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Chapter 11 : Comparative Microbial Genomics and Forensics

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Abstract:

Microbes are phylogenetically diverse and are comprised of viruses, archaea, bacteria, fungi, protozoa, microalgae, and microscopic metazoa. These organisms are invisible to the naked eye, but all contain unique genome DNA sequences (or RNA in the case of some viruses). The genomes of microbes range in size from ∼13 kb for the smallest RNA viruses and up to several hundred megabases in the case of microscopic planarians. Thus, each genome contains a large amount of sequence information that may allow the classification and characterization of these microbes, which often have few morphological characters to allow them to be distinguished. We are now living in an era whereby complete genome sequences can be generated by individual researchers and may be analyzed using computational techniques, revealing a range of insights into the lifestyle, phylogenetic origin, degree of genetic modification, and pathogenic mechanism of the microbes concerned. Such comparison of the complete genome sequences of microbes is termed comparative microbial genomics.

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Figure 1a

Metagenomic fingerprints and their applications. Example of a microbial meta-metabolomic network generated from human skin. Meta-metabolomic networks represent a novel way of interpreting metagenomic data, and certain microhabitats may have characteristic “fingerprints” reflected in the metabolism of the microbial community, irrespective of the particular taxonomic composition. Thus, such a profile can in principle reveal the origin of the sample, using biochemical considerations and comparison with reference datasets. The methodology for construction of the network was as follows. DNA was isolated from microbes isolated from the left retroauricular crease (behind the ear). This was then subjected to shotgun sequencing using the Illumina platform. The sequences were downloaded from the Human Microbiome Project webpage (http://www.hmpdacc.org/HMASM/; identification number SRS ID SRS013258). These were then used to query the NCBI nonredundant database using BLAST. Significant hits were mapped to KEGG K numbers ( ), representing the respective biochemical reaction that each protein is involved in, and then superimposed onto a network of central metabolism using iPath2.0 ( ).

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Image of Figure 1b
Figure 1b

Metagenomic fingerprints and their applications. Comparative metagenomics of soil microbial communities. A comparative metagenomics analysis of bacterial communities present in different soil types is shown. Community profiles were generated from each sample using NGS of 16S rRNA PCR products generated from environmental DNA extracted from each habitat. Then, the different profiles were compared using principal-component analysis. Bacterial communities present in soil obtained from hot deserts, cold deserts, and forests cluster separately. Reproduced from reference .

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Figure 2a

Plotting the phylogenetics of an infectious outbreak. Phylogenetic network of strain O104:H4 and related genomes. A minimum spanning tree of strain O104:H4 was created using allelic profiles of the core genome, which contains 1,144 genes. Each node represents a complete genome; numbers on the lines connecting nodes represent numbers of alleles that differ between genomes. Different colors represent different pathovars (enterohemorrhagic [EHEC], enteroaggregative [EAEC], extraintestinal pathogenic [ExPEC], enteropathogenic [EPEC], enterotoxigenic [ETEC], and commensals). A hypothetical O104:H4 progenitor (green) was created by ancestral sequence reconstruction. Reproduced from reference .

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Figure 2b

Plotting the phylogenetics of an infectious outbreak. Phylogenetic tree of HIV gp120 using sequences from the criminal case ( ). Six case individuals were included in the analysis, WA01 to WA06. WA04 (red) sequences were obtained from the defendant; WA01 to WA03, WA05, and WA06 were from the other case individuals, and black indicates outgroup sequences obtained from the GenBank database. Color gradients represent events of transmission from WA04 to other individuals. The red circle represents the most recent common ancestor of the WA04 sequences. Branch numbers represent statistical support (Bayesian posterior probability/maximum likelihood bootstrap proportion). Values of <0.5 are indicated by a dash or are not shown.

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Figure 3

Genome of strain O104:H4. The nine circles show different strains of O104:H4, 559589 being the original isolate. Annotations on the outside of the circles show positions of transposons, while three plasmids, pTY1 to pTY3, are also included. pTY2 is an aggregative plasmid carrying a fimbria gene that is responsible for the enteroaggregative phenotype of the strain and has been linked to virulence. In green is a variable region, also associated with pathogenicity. Reproduced from reference .

