http://www.ncbi.nlm.nih.gov/books/NBK7971/.
37. Pakalniskiene J,, Falkenhorst G,, Lisby M,, Madsen SB,, Olsen KE,, Nielsen EM,, Mygh A,, Boel J,, Mølbak K . 2009. A foodborne outbreak of enterotoxigenic E. coli and Salmonella anatum infection after a high-school dinner in Denmark, November 2006. Epidemiol Infect 137 : 396 401. [PubMed] [CrossRef]
38. Sekse C,, Muniesa M,, Wasteson Y . 2008. Conserved Stx2 phages from Escherichia coli O103:H25 isolated from patients suffering from hemolytic uremic syndrome. Foodborne Pathog Dis 5 : 801 810.
39. Vojdani JD,, Beuchat LR,, Tauxe RV . 2008. Juice-associated outbreaks of human illness in the United States, 1995 through 2005. J Food Prot 71 : 356 364. [PubMed]
40. Franz E,, van Bruggen AH . 2008. Ecology of E. coli O157:H7 and Salmonella enterica in the primary vegetable production chain. Crit Rev Microbiol 34 : 143 161. [PubMed] [CrossRef]
41. Charatan F . 2006. FDA warns US consumers not to eat spinach after E. coli outbreak. BMJ 333 : 673.
42. Lynch M,, Painter J,, Woodruff R,, Braden C , Centers for Disease Control and Prevention . 2006. Surveillance for foodborne-disease outbreaks—United States, 1998–2002. MMWR Surveill Summ 55 : 1 42. [PubMed]
43. Centers for Disease Control and Prevention (CDC) . 2006. Ongoing multistate outbreak of Escherichia coli serotype O157:H7 infections associated with consumption of fresh spinach—United States, September 2006. MMWR Morb Mortal Wkly Rep 55 : 10451046. [PubMed]
44. Devasia RA,, Jones TF,, Ward J,, Stafford L,, Hardin H,, Bopp C,, Beatty M,, Mintz E,, Schaffner W . 2006. Endemically acquired foodborne outbreak of enterotoxin-producing Escherichia coli serotype O169:H41. Am J Med 119 : 168.e7 168.e10. [PubMed] [CrossRef]
45. Scheutz F,, Nielsen EM,, Frimodt-Møller J,, Boisen N,, Morabito S,, Tozzoli R,, Nataro JP,, Caprioli A . 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. Euro Surveill 16 : pii=19889. http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19889. [PubMed]
46. Mellmann A,, Harmsen D,, Cummings CA,, Zentz EB,, Leopold SR,, Rico A,, Prior K,, Szczepanowski R,, Ji Y,, Zhang W,, McLaughlin SF,, Henkhaus JK,, Leopold B,, Bielaszewska M,, Prager R,, Brzoska PM,, Moore RL,, Guenther S,, Rothberg JM,, Karch H . 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. [PubMed] [CrossRef]
47. Brzuszkiewicz E,, Thürmer A,, Schuldes J,, Leimbach A,, Liesegang H,, Meyer FD,, Boelter J,, Petersen H,, Gottschalk G,, Daniel R . 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. [PubMed] [CrossRef]
48. Freeman BJ . 1951. Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae . J Bacteriol 61 : 675 688. [PubMed]
49. Groman NB . 1953. The relation of bacteriophage to the change of Corynebacterium diphtheriae from avirulence to virulence. Science 117 : 297 299. [PubMed]
