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Chapter 16 : Microbial Genomics and Pathogen Discovery*

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Microbial Genomics and Pathogen Discovery*, Page 1 of 2

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Abstract:

In recent years, our understanding of microbial diversity has grown tremendously as many previously unidentified bacterial, archaeal, and viral species have been discovered and sequenced. In the era of the human microbiome and metagenomics (chapter 15), large-scale DNA sequencing projects and advances in bioinformatics have yielded abundant data regarding human-associated microbes. As human microbiology rapidly expands beyond its past framework of cultured pathogens in the medical microbiology laboratory, opportunities for detection and identification of novel human pathogens associated with infectious diseases abound. In this chapter, we focus on specific or defined sets of pathogens associated with human infections, in contrast to microbial components of disease and microbial ecology. We begin with an overview of historical methodologies, followed by a brief description of the evolution of nucleic acid sequencing technologies. Finally, we describe how microarrays, nucleic acid sequencing technologies, and mass spectrometry are profoundly reshaping strategies aimed at pathogen discovery and identification.

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16
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FIGURE 1

A timeline depicting major landmarks in medical microbiology and molecular microbiology that have enhanced pathogen discovery. doi:10.1128/9781555817381.ch16.f1

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16
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Image of FIGURE 2
FIGURE 2

A proposed workflow for bacterial, WGS-based molecular diagnostics. This workflow uses benchtop sequencing for data generation and implements cloud storage for central data storage and remote data processing. Double-headed arrows indicate constant updating of the central data repository and reference database. Reprinted from reference with permission of Nature Publishing Group. doi:10.1128/9781555817381.ch16.f2

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16
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FIGURE 3

Phylogenetic analysis and genome assembly of , a novel organism associated with cord colitis. Assembly of the genome included unmappable reads generated from WGS of samples from patients with cord colitis. (A) Multisequence alignment of 400 core protein-coding genes was used to generate a rooted phylogenetic tree showing the predicted evolutionary relationships between and related species. (B) Genomic comparison of to . Dark blue lines on the inner circle depict genes present in the genome of that are absent in the genome of . The outer circle depicts amino acid sequence identity of each predicted protein to its closest homologue in . The middle circle is a representation of the contig assembly, with the borders of each contig (dark green) outlined in light green. Reprinted from with permission of Massachusetts Medical Society. doi:10.1128/9781555817381.ch16.f3

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16
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References