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Figure 4a

Pandemics of the past: the Black Death and Spanish flu. Two microbial genomes of pathogens involved in severe historical pandemics have been recovered and sequenced. These are of the bacterial strain that caused the Black Death and the influenza virus strain that caused the Spanish flu. The severe effects of these epidemics are illustrated by these photos. () Plague pit from medieval Venice (photo reproduced with kind permission of Michel Drancourt, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Université de la Méditerranée, Marseille, France). Bodies were unceremoniously thrown into the pit, indicating the severity with which the epidemic struck the community. PCR was used to amplify sequences from ancient DNA obtained from the pit ( ).

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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Figure 4b

Pandemics of the past: the Black Death and Spanish flu. Two microbial genomes of pathogens involved in severe historical pandemics have been recovered and sequenced. These are of the bacterial strain that caused the Black Death and the influenza virus strain that caused the Spanish flu. The severe effects of these epidemics are illustrated by these photos. Treatment center for victims of the Spanish flu in the main drill hall of the Naval Training Center, San Francisco, CA, 1918, showing the scale of the epidemic (U.S. Naval History and Heritage Command photograph).

Citation: Massey S. 2018. Comparative Microbial Genomics and Forensics, p 239-276. In Cano R, Toranzos G (ed), Environmental Microbial Forensics. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.EMF-0001-2013
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References