50. Lenski RE,, Levin BR . 1985. Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communties. Am Nat 125 : 585 602.
51. Waldor MK,, Mekalanos JJ . 1996. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272 : 1910 1914. [PubMed]
52. Davis BM,, Moyer KE,, Boyd EF,, Waldor MK . 2000. CTX prophages in classical biotype Vibrio cholerae: functional phage genes but dysfunctional phage genomes. J Bacteriol 182 : 6992 6998. [PubMed]
53. Ochman H,, Lawrence JG,, Groisman EA . 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405 : 299 304. [PubMed] [CrossRef]
54. Boyd EF,, Davis BM,, Hochhut B . 2001. Bacteriophage-bacteriophage interactions in the evolution of pathogenic bacteria. Trends Microbiol 9 : 137 144. [PubMed]
55. Muniesa M,, Lucena F,, Jofre J . 1999. Study of the potential relationship between the morphology of infectious somatic coliphages and their persistence in the environment. J Appl Microbiol 87 : 402 409. [PubMed]
56. Muniesa M,, Lucena F,, Jofre J . 1999. Comparative survival of free Shiga toxin 2-encoding phages and Escherichia coli strains outside the gut. Appl Environ Microbiol 65 : 5615 5618. [PubMed]
57. Sinton LW,, Hall CH,, Lynch PA,, Davies-Colley RJ . 2002. Sunlight inactivation of fecal indicator bacteria and bacteriophages from waste stabilization pond effluent in fresh and saline waters. Appl Environ Microbiol 68 : 1122 1131. [PubMed]
58. Mocé-Llivina L,, Muniesa M,, Pimenta-Vale H,, Lucena F,, Jofre J . 2003. Survival of bacterial indicator species and bacteriophages after thermal treatment of sludge and sewage. Appl Environ Microbiol 69 : 1452 1456. [PubMed]
59. Tanji Y,, Mizoguchi K,, Yoichi M,, Morita M,, Kijima N,, Kator H,, Unno H . 2003. Seasonal change and fate of coliphages infected to Escherichia coli O157:H7 in a wastewater treatment plant. Water Res 37 : 1136 1142. [PubMed]
60. Dumke R,, Schröter-Bobsin U,, Jacobs E,, Röske I . 2006. Detection of phages carrying the Shiga toxin 1 and 2 genes in waste water and river water samples. Lett Appl Microbiol 42 : 48 53. [PubMed] [CrossRef]
61. Masago Y,, Katayama H,, Watanabe T,, Haramoto E,, Hashimoto A,, Omura T,, Hirata T,, Ohgaki S . 2006. Quantitative risk assessment of noroviruses in drinking water based on qualitative data in Japan. Environ Sci Technol 40 : 7428 7433. [PubMed]
62. McLaughlin MR,, Rose JB . 2006. Application of Bacteroides fragilis phage as an alternative indicator of sewage pollution in Tampa Bay, Florida. Estuar Coast 29 : 246 256.
63. Patz JA,, Daszak P,, Tabor GM,, Aguirre AA,, Pearl M,, Epstein J,, Wolfe ND,, Kilpatrick AM,, Foufopoulos J,, Molyneux D,, Bradley DJ , Working Group on Land Use Change and Disease Emergence . 2004. Unhealthy landscapes: policy recommendations on land use change and infectious disease emergence. Environ Health Perspect 112 : 1092 1098. [PubMed]
64. Schmidt KA,, Ostfeld RS . 2001. Biodiversity and the dilution effect in disease ecology. Ecology 82 : 609 619.
65. Chua KB,, Goh KJ,, Wong KT,, Kamarulzaman A,, Tan PS,, Ksiazek TG,, Zaki SR,, Paul G,, Lam SK,, Tan CT . 1999. Fatal encephalitis due to Nipah virus among pig-farmers in Malaysia. Lancet 354 : 1257 1259. [PubMed] [CrossRef]
66. Lam SK,, Chua KB . 2002. Nipah virus encephalitis outbreak in Malaysia. Clin Infect Dis 34( Suppl 2) : S48 S51. [PubMed] [CrossRef]
67. Rose JB,, Epstein PR,, Lipp EK,, Sherman BH,, Bernard SM,, Patz JA . 2001. Climate variability and change in the United States: potential impacts on water- and foodborne diseases caused by microbiologic agents. Environ Health Perspect 109 : 211 221. [PubMed] [CrossRef]
68. Ford TE,, Colwell RR,, Rose JB,, Morse SS,, Rogers DJ,, Yates TL . 2009. Using satellite images of environmental changes to predict infectious disease outbreaks. Emerg Infect Dis 15 : 1341 1346. [PubMed] [CrossRef]

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error