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Currently Supported Large-Scale Genome Sequencing Projects

Advances in molecular biology

have led to remarkably fast and accurate methods for sequencing the genomes of disease-causing microorganisms. Genome sequencing reveals the lineup of paired chemical bases that make up the pathogen's DNA, the language of life. The potential payoffs of sequencing pathogens have begun stirring scientific excitement. Sequence information can be exploited in many ways: to demarcate genes, to locate therapeutic targets, to identify mutations that contribute to drug resistance, and to compare the genomes of variant strains to note differences that may affect the antigenicity or virulence of the microbe.

When scientists identify genes that are unique to a particular microbe, drugs can be targeted to these genes, and the products of these genes can be incorporated into experimental vaccines. Strategies can be devised to counteract genetic mutations that cause a microbe to become drug resistant. Once virulence genes are found, researchers can attempt to disable them. Genetic variations detected in different strains of the same pathogen can be used to study the population dynamics of these strains, such as the spread of a virulent or drug-resistant form of a pathogen in a susceptible population. Finally, understanding the genetic basis for both virulence and drug resistance may also help predict disease prognosis and influence the type and extent of patient care and treatment.

Recognizing the tremendous benefits of genome sequencing, NIAID has funded projects to sequence the full genomes of a number of medically important microbes, including the bacteria that cause tuberculosis, gonorrhea, chlamydia and cholera (see Table). In addition, NIAID collaborates with other funding agencies to sequence the larger genomes of protozoan pathogens such as that of the organism causing malaria. Many of these microbes have been completely sequenced and are now being annotated and analyzed. During annotation, each gene's position or placement on the genome is determined. This information is further analyzed to provide insight on important features of the genome that may affect the biology of the microbe and its ability to cause disease. Sequence information as well as annotation data are continually being provided to the scientific community by means of publicly accessible Websites.

The following table identifies the projects supported by NIAID as well as the Web sites where the data and additional information can be found.

Pathogen Strain Awardee/Grant Info Website/Reference

COMPLETED GENOME PROJECTS

Anopheles gambiae PEST Celera Genomics
U01AI50687 		Holt et al Science 298 (5591): 129-49 (2002)

http://www.niaid.nih.gov/dmid/genomes/anopheles.htm

 
Bacillus anthracis Ames Office of Naval Research & TIGR
 Read et al Nature 423: 81-82 (2003)

Read et al Science 296: (5575):2028 (2002)

http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Bacillus anthracis Kruger B1 The Institute for Genomic Research (TIGR)
NIAID Contract 		 
Bacillus anthracis Western North America The Institute for Genomic Research (TIGR)
NIAID Contract 		 
Bacillus cereus 10987 The Institute for Genomic Research (TIGR)
NIAID Contract 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Brucella suis 1330 The Institute for Genomic Research (TIGR)
U01 AI49036 		Paulsen, I et al PNAS 99 (20): 13148-13153 (2002)

http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Burkholderia mallei ATCC23344 The Institute for Genomic Research (TIGR)
U01AI49037 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Chlamydia pneumoniae AR39 The Institute for Genomic Research (TIGR)
R01AI43359 		Read et al. Nucleic Acids Research 28 (6):1397-1406 (2000)

http://www.tigr.org/tdb/mdb/mdbcomplete.html

 
Chlamydia trachomatis serovar D University of California, Berkeley
R01AI39258 		Stephens et al. Science 282 (5389):754-59 (1998)

http://www.stdgen.lanl.gov/

 
Chlamydia trachomatis Mouse pneumonitis The Institute for Genomic Research (TIGR)
R01AI43359 		Read et al. Nucleic Acids Research 28 (6):1397-1406 (2000)

http://www.tigr.org/tdb/mdb/mdbcomplete.html

 
Clostridium perfringens ATCC 13124 The Institute for Genomic Research (TIGR)
U01AI49921 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Coxiella burnetii Nine Mile phase I RSA 493 The Institute for Genomic Research (TIGR)
U01AI49034 		Seshadri et al PNAS 100 (9): 5455 - 5460 (2003)

http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Cryptococcus neoformans JEC21 serotypeD The Institute for Genomic Research (TIGR)
U01AI48594 		http://www.tigr.org/tdb/e2k1/cna1/

 
Cryptococcus neoformans B3501 serotypeD Stanford University
U01 AI47087 		http://www-sequence.stanford.edu/group/C.neoformans/index.html

 
Cryptosporidum parvum Iowa University of Minnesota
U01 AI46397 		http://www.cbc.umn.edu/ResearchProjects/AGAC/Cp/index.htm

 
Enterococcus faecalis V583 (vancomycin resistant) The Institute for Genomic Research (TIGR)
U01AI40963 		Paulsen et al Science 299 (5615) 2071-2074 (2003)

http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Escherichia coli K1 RS218 meningitis strain University of Wisconsin
U01AI44387 		http://www.genome.wisc.edu

 
Escherichia coli CFT073 uropathogenic strain University of Wisconsin
U0144387 		http://www.genome.wisc.edu