/content/book/10.1128/9781555818852.chap11
1. Fleischmann RD, , et al . 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269 : 496 512.[PubMed][CrossRef]
2. Miller RR,, Montoya V,, Gardy JL,, Patrick DM,, Tang P . 2013. Metagenomics for pathogen detection in public health. Genome Med 5 : 81.[PubMed][CrossRef]
3. Padmanabhan R,, Mishra AK,, Raoult D,, Fournier PE . 2013. Genomics and metagenomics in medical microbiology. J Microbiol Methods 95 : 415 424.[PubMed][CrossRef]
4. Bromham L,, Penny D . 2003. The modern molecular clock. Nat Rev Genet 4 : 216 224.[PubMed][CrossRef]
5. Pulquério MJ,, Nichols RA . 2007. Dates from the molecular clock: how wrong can we be? Trends Ecol Evol 22 : 180 184.[PubMed][CrossRef]
6. Metzker ML,, Mindell DP,, Liu X-M,, Ptak RG,, Gibbs RA,, Hillis DM . 2002. Molecular evidence of HIV-1 transmission in a criminal case. Proc Natl Acad Sci USA 99 : 14292 14297.[PubMed][CrossRef]
7. Albert J,, Wahlberg J,, Leitner T,, Escanilla D,, Uhlén M . 1994. Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes. J Virol 68 : 5918 5924.[PubMed]
8. Birch CJ,, McCaw RF,, Bulach DM,, Revill PA,, Carter JT,, Tomnay J,, Hatch B,, Middleton TV,, Chibo D,, Catton MG,, Pankhurst JL,, Breschkin AM,, Locarnini SA,, Bowden DS . 2000. Molecular analysis of human immunodeficiency virus strains associated with a case of criminal transmission of the virus. J Infect Dis 182 : 941 944.[PubMed][CrossRef]
9. Banaschak S,, Werwein M,, Brinkmann B,, Hauber I . 2000. Human immunodeficiency virus type 1 infection after sexual abuse: value of nucleic acid sequence analysis in identifying the offender. Clin Infect Dis 31 : 1098 1100.[PubMed][CrossRef]
10. Machuca R,, Jørgensen LB,, Theilade P,, Nielsen C . 2001. Molecular investigation of transmission of human immunodeficiency virus type 1 in a criminal case. Clin Diagn Lab Immunol 8 : 884 890.[PubMed][CrossRef]
11. Lemey P,, Van Dooren S,, Van Laethem K,, Schrooten Y,, Derdelinckx I,, Goubau P,, Brun-Vézinet F,, Vaira D,, Vandamme AM . 2005. Molecular testing of multiple HIV-1 transmissions in a criminal case. AIDS 19 : 1649 1658.[PubMed][CrossRef]
12. Achtman M . 2012. Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 367 : 860 867.[PubMed][CrossRef]
13. Bos KI,, Schuenemann VJ,, Golding GB,, Burbano HA,, Waglechner N,, Coombes BK,, McPhee JB,, DeWitte SN,, Meyer M,, Schmedes S,, Wood J,, Earn DJ,, Herring DA,, Bauer P,, Poinar HN,, Krause J . 2011. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478 : 506 510.[PubMed][CrossRef]
14. Jolley KA,, Maiden MCJ . 2010. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11 : 595.[PubMed][CrossRef]
15. Jolley KA,, Hill DM,, Bratcher HB,, Harrison OB,, Feavers IM,, Parkhill J,, Maiden MC . 2012. Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods. J Clin Microbiol 50 : 3046 3053.[PubMed][CrossRef]
16. Bryant D,, Moulton V . 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21 : 255 265.[PubMed][CrossRef]
17. Huson DH,, Bryant D . 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23 : 254 267.[PubMed][CrossRef]
18. Didelot X,, Falush D . 2007. Inference of bacterial microevolution using multilocus sequence data. Genetics 175 : 1251 1266.[PubMed][CrossRef]
19. Gardy JL,, Johnston JC,, Ho Sui SJ,, 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 SJ,, Brinkman FS,, Brunham RC,, Tang P . 2011. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364 : 730 739.[PubMed][CrossRef]