/content/book/10.1128/9781555817381.mcm11.ch16
1. Brosius J,, Palmer ML,, Kennedy PJ,, Noller HF. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 75:48014805.
2. Relman DA,, Loutit JS,, Schmidt TM,, Falkow S,, Tompkins LS. 1990. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med 323:15731580.
3. Relman DA,, Schmidt TM,, MacDermott RP,, Falkow S. 1992. Identification of the uncultured bacillus of Whipple’s disease. N Engl J Med 327:293301.
4. Nichol ST,, Spiropoulou CF,, Morzunov S,, Rollin PE,, Ksiazek TG,, Feldmann H,, Sanchez A,, Childs J,, Zaki S,, Peters CJ. 1993. Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness. Science 262:914917.
5. Kistler A,, Avila PC,, Rouskin S,, Wang D,, Ward T,, Yagi S,, Schnurr D,, Ganem D,, DeRisi JL,, Boushey HA. 2007. Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. J Infect Dis 196:817825.
6. Lamson D,, Renwick N,, Kapoor V,, Liu Z,, Palacios G,, Ju J,, Dean A,, St. George K,, Briese T,, Lipkin WI. 2006. MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004–2005. J Infect Dis 194:13981402.
7. Lau SK,, Yip CC,, Tsoi HW,, Lee RA,, So LY,, Lau YL,, Chan KH,, Woo PC,, Yuen KY. 2007. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children. J Clin Microbiol 45:36553664.
8. Lee WM,, Kiesner C,, Pappas T,, Lee I,, Grindle K,, Jartti T,, Jakiela B,, Lemanske RFJr,., Shult PA,, Gern JE. 2007. A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS One 2:e966. 10.1371/journal.pone.0000966.
9. McErlean P,, Shackelton LA,, Lambert SB,, Nissen MD,, Sloots TP,, Mackay IM. 2007. Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis. J Clin Virol 39:6775.
10. Al-Sunaidi M,, Williams CH,, Hughes PJ,, Schnurr DP,, Stanway G. 2007. Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains. J Virol 81:10131021.
11. Baumgarte S,, de Souza Luna LK,, Grywna K,, Panning M,, Drexler JF,, Karsten C,, Huppertz HI,, Drosten C. 2008. Prevalence, types, and RNA concentrations of human parechoviruses, including a sixth parechovirus type, in stool samples from patients with acute enteritis. J Clin Microbiol 46:242248.
12. Benschop KS,, Schinkel J,, Luken ME,, van den Broek PJ,, Beersma MF,, Menelik N,, van Eijk HW,, Zaaijer HL,, VandenBroucke-Grauls CM,, Beld MG,, Wolthers KC. 2006. Fourth human parechovirus serotype. Emerg Infect Dis 12:15721575.
13. Drexler JF,, Luna LK,, Stocker A,, Almeida PS,, Ribeiro TC,, Petersen N,, Herzog P,, Pedroso C,, Huppertz HI,, Ribeiro Hda CJr,, Baumgarte S,, Drosten C. 2008. Circulation of 3 lineages of a novel Saffold cardiovirus in humans. Emerg Infect Dis 14:13981405.
14. Li L,, Victoria J,, Kapoor A,, Naeem A,, Shaukat S,, Sharif S,, Alam MM,, Angez M,, Zaidi SZ,, Delwart E. 2009. Genomic characterization of novel human parechovirus type. Emerg Infect Dis 15:288291.
15. Watanabe K,, Oie M,, Higuchi M,, Nishikawa M,, Fujii M. 2007. Isolation and characterization of novel human parechovirus from clinical samples. Emerg Infect Dis 13:889895.
16. Delgado S,, Erickson BR,, Agudo R,, Blair PJ,, Vallejo E,, Albarino CG,, Vargas J,, Comer JA,, Rollin PE,, Ksiazek TG,, Olson JG,, Nichol ST. 2008. Chapare virus, a newly discovered arenavirus isolated from a fatal hemorrhagic fever case in Bolivia. PLoS Pathog 4:e1000047. 10.1371/journal.ppat.1000047.
17. Towner JS,, Sealy TK,, Khristova ML,, Albarino CG,, Conlan S,, Reeder SA,, Quan PL,, Lipkin WI,, Downing R,, Tappero JW,, Okware S,, Lutwama J,, Bakamutumaho B,, Kayiwa J,, Comer JA,, Rollin PE,, Ksiazek TG,, Nichol ST. 2008. Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 4:e1000212. 10.1371/journal.ppat.1000212.
18. Cotten M,, Watson SJ,, Kellam P,, Al-Rabeeah AA,, Makhdoom HQ,, Assiri A,, Al-Tawfiq JA,, Alhakeem RF,, Madani H,, AlRabiah FA,, Al Hajjar S,, Al-nassir WN,, Albarrak A,, Flemban H,, Balkhy HH,, Alsubaie S,, Palser AL,, Gall A,, Bashford-Rogers R,, Rambaut A,, Zumla AI,, Memish ZA. 2013. Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet 382:19932002.
