Computational resources in infectious disease: Limitations and challenges

PLoS Computational Biology

Volumn 5, Issue 10, 2009, Pages

  Berglund, Eva C ^a   Nystedt, Björn ^a   Andersson, Siv G E ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL RESOURCES; INFECTIOUS DISEASE;

DISEASES;

BACTERIAL DNA; BACTERIAL RNA; BACTERIAL VACCINE; RNA 16S; VIRULENCE FACTOR;

AMPLICON; ANTIBIOTIC RESISTANCE; BACTERIAL ARTIFICIAL CHROMOSOME; BACTERIAL INFECTION; BACTERIAL VIRULENCE; BACTERIOPHAGE; BACTERIUM ISOLATE; BIOLOGY; CAUSE OF DEATH; COMPARATIVE GENE MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; DIAGNOSTIC PROCEDURE; GENE FUNCTION; GENE INTERACTION; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; GENOTYPE; HORIZONTAL GENE TRANSFER; HOST PATHOGEN INTERACTION; HUMAN; INFECTION RISK; MICROBIAL COMMUNITY; MULTILOCUS SEQUENCE TYPING; MYCOBACTERIUM MARINUM; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM ULCERANS; NONHUMAN; PATHOGENICITY; PLASMID; PROTEIN SECRETION; PSEUDOGENE; REVIEW; RICKETTSIA PROWAZEKII; RISK ASSESSMENT; SARS CORONAVIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; VACCINE PRODUCTION; ANIMAL; COMMUNICABLE DISEASE; DISEASE CARRIER; DISEASE TRANSMISSION; EPIDEMIC; GENETICS; GENOME; HEALTH SURVEY; INFECTION CONTROL; INTERNATIONAL COOPERATION; INTERNET; METHODOLOGY; MICROBIOLOGY; PROGRAM DEVELOPMENT; UNITED STATES; VIRULENCE;

ANIMALS; BACTERIAL INFECTIONS; COMMUNICABLE DISEASE CONTROL; COMMUNICABLE DISEASES; DISEASE OUTBREAKS; DISEASE RESERVOIRS; GENOME; HUMANS; INTERNATIONALITY; INTERNET; MICROBIOLOGY; POPULATION SURVEILLANCE; PROGRAM DEVELOPMENT; UNITED STATES; VIRULENCE;

EID: 70350467875     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000481     Document Type: Review

References (43)

1. Rappuoli R (2004) From Pasteur to genomics: Progress and challenges in infectious diseases. Nat Med 10: 1177-1185.
2. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, et al. (2003) The genome sequence of the SARS-associated coronavirus. Science 300: 1399-1404.
3. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, et al. (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300: 1394-1399.
4. Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413: 523-527.
5. Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 99: 17020-17024.
6. Dziejman M, Balon E, Boyd D, Fraser CM, Heidelberg JF, et al. (2002) Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc Natl Acad Sci U S A 99: 1556-1561.
7. Wolfgang MC, Kulasekara BR, Liang X, Boyd D, Wu K, et al. (2003) Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 100: 8484-8489.
8. Seshadri R, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, et al. (2004) Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A 101: 5646-5651.
9. Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, et al. (2005) Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol 187: 2426-2438.
10. Fuxelius HH, Darby AC, Cho NH, Andersson SG (2008) Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol 9: R42.
11. Berglund EC, Frank AC, Calteau A, Vinnere Pettersson O, Granberg F, et al. (2009) Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. PLoS Genet 5: e1000546. doi:10.1371/journal. pgen.1000546.
12. Deitsch KW, Moxon ER, Wellems TE (1997) Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections. Microbiol Mol Biol Rev 61: 281-293.
13. Brayton KA, Knowles DP, McGuire TC, Palmer GH (2001) Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens. Proc Natl Acad Sci U S A 98: 4130-4135.
14. Nystedt B, Frank AC, Thollesson M, Andersson SG (2008) Diversifying selection and concerted evolution of a type IV secretion system in Bartonella. Mol Biol Evol 25: 287-300.
15. Bilek N, Ison CA, Spratt BG (2009) Relative contributions of recombination and mutation to the diversification of the opa gene repertoire of Neisseria gonorrhoeae. J Bacteriol 191: 1878-1890.
16. Gupta PK (2008) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26: 602-611.
17. The Gene Ontology's Reference Genome Project: A unified framework for functional annotation across species. PLoS Comput Biol 5: e1000431.
18. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33: 6083-6089.
19. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, et al. (1998) Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95: 3140-3145.
20. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
21. Turner KM, Feil EJ (2007) The secret life of the multilocus sequence type. Int J Antimicrob Agents 29: 129-135.
22. Bambini S, Rappuoli R (2009) The use of genomics in microbial vaccine development. Drug Discov Today 14: 252-260.
23. Raes J, Bork P (2008) Molecular eco-systems biology: Towards an understanding of community function. Nat Rev Microbiol 6: 693-699.
24. Kunin V, Copeland A, Lapidus A,Mavromatis K, Hugenholtz P (2008) A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 72: 557-578.
25. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC (2008) The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36: D475-479.
26. Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280. doi:10.1371/journal.pbio.0060280.
27. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
28. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, et al. (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A 106: 5859-5864.
29. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, et al. (2008) Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87: 1016-1020.
30. Spear GT, Sikaroodi M, Zariffard MR, Landay AL, French AL, et al. (2008) Comparison of the diversity of the vaginal microbiota in HIV-infected and HIV-uninfected women with or without bacterial vaginosis. J Infect Dis 198: 1131-1140.
31. Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: Computational analysis of environmental sequence data. Curr Opin Microbiol 10: 490-498.
32. Andersson SG, Kurland CG (1998) Reductive evolution of resident genomes. Trends Microbiol 6: 263-268.
33. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409: 1007-1011.
34. Alsmark CM, Frank AC, Karlberg EO, Legault BA, Ardell DH, et al. (2004) The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc Natl Acad Sci U S A 101: 9716-9721.
35. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
36. Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, et al. (2003) Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 35: 32-40.
37. Yip MJ, Porter JL, Fyfe JA, Lavender CJ, Portaels F, et al. (2007) Evolution of Mycobacterium ulcerans and other mycolactone-producing mycobacteria from a common Mycobacterium marinum progenitor. J Bacteriol 189: 2021-2029.
38. Rondini S, Kaser M, Stinear T, Tessier M, Mangold C, et al. (2007) Ongoing genome reduction in Mycobacterium ulcerans. Emerg Infect Dis 13: 1008-1015.
39. Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, et al. (2007) Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res 17: 192-200.
40. Huber CA, Ruf MT, Pluschke G, Kaser M (2008) Independent loss of immunogenic proteins in Mycobacterium ulcerans suggests immune evasion. Clin Vaccine Immunol 15: 598-606.
41. Stinear TP, Mve-Obiang A, Small PL, Frigui W, Pryor MJ, et al. (2004) Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc Natl Acad Sci U S A 101: 1345-1349.
42. Pidot SJ, Hong H, Seemann T, Porter JL, Yip MJ, et al. (2008) Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones. BMC Genomics 9: 462.
43. Tay CY, Reeves PR, Lan R (2008) Importation of the major pilin TcpA gene and frequent recombination drive the divergence of the Vibrio pathogenicity island in Vibrio cholerae. FEMS Microbiol Lett 289: 210-218.