20. Linz B,, Balloux F,, Moodley Y,, Manica A,, Liu H,, Roumagnac P,, Falush D,, Stamer C,, Prugnolle F,, van der Merwe SW,, Yamaoka Y,, Graham DY,, Perez-Trallero E,, Wadstrom T,, Suerbaum S,, Achtman M . 2007. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445 : 915 918.[PubMed][CrossRef]
21. Ong C-K,, Chan SY,, Campo MS,, Fujinaga K,, Mavromara-Nazos P,, Labropoulou V,, Pfister H,, Tay SK,, ter Meulen J,, Villa LL,, Bernard H-U . 1993. Evolution of human papillomavirus type 18: an ancient phylogenetic root in Africa and intratype diversity reflect coevolution with human ethnic groups. J Virol 67 : 6424 6431.[PubMed]
22. Gessain A,, Boeri E,, Yanagihara R,, Gallo RC,, Franchini G . 1993. Complete nucleotide sequence of a highly divergent human T-cell leukemia (lymphotropic) virus type I (HTLV-I) variant from melanesia: genetic and phylogenetic relationship to HTLV-I strains from other geographical regions. J Virol 67 : 1015 1023.[PubMed]
23. Fierer N,, Lauber CL,, Zhou N,, McDonald D,, Costello EK,, Knight R . 2010. Forensic identification using skin bacterial communities. Proc Natl Acad Sci USA 107 : 6477 6481.[PubMed][CrossRef]
24. Tims S,, van Wamel W,, Endtz HP,, van Belkum A,, Kayser M . 2010. Microbial DNA fingerprinting of human fingerprints: dynamic colonization of fingertip microflora challenges human host inferences for forensic purposes. Int J Legal Med 124 : 477 481.[PubMed][CrossRef]
25. Meyer F,, Paarmann D,, D’Souza M,, Olson R,, Glass EM,, Kubal M,, Paczian T,, Rodriguez A,, Stevens R,, Wilke A,, Wilkening J,, Edwards RA . 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9 : 386.[PubMed][CrossRef]
26. Henry JB,, Smith FA . 1980. Estimation of the postmortem interval by chemical means. Am J Forensic Med Pathol 1 : 341 347.[PubMed][CrossRef]
27. Huang P,, Tian W,, Tuo Y,, Wang Z,, Yang G . 2009. Estimation of postmortem interval in rat liver and spleen using Fourier transform infrared spectroscopy. Spectrosc Lett 42 : 108 116.[CrossRef]
28. Wheelis M . 2002. Biological warfare at the 1346 siege of Caffa. Emerg Infect Dis 8 : 971 975.[PubMed][CrossRef]
29. Riedel S . 2004. Biological warfare and terrorism: a historical review. Proc (Bayl Univ Med Cent) 17 : 400 406.[PubMed]
30. Robertson AG,, Robertson LJ . 1995. From asps to allegations: biological warfare in history. Mil Med 160 : 369 373.[PubMed]
31. Mayor A . 2003. Greek Fire, Poison Arrows, and Scorpion Bombs: Biological and Chemical Warfare in the Ancient World. The Overlook Press, Woodstock, NY.
32. Christopher GW,, Cieslak TJ,, Pavlin JA,, Eitzen, Jr . 1997. Biological warfare. A historical perspective. JAMA 278 : 412 417.[PubMed][CrossRef]
33. Takahashi H,, Keim P,, Kaufmann AF,, Keys C,, Smith KL,, Taniguchi K,, Inouye S,, Kurata T . 2004. Bacillus anthracis incident, Kameido, Tokyo, 1993. Emerg Infect Dis 10 : 117 120.[PubMed][CrossRef]
34. 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.[PubMed][CrossRef]
35. 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 USA 108 : 5027 5032.[PubMed][CrossRef]
36. Meselson M,, Guillemin J,, Hugh-Jones M,, Langmuir A,, Popova I,, Shelokov A,, Yampolskaya O . 1994. The Sverdlovsk anthrax outbreak of 1979. Science 266 : 1202 1208.[PubMed][CrossRef]
37. Gao F,, Bailes E,, Robertson DL,, Chen Y,, Rodenburg CM,, Michael SF,, Cummins LB,, Arthur LO,, Peeters M,, Shaw GM,, Sharp PM,, Hahn BH . 1999. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397 : 436 441.[PubMed][CrossRef]