19. Bhatt AS,, Freeman SS,, Herrera AF,, Pedamallu CS,, Gevers D,, Duke F,, Jung J,, Michaud M,, Walker BJ,, Young S,, Earl AM,, Kostic AD,, Ojesina AI,, Hasserjian R,, Ballen KK,, Chen YB,, Hobbs G,, Antin JH,, Soiffer RJ,, Baden LR,, Garrett WS,, Hornick JL,, Marty FM,, Meyerson M. 2013. Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med 369:517528.
20. Choo QL,, Kuo G,, Weiner AJ,, Overby LR,, Bradley DW,, Houghton M. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359362.
21. Chang Y,, Cesarman E,, Pessin MS,, Lee F,, Culpepper J,, Knowles DM,, Moore PS. 1994. Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi’s sarcoma. Science 266:18651869.
22. Woese CR,, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:50885090.
23. Fleischmann RD,, Adams MD,, White O,, Clayton RA,, Kirkness EF,, Kerlavage AR,, Bult CJ,, Tomb JF,, Dougherty BA,, Merrick JM, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
24. Goffeau A,, Barrell BG,, Bussey H,, Davis RW,, Dujon B,, Feldmann H,, Galibert F,, Hoheisel JD,, Jacq C,, Johnston M,, Louis EJ,, Mewes HW,, Murakami Y,, Philippsen P,, Tettelin H,, Oliver SG. 1996. Life with 6000 genes. Science 274:546, 563567.
25. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:20122018.
26. Cole ST,, Brosch R,, Parkhill J,, Garnier T,, Churcher C,, Harris D,, Gordon SV,, Eiglmeier K,, Gas S,, Barry CEIII,, Tekaia F,, Badcock K,, Basham D,, Brown D,, Chillingworth T,, Connor R,, Davies R,, Devlin K,, Feltwell T,, Gentles S,, Hamlin N,, Holroyd S,, Hornsby T,, Jagels K,, Krogh A,, McLean J,, Moule S,, Murphy L,, Oliver K,, Osborne J,, Quail MA,, Rajandream MA,, Rogers J,, Rutter S,, Seeger K,, Skelton J,, Squares R,, Squares S,, Sulston JE,, Taylor K,, Whitehead S,, Barrell BG. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537544.
27. Parkhill J,, Wren BW,, Thomson NR,, Titball RW,, Holden MT,, Prentice MB,, Sebaihia M,, James KD,, Churcher C,, Mungall KL,, Baker S,, Basham D,, Bentley SD,, Brooks K,, Cerdeno-Tarraga AM,, Chillingworth T,, Cronin A,, Davies RM,, Davis P,, Dougan G,, Feltwell T,, Hamlin N,, Holroyd S,, Jagels K,, Karlyshev AV,, Leather S,, Moule S,, Oyston PC,, Quail M,, Rutherford K,, Simmonds M,, Skelton J,, Stevens K,, Whitehead S,, Barrell BG. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523527.
28. Gardner MJ,, Hall N,, Fung E,, White O,, Berriman M,, Hyman RW,, Carlton JM,, Pain A,, Nelson KE,, Bowman S,, Paulsen IT,, James K,, Eisen JA,, Rutherford K,, Salzberg SL,, Craig A,, Kyes S,, Chan MS,, Nene V,, Shallom SJ,, Suh B,, Peterson J,, Angiuoli S,, Pertea M,, Allen J,, Selengut J,, Haft D,, Mather MW,, Vaidya AB,, Martin DM,, Fairlamb AH,, Fraunholz MJ,, Roos DS,, Ralph SA,, McFadden GI,, Cummings LM,, Subramanian GM,, Mungall C,, Venter JC,, Carucci DJ,, Hoffman SL,, Newbold C,, Davis RW,, Fraser CM,, Barrell B. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:498511.
29. Raoult D,, Audic S,, Robert C,, Abergel C,, Renesto P,, Ogata H,, La Scola B,, Suzan M,, Claverie JM. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306:13441350.
30. Mardis ER. 2008. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387402.
31. DeRisi JL,, Iyer VR,, Brown PO. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680686.
32. Wang D,, Coscoy L,, Zylberberg M,, Avila PC,, Boushey HA,, Ganem D,, DeRisi JL. 2002. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 99:1568715692.
33. Wang D,, Urisman A,, Liu YT,, Springer M,, Ksiazek TG,, Erdman DD,, Mardis ER,, Hickenbotham M,, Magrini V,, Eldred J,, Latreille JP,, Wilson RK,, Ganem D,, DeRisi JL. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol 1:E2. 10.1371/journal.pbio.0000002.
34. Eisen MB,, Spellman PT,, Brown PO,, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95:1486314868.