38. Corbet S,, Müller-Trutwin MC,, Versmisse P,, Delarue S,, Ayouba A,, Lewis J,, Brunak S,, Martin P,, Brun-Vezinet F,, Simon F,, Barre-Sinoussi F,, Mauclere P . 2000. env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area. J Virol 74 : 529 534.[PubMed][CrossRef]
39. Plantier J-C,, Leoz M,, Dickerson JE,, De Oliveira F,, Cordonnier F,, Lemée V,, Damond F,, Robertson DL,, Simon F . 2009. A new human immunodeficiency virus derived from gorillas. Nat Med 15 : 871 872.[PubMed][CrossRef]
40. Santiago ML,, Range F,, Keele BF,, Li Y,, Bailes E,, Bibollet-Ruche F,, Fruteau C,, Noë R,, Peeters M,, Brookfield JF,, Shaw GM,, Sharp PM,, Hahn BH . 2005. Simian immunodeficiency virus infection in free-ranging sooty mangabeys ( Cercocebus atys atys) from the Taï Forest, Côte d’Ivoire: implications for the origin of epidemic human immunodeficiency virus type 2. J Virol 79 : 12515 12527.[PubMed][CrossRef]
41. Lemey P,, Pybus OG,, Rambaut A,, Drummond AJ,, Robertson DL,, Roques P,, Worobey M,, Vandamme A-M . 2004. The molecular population genetics of HIV-1 group O. Genetics 167 : 1059 1068.[PubMed][CrossRef]
42. Korber B,, Muldoon M,, Theiler J,, Gao F,, Gupta R,, Lapedes A,, Hahn BH,, Wolinsky S,, Bhattacharya T . 2000. Timing the ancestor of the HIV-1 pandemic strains. Science 288 : 1789 1796.[PubMed][CrossRef]
43. Lemey P,, Pybus OG,, Wang B,, Saksena NK,, Salemi M,, Vandamme A-M . 2003. Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci USA 100 : 6588 6592.[PubMed][CrossRef]
44. Zhao K,, Ishida Y,, Oleksyk TK,, Winkler CA,, Roca AL . 2012. Evidence for selection at HIV host susceptibility genes in a West Central African human population. BMC Evol Biol 12 : 237.[PubMed][CrossRef]
45. Pomerantsev AP,, Staritsin NA,, Mockov YV,, Marinin LI . 1997. Expression of cereolysine AB genes in Bacillus anthracis vaccine strain ensures protection against experimental hemolytic anthrax infection. Vaccine 15 : 1846 1850.[CrossRef]
46. Herfst S,, Schrauwen EJ,, Linster M,, Chutinimitkul S,, de Wit E,, Munster VJ,, Sorrell EM,, Bestebroer TM,, Burke DF,, Smith DJ,, Rimmelzwaan GF,, Osterhaus AD,, Fouchier RA . 2012. Airborne transmission of influenza A/H5N1 virus between ferrets. Science 336 : 1534 1541.[PubMed][CrossRef]
47. Imai M,, Watanabe T,, Hatta M,, Das SC,, Ozawa M,, Shinya K,, Zhong G,, Hanson A,, Katsura H,, Watanabe S,, Li C,, Kawakami E,, Yamada S,, Kiso M,, Suzuki Y,, Maher EA,, Neumann G,, Kawaoka Y . 2012. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 486 : 420 428.[PubMed][CrossRef]
48. Cello J,, Paul AV,, Wimmer E . 2002. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297 : 1016 1018.[PubMed][CrossRef]
49. Kobasa D,, Jones SM,, Shinya K,, Kash JC,, Copps J,, Ebihara H,, Hatta Y,, Kim JH,, Halfmann P,, Hatta M,, Feldmann F,, Alimonti JB,, Fernando L,, Li Y,, Katze MG,, Feldmann H,, Kawaoka Y . 2007. Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 445 : 319 323.[PubMed][CrossRef]
50. Altschul SF,, Gish W,, Miller W,, Myers EW,, Lipman DJ . 1990. Basic local alignment search tool. J Mol Biol 215 : 403 410.[PubMed][CrossRef]
51. Ewald PW . 1996. Guarding against the most dangerous emerging pathogens. Emerg Infect Dis 2 : 245 257.[PubMed][CrossRef]
52. Snitkin ES,, Zelazny AM,, Thomas PJ,, Stock F,, Henderson DK,, Palmore TN,, Segre JA, NISC Comparative Sequencing Program Group . 2012. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4 : 148ra116.[PubMed][CrossRef]