35. Palacios G,, Quan PL,, Jabado OJ,, Conlan S,, Hirschberg DL,, Liu Y,, Zhai J,, Renwick N,, Hui J,, Hegyi H,, Grolla A,, Strong JE,, Towner JS,, Geisbert TW,, Jahrling PB,, Buchen-Osmond C,, Ellerbrok H,, Sanchez-Seco MP,, Lussier Y,, Formenty P,, Nichol MS,, Feldmann H,, Briese T,, Lipkin WI. 2007. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis 13:7381.
36. Urisman A,, Fischer KF,, Chiu CY,, Kistler AL,, Beck S,, Wang D,, DeRisi JL. 2005. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol 6:R78. 10.1186/gb-2005-6-9-r78.
37. Watson M,, Dukes J,, Abu-Median AB,, King DP,, Britton P. 2007. DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data. Genome Biol 8:R190. 10.1186/gb-2007-8-9-r190.
38. Rehrauer H,, Schonmann S,, Eberl L,, Schlapbach R. 2008. PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics 24:i83i89.
39. Allred AF,, Wu G,, Wulan T,, Fischer KF,, Holbrook MR,, Tesh RB,, Wang D. 2010. VIPR: a probabilistic algorithm for analysis of microbial detection microarrays. BMC Bioinformatics 11:384. 10.1186/1471-2105-11-384.
40. Allred AF,, Renshaw H,, Weaver S,, Tesh RB,, Wang D. 2012. VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays. Bioinformatics 28:29222929.
41. Ksiazek TG,, Erdman D,, Goldsmith CS,, Zaki SR,, Peret T,, Emery S,, Tong S,, Urbani C,, Comer JA,, Lim W,, Rollin PE,, Dowell SF,, Ling AE,, Humphrey CD,, Shieh WJ,, Guarner J,, Paddock CD,, Rota P,, Fields B,, DeRisi J,, Yang JY,, Cox N,, Hughes JM,, LeDuc JW,, Bellini WJ,, Anderson LJ. 2003. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348:19531966.
42. Rota PA,, Oberste MS,, Monroe SS,, Nix WA,, Campagnoli R,, Icenogle JP,, Penaranda S,, Bankamp B,, Maher K,, Chen MH,, Tong S,, Tamin A,, Lowe L,, Frace M,, DeRisi JL,, Chen Q,, Wang D,, Erdman DD,, Peret TC,, Burns C,, Ksiazek TG,, Rollin PE,, Sanchez A,, Liffick S,, Holloway B,, Limor J,, McCaustland K,, Olsen-Rasmussen M,, Fouchier R,, Gunther S,, Osterhaus AD,, Drosten C,, Pallansch MA,, Anderson LJ,, Bellini WJ. 2003. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300: 13941399.
43. Chiu CY,, Alizadeh AA,, Rouskin S,, Merker JD,, Yeh E,, Yagi S,, Schnurr D,, Patterson BK,, Ganem D,, DeRisi JL. 2007. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. J Clin Microbiol 45:23402343.
44. Chiu CY,, Rouskin S,, Koshy A,, Urisman A,, Fischer K,, Yagi S,, Schnurr D,, Eckburg PB,, Tompkins LS,, Blackburn BG,, Merker JD,, Patterson BK,, Ganem D,, DeRisi JL. 2006. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Clin Infect Dis 43:e71e76.
45. Lin B,, Malanoski AP,, Wang Z,, Blaney KM,, Ligler AG,, Rowley RK,, Hanson EH,, von Rosenvinge E,, Ligler FS,, Kusterbeck AW,, Metzgar D,, Barrozo CP,, Russell KL,, Tibbetts C,, Schnur JM,, Stenger DA. 2007. Application of broad-spectrum, sequence-based pathogen identification in an urban population. PLoS One 2:e419. 10.1371/journal.pone.0000419.
46. Quan PL,, Palacios G,, Jabado OJ,, Conlan S,, Hirschberg DL,, Pozo F,, Jack PJ,, Cisterna D,, Renwick N,, Hui J,, Drysdale A,, Amos-Ritchie R,, Baumeister E,, Savy V,, Lager KM,, Richt JA,, Boyle DB,, Garcia-Sastre A,, Casas I,, Perez-Brena P,, Briese T,, Lipkin WI. 2007. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J Clin Microbiol 45:23592364.
47. Wong CW,, Heng CL,, Wan Yee L,, Soh SW,, Kartasasmita CB,, Simoes EA,, Hibberd ML,, Sung WK,, Miller LD. 2007. Optimization and clinical validation of a pathogen detection microarray. Genome Biol 8:R93. 10.1186/gb-2007-8-5-r93.
48. Gardner SN,, Jaing CJ,, McLoughlin KS,, Slezak TR. 2010. A microbial detection array (MDA) for viral and bacterial detection. BMC Genomics 11:668. 10.1186/1471-2164-11-668.
49. Jaing C,, Gardner S,, McLoughlin K,, Mulakken N,, Alegria-Hartman M,, Banda P,, Williams P,, Gu P,, Wagner M,, Manohar C,, Slezak T. 2008. A functional gene array for detection of bacterial virulence elements. PLoS One 3:e2163. 10.1371/journal.pone.0002163.
50. Erlandsson L,, Rosenstierne MW,, McLoughlin K,, Jaing C,, Fomsgaard A. 2011. The microbial detection array combined with random Phi29-amplification used as a diagnostic tool for virus detection in clinical samples. PLoS One 6:e22631. s10.1371/journal.pone.0022631.
51. Simoes EA,, Patel C,, Sung WK,, Lee CW,, Loh KH,, Lucero M,, Nohynek H,, Nai G,, Thien PL,, Koh CW,, Chan YS,, Ma J,, Maurer-Stroh S,, Carosone-Link P,, Hibberd ML,, Wong CW,, ARIVAC Consortium. 2013. Pathogen chip for respiratory tract infections. J Clin Microbiol 51:945953.
52. Ryabinin VA,, Kostina EV,, Maksakova GA,, Neverov AA,, Chumakov KM,, Sinyakov AN. 2011. Universal oligonucleotide microarray for sub-typing of Influenza A virus. PLoS One 6:e17529. 10.1371/journal.pone.0017529.
53. DeSantis TZ,, Brodie EL,, Moberg JP,, Zubieta IX,, Piceno YM,, Andersen GL. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53:371383.
54. Palmer C,, Bik EM,, DiGiulio DB,, Relman DA,, Brown PO. 2007. Development of the human infant intestinal microbiota. PLoS Biol 5:e177. 10.1371/journal.pbio .0050177.
55. Samuel LP,, Tibbetts RJ,, Agotesku A,, Fey M,, Hensley R,, Meier FA. 2013. Evaluation of a microarray-based assay for rapid identification of Gram-positive organisms and resistance markers in positive blood cultures. J Clin Microbiol 51:11881192.
56. Yoo SM,, Choi JY,, Yun JK,, Choi JK,, Shin SY,, Lee K,, Kim JM,, Lee SY. 2010. DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections. Mol Cell Probes 24:4452.
57. Tissari P,, Zumla A,, Tarkka E,, Mero S,, Savolainen L,, Vaara M,, Aittakorpi A,, Laakso S,, Lindfors M,, Piiparinen H,, Maki M,, Carder C,, Huggett J,, Gant V. 2010. Accurate and rapid identification of bacterial species from positive blood cultures with a DNA-based microarray platform: an observational study. Lancet 375:224230.
58. Dols JA,, Smit PW,, Kort R,, Reid G,, Schuren FH,, Tempelman H,, Bontekoe TR,, Korporaal H,, Boon ME. 2011. Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis. Am J Obstet Gynecol 204:305.e1305.e7.
59. Chung WY,, Jung YL,, Park KS,, Jung C,, Shin SC,, Hwang SJ,, Cho DY,, Cha SH,, Lim SK,, Park HG. 2011. A Sexually Transmitted Disease (STD) DNA chip for the diagnosis of genitourinary infections. Biosens Bioelectron 26:43144319.
60. Donatin E,, Buffet S,, Leroy Q,, Raoult D,, Drancourt M. 2013. A DNA microarray for the versatile diagnosis of infectious diarrhea. APMIS 121:634642.
61. Leinberger DM,, Schumacher U,, Autenrieth IB,, Bachmann TT. 2005. Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses. J Clin Microbiol 43:49434953.
62. Spiess B,, Seifarth W,, Hummel M,, Frank O,, Fabarius A,, Zheng C,, Morz H,, Hehlmann R,, Buchheidt D. 2007. DNA microarray-based detection and identification of fungal pathogens in clinical samples from neutropenic patients. J Clin Microbiol 45:37433753.
63. van den Hoogen BG,, de Jong JC,, Groen J,, Kuiken T,, de Groot R,, Fouchier RA,, Osterhaus AD. 2001. A newly discovered human pneumovirus isolated from young children with respiratory tract disease. Nat Med 7:719724.
64. Deffrasnes C,, Hamelin ME,, Boivin G. 2007. Human metapneumovirus. Semin Respir Crit Care Med 28:213221.
65. Allander T,, Emerson SU,, Engle RE,, Purcell RH,, Bukh J. 2001. A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A 98:1160911614.
66. Allander T,, Tammi MT,, Eriksson M,, Bjerkner A,, Tiveljung-Lindell A,, Andersson B. 2005. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A 102:1289112896.
67. Endo R,, Ishiguro N,, Kikuta H,, Teramoto S,, Shirkoohi R,, Ma X,, Ebihara T,, Ishiko H,, Ariga T. 2007. Seroepidemiology of human bocavirus in Hokkaido prefecture, Japan. J Clin Microbiol 45:32183223.
68. Kantola K,, Hedman L,, Allander T,, Jartti T,, Lehtinen P,, Ruuskanen O,, Hedman K,, Soderlund-Venermo M. 2008. Serodiagnosis of human bocavirus infection. Clin Infect Dis 46:540546.
69. Feng H,, Shuda M,, Chang Y,, Moore PS. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:10961100.
70. Briese T,, Paweska JT,, McMullan LK,, Hutchison SK,, Street C,, Palacios G,, Khristova ML,, Weyer J,, Swanepoel R,, Egholm M,, Nichol ST,, Lipkin WI. 2009. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog 5:e1000455. 10.1371/journal.ppat.1000455.