53. Harris SR,, Cartwright EJ,, Török ME,, Holden MT,, Brown NM,, Ogilvy-Stuart AL,, Ellington MJ,, Quail MA,, Bentley SD,, Parkhill J,, Peacock SJ . 14 November 2012. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis.http://dx.doi.org/10.1016/S1473-3099(12)70268-2
54. Ben Zakour NL,, Venturini C,, Beatson SA,, Walker MJ . 2012. Analysis of a Streptococcus pyogenes puerperal sepsis cluster by use of whole-genome sequencing. J Clin Microbiol 50 : 2224 2228.[PubMed][CrossRef]
55. Allen HK,, Donato J,, Wang HH,, Cloud-Hansen KA,, Davies J,, Handelsman J . 2010. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 8 : 251 259.[PubMed][CrossRef]
56. Cantón R . 2009. Antibiotic resistance genes from the environment: a perspective through newly identified antibiotic resistance mechanisms in the clinical setting. Clin Microbiol Infect 15( Suppl 1) : 20 25.[PubMed][CrossRef]
57. Rohde H,, Qin J,, Cui Y,, Li D,, Loman NJ,, Hentschke M,, Chen W,, Pu F,, Peng Y,, Li J,, Xi F,, Li S,, Li Y,, Zhang Z,, Yang X,, Zhao M,, Wang P,, Guan Y,, Cen Z,, Zhao X,, Christner M,, Kobbe R,, Loos S,, Oh J,, Yang L,, Danchin A,, Gao GF,, Song Y,, Li Y,, Yang H,, Wang J,, Xu J,, Pallen MJ,, Wang J,, Aepfelbacher M,, Yang R, E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium . 2011. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365 : 718 724.[PubMed][CrossRef]
58. Loman NJ,, Constantinidou C,, Christner M,, Rohde H,, Chan JZM,, Quick J,, Weir JC,, Quince C,, Smith GP,, Betley JR,, Aepfelbacher M,, Pallen MJ . 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.[PubMed][CrossRef]
59. Surowiecki J . 2004. The Wisdom of Crowds: Why the Many Are Smarter Than the Few and How Collective Wisdom Shapes Business, Economies, Societies and Nations. Doubleday, New York, NY.[PubMed]
60. Whitby S,, Rogers P . 1997. Anti-crop biological warfare—implications of the Iraqi and US programs. Def Anal 13 : 303 318.[CrossRef]
61. Cottam EM,, Wadsworth J,, Knowles NJ,, King DP . 2009. Full sequencing of viral genomes: practical strategies used for the amplification and characterization of foot-and-mouth disease virus. Methods Mol Biol 551 : 217 230.[PubMed][CrossRef]
62. Cottam EM,, Thébaud G,, Wadsworth J,, Gloster J,, Mansley L,, Paton DJ,, King DP,, Haydon DT . 2008. Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc Biol Sci 275 : 887 895.[PubMed][CrossRef]
63. Flowerdew JR,, Trout RC,, Ross J . 1992. Myxomatosis: population dynamics of rabbits ( Oryctolagus cuniculus Linnaeus, 1758) and ecological effects in the United Kingdom. Rev Sci Tech 11 : 1109 1113.[PubMed][CrossRef]
64. dos Santos HF,, Cury JC,, do Carmo FL,, dos Santos AL,, Tiedje J,, van Elsas JD,, Rosado AS,, Peixoto RS . 2011. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS One 6 : e16943.[PubMed][CrossRef]
65. Lazzaro A,, Widmer F,, Sperisen C,, Frey B . 2008. Identification of dominant bacterial phylotypes in a cadmium-treated forest soil. FEMS Microbiol Ecol 63 : 143 155.[PubMed][CrossRef]
66. Hemme CL,, Deng Y,, Gentry TJ,, Fields MW,, Wu L,, Barua S,, Barry K,, Tringe SG,, Watson DB,, He Z,, Hazen TC,, Tiedje JM,, Rubin EM,, Zhou J . 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4 : 660 672.[PubMed][CrossRef]
67. Tringe SG,, Zhang T,, Liu X,, Yu Y,, Lee WH,, Yap J,, Yao F,, Suan ST,, Ing SK,, Haynes M,, Rohwer F,, Wei CL,, Tan P,, Bristow J,, Rubin EM,, Ruan Y . 2010. The airborne metagenome in an indoor urban environment. PLoS One 3 : e1862.[PubMed]