71. Blazes DL,, Mullins K,, Smoak BL,, Jiang J,, Canal E,, Solorzano N,, Hall E,, Meza R,, Maguina C,, Myers T,, Richards AL,, Laughlin L. 2013. Novel Bartonella agent as cause of verruga peruana. Emerg Infect Dis 19:11111114.
72. Wright AM,, Beres SB,, Consamus EN,, Long SW,, Flores AR,, Barrios R,, Richter GS,, Oh SY,, Garufi G,, Maier H,, Drews AL,, Stockbauer KE,, Cernoch P,, Schneewind O,, Olsen RJ,, Musser JM. 2011. Rapidly progressive, fatal, inhalation anthrax-like infection in a human: case report, pathogen genome sequencing, pathology, and coordinated response. Arch Pathol Lab Med 135:14471459.
73. Roetzer A,, Diel R,, Kohl TA,, Ruckert C,, Nubel U,, Blom J,, Wirth T,, Jaenicke S,, Schuback S,, Rusch-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. 10.1371/journal.pmed.1001387.
74. Flores AR,, Sahasrabhojane P,, Saldana M,, Galloway-Pena J,, Olsen RJ,, Musser JM,, Shelburne SA. 2014. Molecular characterization of an invasive phenotype of group A Streptococcus arising during human infection using whole genome sequencing of multiple isolates from the same patient. J Infect Dis 209:15201523.
75. Xiao YL,, Kash JC,, Beres SB,, Sheng ZM,, Musser JM,, Taubenberger JK. 2013. High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. J Pathol 229:535545.
76. Taubenberger JK,, Hultin JV,, Morens DM. 2007. Discovery and characterization of the 1918 pandemic influenza virus in historical context. Antivir Ther 12:581591.
77. Desnues C,, La Scola B,, Yutin N,, Fournous G,, Robert C,, Azza S,, Jardot P,, Monteil S,, Campocasso A,, Koonin EV,, Raoult D. 2012. Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A 109:1807818083.
78. Sberro H,, Leavitt A,, Kiro R,, Koh E,, Peleg Y,, Qimron U,, Sorek R. 2013. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning. Mol Cell 50:136148.
79. Ravn U,, Didelot G,, Venet S,, Ng KT,, Gueneau F,, Rousseau F,, Calloud S,, Kosco-Vilbois M,, Fischer N. 2013. Deep sequencing of phage display libraries to support antibody discovery. Methods 60:99110.
80. Fowler DM,, Araya CL,, Fleishman SJ,, Kellogg EH,, Stephany JJ,, Baker D,, Fields S. 2010. High-resolution mapping of protein sequence-function relationships. Nat Methods 7:741746.
81. ’t Hoen PA,, Jirka SM,, Ten Broeke BR,, Schultes EA,, Aguilera B,, Pang KH,, Heemskerk H,, Aartsma-Rus A,, van Ommen GJ,, den Dunnen JT. 2012. Phage display screening without repetitious selection rounds. Anal Biochem 421:622631.
82. Matochko WL,, Chu K,, Jin B,, Lee SW,, Whitesides GM,, Derda R. 2012. Deep sequencing analysis of phage libraries using Illumina platform. Methods 58:4755.
83. Dias-Neto E,, Nunes DN,, Giordano RJ,, Sun J,, Botz GH,, Yang K,, Setubal JC,, Pasqualini R,, Arap W. 2009. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS One 4:e8338. 10.1371/journal.pone.0008338.
84. Di Niro R,, Sulic AM,, Mignone F,, D’Angelo S,, Bordoni R,, Iacono M,, Marzari R,, Gaiotto T,, Lavric M,, Bradbury AR,, Biancone L,, Zevin-Sonkin D,, De Bellis G,, Santoro C,, Sblattero D. 2010. Rapid interactome profiling by massive sequencing. Nucleic Acids Res 38:e110. 10.1093/nar/gkq052.
85. Zhang H,, Torkamani A,, Jones TM,, Ruiz DI,, Pons J,, Lerner RA. 2011. Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems. Proc Natl Acad Sci U S A 108:1345613461.
86. Kuenne C,, Billion A,, Mraheil MA,, Strittmatter A,, Daniel R,, Goesmann A,, Barbuddhe S,, Hain T,, Chakraborty T. 2013. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genomics 14:47. 10.1186/1471-2164-14-47.
87. Muller SA,, Findeiss S,, Pernitzsch SR,, Wissenbach DK,, Stadler PF,, Hofacker IL,, von Bergen M,, Kalkhof S. 2013. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteomics 86:2742.
88. Chaudhury S,, Abdulhameed MD,, Singh N,, Tawa GJ,, D’Haeseleer P M,, Zemla AT,, Navid A,, Zhou CE,, Franklin MC,, Cheung J,, Rudolph MJ,, Love J,, Graf JF,, Rozak DA,, Dankmeyer JL,, Amemiya K,, Daefler S,, Wallqvist A. 2013. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLoS One 8:e63369. 10.1371/journal.pone.0063369.
89. Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207214.
90. Caporaso JG,, Kuczynski J,, Stombaugh J,, Bittinger K,, Bushman FD,, Costello EK,, Fierer N,, Pena AG,, Goodrich JK,, Gordon JI,, Huttley GA,, Kelley ST,, Knights D,, Koenig JE,, Ley RE,, Lozupone CA,, McDonald D,, Muegge BD,, Pirrung M,, Reeder J,, Sevinsky JR,, Turnbaugh PJ,, Walters WA,, Widmann J,, Yatsunenko T,, Zaneveld J,, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335336.
91. Zhao G,, Krishnamurthy S,, Cai Z,, Popov VL,, Travassos da Rosa AP,, Guzman H,, Cao S,, Virgin HW,, Tesh RB,, Wang D. 2013. Identification of novel viruses using VirusHunter—an automated data analysis pipeline. PLoS One 8:e78470. 10.1371/journal.pone.0078470.
92. Cosentino S,, Voldby Larsen M,, Moller Aarestrup F,, Lund O. 2013. PathogenFinder—distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 8:e77302. 10.1371/journal.pone.0077302.
93. Iwasaki Y,, Abe T,, Wada Y,, Wada K,, Ikemura T. 2013. Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains. BMC Infect Dis 13:386. 10.1186/1471-2334-13-386.
94. Borozan I,, Watt SN,, Ferretti V. 2013. Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq. PLoS One 8:e76935. 10.1371/journal.pone.0076935.
95. He B,, Li Z,, Yang F,, Zheng J,, Feng Y,, Guo H,, Li Y,, Wang Y,, Su N,, Zhang F,, Fan Q,, Tu C. 2013. Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel mammalian viruses. PLoS One 8:e61950. 10.1371/journal.pone.0061950.
96. Tao Y,, Shi M,, Conrardy C,, Kuzmin IV,, Recuenco S,, Agwanda B,, Alvarez DA,, Ellison JA,, Gilbert AT,, Moran D,, Niezgoda M,, Lindblade KA,, Holmes EC,, Breiman RF,, Rupprecht CE,, Tong S. 2013. Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. J Gen Virol 94:738748.
97. Tse H,, Tsang AK,, Tsoi HW,, Leung AS,, Ho CC,, Lau SK,, Woo PC,, Yuen KY. 2012. Identification of a novel bat papillomavirus by metagenomics. PLoS One 7:e43986. 10.1371/journal.pone.0043986.
98. Koch R. 1890. An address on bacteriological research. Br Med J 2:380383.
99. Hill AB. 1965. The environment and disease: association or causation? Proc R Soc Med 58:295300.
100. Evans AS. 1976. Causation and disease: the Henle-Koch postulates revisited. Yale J Biol Med 49:175195.
101. Fredericks DN,, Relman DA. 1996. Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin Microbiol Rev 9:1833.
102. Hemarajata P,, Versalovic J. 2013. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol 6:3951.
103. Turnbaugh PJ,, Hamady M,, Yatsunenko T,, Cantarel BL,, Duncan A,, Ley RE,, Sogin ML,, Jones WJ,, Roe BA,, Affourtit JP,, Egholm M,, Henrissat B,, Heath AC,, Knight R,, Gordon JI. 2009. A core gut microbiome in obese and lean twins. Nature 457:480484.
104. Morgan XC,, Tickle TL,, Sokol H,, Gevers D,, Devaney KL,, Ward DV,, Reyes JA,, Shah SA,, Leleiko N,, Snapper SB,, Bousvaros A,, Korzenik J,, Sands BE,, Xavier RJ,, Huttenhower C. 2012. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13:R79. 10.1186/gb-2012-13-9-r79.
105. Proal AD,, Albert PJ,, Marshall TG. 2013. The human microbiome and autoimmunity. Curr Opin Rheumatol 25:234240.
106. Brown EM,, Arrieta MC,, Finlay BB. 2013. A fresh look at the hygiene hypothesis: how intestinal microbial exposure drives immune effector responses in atopic disease. Semin Immunol 25:378387.
107. Relman DA. 2013. Metagenomics, infectious disease diagnostics, and outbreak investigations: sequence first, ask questions later? JAMA 309:15311532.
108. Ley RE,, Turnbaugh PJ,, Klein S,, Gordon JI. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:10221023.
109. Olsen RJ,, Long SW,, Musser JM. 2012. Bacterial genomics in infectious disease and the clinical pathology laboratory. Arch Pathol Lab Med 136:14141422.