68. Tran TN,, Signoli M,, Fozzati L,, Aboudharam G,, Raoult D,, Drancourt M . 2011. High throughput, multiplexed pathogen detection authenticates plague waves in medieval Venice, Italy. PLoS One 6 : e16735.[PubMed][CrossRef]
69. Stephens JC,, Reich DE,, Goldstein DB,, Shin HD,, Smith MW,, Carrington M,, Winkler C,, Huttley GA,, Allikmets R,, Schriml L,, Gerrard B,, Malasky M,, Ramos MD,, Morlot S,, Tzetis M,, Oddoux C,, di Giovine FS,, Nasioulas G,, Chandler D,, Aseev M,, Hanson M,, Kalaydjieva L,, Glavac D,, Gasparini P,, Kanavakis E,, Claustres M,, Kambouris M,, Ostrer H,, Duff G,, Baranov V,, Sibul H,, Metspalu A,, Goldman D,, Martin N,, Duffy D,, Schmidtke J,, Estivill X,, O’Brien SJ,, Dean M . 1998. Dating the origin of the CCR5-Δ32 AIDS-resistance allele by the coalescence of haplotypes. Am J Hum Genet 62 : 1507 1515.[PubMed][CrossRef]
70. Bos KI,, Stevens P,, Nieselt K,, Poinar HN,, Dewitte SN,, Krause J . 2012. Yersinia pestis: new evidence for an old infection. PLoS One 7 : e49803.[PubMed][CrossRef]
71. Johnson NP,, Mueller J . 2002. Updating the accounts: global mortality of the 1918–1920 “Spanish” influenza pandemic. Bull Hist Med 76 : 105 115.[PubMed][CrossRef]
72. Taubenberger JK,, Reid AH,, Lourens RM,, Wang R,, Jin G,, Fanning TG . 2005. Characterization of the 1918 influenza virus polymerase genes. Nature 437 : 889 893.[PubMed][CrossRef]
73. Kobasa D,, Takada A,, Shinya K,, Hatta M,, Halfmann P,, Theriault S,, Suzuki H,, Nishimura H,, Mitamura K,, Sugaya N,, Usui T,, Murata T,, Maeda Y,, Watanabe S,, Suresh M,, Suzuki T,, Suzuki Y,, Feldmann H,, Kawaoka Y . 2004. Enhanced virulence of influenza A viruses with the haemagglutinin of the 1918 pandemic virus. Nature 431 : 703 707.[PubMed][CrossRef]
74. Neumann G,, Watanabe T,, Ito H,, Watanabe S,, Goto H,, Gao P,, Hughes M,, Perez DR,, Donis R,, Hoffmann E,, Hobom G,, Kawaoka Y . 1999. Generation of influenza A viruses entirely from cloned cDNAs. Proc Natl Acad Sci USA 96 : 9345 9350.[PubMed][CrossRef]
75. Vana G,, Westover KM . 2008. Origin of the 1918 Spanish influenza virus: a comparative genomic analysis. Mol Phylogenet Evol 47 : 1100 1110.[PubMed][CrossRef]
76. de Oviedo GF . 1526. Sumario de la natural historia de las Indias. Toledo, Spain.
77. Steinbock RT . 1976. Paleopathological Diagnosis and Interpretation: Bone Disease in Ancient Human Populations. CC Thomas, Springfield, IL.[PubMed]
78. Harper KN,, Ocampo PS,, Steiner BM,, George RW,, Silverman MS,, Bolotin S,, Pillay A,, Saunders NJ,, Armelagos GJ . 2008. On the origin of the treponematoses: a phylogenetic approach. PLoS Negl Trop Dis 2 : e148.[PubMed][CrossRef]
79. Papagrigorakis MJ,, Yapijakis C,, Synodinos PN,, Baziotopoulou-Valavani E . 2006. DNA examination of ancient dental pulp incriminates typhoid fever as a probable cause of the Plague of Athens. Int J Infect Dis 10 : 206 214.[PubMed][CrossRef]
80. Shapiro B,, Rambaut A,, Gilbert MTP . 2006. No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.). Int J Infect Dis 10 : 334 335. (Author reply, 335–336).[PubMed][CrossRef]
81. Cunha BA . 2004. The cause of the plague of Athens: plague, typhoid, typhus, smallpox, or measles? Infect Dis Clin North Am 18 : 29 43.[PubMed][CrossRef]
82. Olson PE,, Hames CS,, Benenson AS,, Genovese EN . 1996. The Thucydides syndrome: Ebola déjà vu? (or Ebola reemergent?). Emerg Infect Dis 2 : 155 156.[PubMed][CrossRef]