110. Dunne WMJr,, Westblade LF,, Ford B. 2012. Nextgeneration and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31:17191726.
111. van der Hoek L,, Pyrc K,, Jebbink MF,, Vermeulen-Oost W,, Berkhout RJ,, Wolthers KC,, Wertheim-van Dillen PM,, Kaandorp J,, Spaargaren J,, Berkhout B. 2004. Identification of a new human coronavirus. Nat Med 10:368373.
112. Jones MS,, Kapoor A,, Lukashov VV,, Simmonds P,, Hecht F,, Delwart E. 2005. New DNA viruses identified in patients with acute viral infection syndrome. J Virol 79:82308236.
113. Breitbart M,, Rohwer F. 2005. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39:729736.
114. Allander T,, Andreasson K,, Gupta S,, Bjerkner A,, Bogdanovic G,, Persson MA,, Dalianis T,, Ramqvist T,, Andersson B. 2007. Identification of a third human polyomavirus. J Virol 81:41304136.
115. Gaynor AM,, Nissen MD,, Whiley DM,, Mackay IM,, Lambert SB,, Wu G,, Brennan DC,, Storch GA,, Sloots TP,, Wang D. 2007. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog 3:e64. 10.1371/journal.ppat.0030064.
116. Jones MSII,, Harrach B,, Ganac RD,, Gozum MM,, Dela Cruz WP,, Riedel B,, Pan C,, Delwart EL,, Schnurr DP. 2007. New adenovirus species found in a patient presenting with gastroenteritis. J Virol 81:59785984.
117. Finkbeiner SR,, Le BM,, Holtz LR,, Storch GA,, Wang D. 2009. Detection of newly described astrovirus MLB1 in stool samples from children. Emerg Infect Dis 15:441444.
118. Kapoor A,, Victoria J,, Simmonds P,, Wang C,, Shafer RW,, Nims R,, Nielsen O,, Delwart E. 2008. A highly divergent picornavirus in a marine mammal. J Virol 82: 311320.
119. Hales LM,, Knowles NJ,, Reddy PS,, Xu L,, Hay C,, Hallenbeck PL. 2008. Complete genome sequence analysis of Seneca Valley virus-001, a novel oncolytic picornavirus. J Gen Virol 89:12651275.
120. Holtz LR,, Finkbeiner SR,, Kirkwood CD,, Wang D. 2008. Identification of a novel picornavirus related to cosaviruses in a child with acute diarrhea. Virol J 5:159. 10.1186/1743-422X-5-159.
121. Arthur JL,, Higgins GD,, Davidson GP,, Givney RC,, Ratcliff RM. 2009. A novel bocavirus associated with acute gastroenteritis in Australian children. PLoS Pathog 5:e1000391. 10.1371/journal.ppat.1000391.
122. Kapoor A,, Slikas E,, Simmonds P,, Chieochansin T,, Naeem A,, Shaukat S,, Alam MM,, Sharif S,, Angez M,, Zaidi S,, Delwart E. 2009. A newly identified bocavirus species in human stool. J Infect Dis 199:196200.
123. Kwok H,, Tong AH,, Lin CH,, Lok S,, Farrell PJ,, Kwong DL,, Chiang AK. 2012. Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One 7:e36939. 10.1371/journal.pone.0036939.
124. DeBoever C,, Reid EG,, Smith EN,, Wang X,, Dumaop W,, Harismendy O,, Carson D,, Richman D,, Masliah E,, Frazer KA. 2013. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS One 8:e73956. 10.1371/journal.pone.0073956.
125. Greninger AL,, Runckel C,, Chiu CY,, Haggerty T,, Parsonnet J,, Ganem D,, DeRisi JL. 2009. The complete genome of klassevirus—a novel picornavirus in pediatric stool. Virol J 6:82. 10.1186/1743-422X-6-82.
126. Holtz LR,, Finkbeiner SR,, Zhao G,, Kirkwood CD,, Girones R,, Pipas JM,, Wang D. 2009. Klassevirus 1, a previously undescribed member of the family Picornaviridae, is globally widespread. Virol J 6:86. 10.1186/1743-422X-6-86.
127. Finkbeiner SR,, Li Y,, Ruone S,, Conrardy C,, Gregoricus N,, Toney D,, Virgin HW,, Anderson LJ,, Vinje J,, Wang D,, Tong S. 2009. Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J Virol 83:1083610839.
128. Fricke WF,, Rasko DA. 2014. Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 15:4955.

Tables

Generic image for table
TABLE 1

Novel viruses discovered by Sanger sequencing methods

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16
Generic image for table
TABLE 2

Novel viruses discovered by NGS methods

Citation: Spinler J, Hemarajata P, Versalovic J. 2015. Microbial Genomics and Pathogen Discovery*, p 238-251. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch16

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