83. Hawass Z,, Shafik M,, Rühli FJ,, Selim A,, El-Sheik E,, Abdel Fatah S,, Amer H,, Gaballa F,, Gamal Eldin A,, Egarter-Vigl E,, Gostner P . 2009. Computed tomographic evaluation of King Tutankhamun, ca. 1300 BC. Ann Serv Antiq Egypte 81 : 159 174.
84. Ashrafian H . 2012. Familial epilepsy in the pharaohs of ancient Egypt’s eighteenth dynasty. Epilepsy Behav 25 : 23 31.[PubMed][CrossRef]
85. Pays JF . 2010. Tutankhamun and sickle-cell anaemia. Bull Soc Pathol Exot 103 : 346 347(InFrench).[PubMed][CrossRef]
86. Hawass Z,, Gad YZ,, Ismail S,, Khairat R,, Fathalla D,, Hasan N,, Ahmed A,, Elleithy H,, Ball M,, Gaballah F,, Wasef S,, Fateen M,, Amer H,, Gostner P,, Selim A,, Zink A,, Pusch CM . 2010. Ancestry and pathology in King Tutankhamun’s family. JAMA 303 : 638 647.[PubMed][CrossRef]
87. López C,, Saravia C,, Gomez A,, Hoebeke J,, Patarroyo MA . 2010. Mechanisms of genetically-based resistance to malaria. Gene 467 : 1 12.[PubMed][CrossRef]
88. Cunha BA . 2004. The death of Alexander the Great: malaria or typhoid fever? Infect Dis Clin North Am 18 : 53 63.[PubMed][CrossRef]
89. Ashrafian H . 2004. The death of Alexander the Great—a spinal twist of fate. J Hist Neurosci 13 : 138 142.[PubMed][CrossRef]
90. Oldach DW,, Richard RE,, Borza EN,, Benitez RM . 1998. A mysterious death. N Engl J Med 338 : 1764 1769.[PubMed][CrossRef]
91. Marr JS,, Calisher CH . 2003. Alexander the Great and West Nile virus encephalitis. Emerg Infect Dis 9 : 1599 1603.[PubMed][CrossRef]
92. Orlova A . 1990. Tchaikovsky: A Self-Portrait. Oxford University Press, Oxford, United Kingdom.
93. Kornhauser P . 2010. The cause of P.I. Tchaikovsky’s (1840–1893) death: cholera, suicide, or both? Acta Med Hist Adriat 8 : 145 172.[PubMed]
94. Holden A . 1996. Tchaikovsky: A biography. Random House, New York, NY.
95. Thornton JW,, Need E,, Crews D . 2003. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301 : 1714 1717.[PubMed][CrossRef]
96. Ugalde JA,, Chang BSW,, Matz MV . 2004. Evolution of coral pigments recreated. Science 305 : 1433.[PubMed][CrossRef]
97. Tuller T,, Birin H,, Gophna U,, Kupiec M,, Ruppin E . 2010. Reconstructing ancestral gene content by coevolution. Genome Res 20 : 122 132.[PubMed][CrossRef]
98. Tanabe M,, Kanehisa M . 2012. Using the KEGG database resource. Curr Protoc Bioinformatics Chapter 1: Unit 1.12.[CrossRef]
99. Yamada T,, Letunic I,, Okuda S,, Kanehisa M,, Bork P . 2011. iPath2.0: interactive pathway explorer. Nucleic Acids Res 39( Suppl) : W412 W415.[PubMed][CrossRef]
100. Fierer N,, Leff JW,, Adams BJ,, Nielsen UN,, Bates ST,, Lauber CL,, Owens S,, Gilbert JA,, Wall DH,, Caporaso JG . 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109 : 21390 21395.[PubMed][CrossRef]
101. 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.[PubMed][CrossRef]
102. Scaduto DI,, Brown JM,, Haaland WC,, Zwickl DJ,, Hillis DM,, Metzker ML . 2010. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences. Proc Natl Acad Sci USA 107 : 21242 21247.[PubMed][CrossRef]
103. Grad YH,, Godfrey P,, Cerquiera GC,, Mariani-Kurkdjian P,, Gouali M,, Bingen E,, Shea TP,, Haas BJ,, Griggs A,, Young S,, Zeng Q,, Lipsitch M,, Waldor MK,, Weill FX,, Wortman JR,, Hanage WP . 2013. Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. mBio 4 : e00452-12.[PubMed][CrossRef]

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