 
Escherichia coli 0157:H7 University of Wisconsin
U01AI41329 		Perna et al Nature 409 (6819): 529-533(2001)

http://www.genome.wisc.edu

 
Group B streptococcus A909 The Institute for Genomic Research (TIGR)
U01AI50909 		Tettelin Proc. Natl. Acad. Sci. 99: 12391-12396 (2002)

 
Haemophilus ducreyi 35000HP Ohio State University
R01AI45091 		http://www.microbial-pathogenesis.org

 
Klebsiella pneumoniae MGH 78578 Washington University , St Louis
U01AI43283 		 
Leishmania major Friedlin Chromosome 1 Seattle Biomedical Research Institute
U01AI40599 		Myler et al. Proc. Natl. Acad. Sci. USA 96:2902-06 (1999)

http://www.genedb.org/genedb/leish/index.jsp

 
Leishmania major Friedlin Seattle Biomedical Research Institute
U01AI40599 		http://www.genedb.org/genedb/leish/index.jsp

 
Mycobacterium avium 104 The Institute for Genomic Research (TIGR)
R01AI41943 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Mycobacterium tuberculosis CSU 93 (Virulent clinical isolate) The Institute for Genomic Research (TIGR)
R01AI40125 		Fleishcmann et al J.Bacteriol. 184 (19): 5479 - 5490 (2002)

http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Neisseria gonorrhoeae FA1090 University of Oklahoma
R01AI38399 		http://www.genome.ou.edu/gono.html

 
Nematode EST project   Washington University, St. Louis
U01 AI46593 		http://www.nematode.net

 
Plasmodium falciparum 3D7 TIGR & Naval Medical Research Institute
U01 AI42243 		Gardner et al Nature 419 (6906) 498-511 (2002)

Gardner et al Nature 419 (6906) 531-534 (2002)

Gardner et al Science 282 (5391): 1126-1132 (1998)

http://PlasmoDB.org

 
Rickettsia rickettsii Sheila Smith Institute for Systems Biology
U01AI50942 		 
Rickettsia typhi Wilmington University of Texas, Galveston
U01AI49040 		http://www.hgsc.bcm.tmc.edu

 
Salmonella paratyphi A ATCC 9150 Washington University , St Louis
U01AI43283 		 
Salmonella typhi TY2 University of Wisconsin
U01 AI44387 		http://www.genome.wisc.edu

 
Salmonella typhimurium LT2 Washington University, St. Louis
U01AI43283 		McClelland et al. Nature 413: 852-856 (2001)

http://genome.wustl.edu/projects/bacterial/styphimurium/

 
Shigella flexneri Serotype 2a University of Wisconsin
U01AI44387 		http://www.genome.wisc.edu

 
Staphylococcus aureus COL(methicillin resistant) The Institute for Genomic Research (TIGR)
R01AI43567 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Staphylococcus aureus 8325(antibiotic sensitive) University of Oklahoma
R01AI43568 		http://www.genome.ou.edu/staph.html

 
Staphylococcus epidermidis RP62A The Institute for Genomic Research (TIGR)
U01 AI45667 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Streptococcus pneumoniae serotype 4 University of Alabama, Birmingham
R01AI40645 		Tettelin, H et al Science 293 (5529): 498-506 (2001)

http://genome.microbio.uab.edu//strep/

 
Streptococcus pyogenes M1 GAS University of Oklahoma
R01AI38406 		Ferretti et al Proc. Natl. Acad. Sci. USA 98 (8): 4658-63 (2001)

http://www.genome.ou.edu/strep.html

 
Treponema pallidum Nichols University of Texas Health Science Center & TIGR
R01AI40390 		Fraser et al. Science 281 (5375):375-88 (1998)

http://www.tigr.org/tdb/mdb/mdbcomplete.html

http://www.stdgen.lanl.gov

 
Trypanosoma cruzi CL Brener University of Karolinska
U01 AI 45061 		 
Trypanosoma cruzi CL Brener Seattle Biomedical Research Institute
U01 AI45039 		 
Trypanosoma cruzi CL Brener The Institute for Genomic Research (TIGR)
U01 AI45038 		http://www.tigr.org/tdb/e2k1/tca1

 
Ureaplasma urealyticum serovar 3 University of Alabama, Birmingham
R01AI28279 		Glass et al Nature 407 (6805): 757-762 (2000)

http://www.stdgen.lanl.gov

http://genome.microbio.uab.edu/uu/uugen.htm

 
Vibrio cholerae N16961 Serotype 01, biotype El Tor The Institute for Genomic Research (TIGR)
R01AI40535 		Heidelberg et al Nature 406 (6795): 477-83 (2000)

http://www.tigr.org/tdb/mdb/mdbcomplete.html

 
Wolbachia spp. Drosophila and Brugia malayi Yale University
U01 AI47409 		http://www.tigr.org/cgi-bin/BlastSearch/blast.cgi

 
Yersinia pestis KIM5 P12 University of Wisconsin
U01 AI44387 		Deng et al J.Bacteriol. 184 (16): 4601-11 (2002)

http://www.genome.wisc.edu

 

ONGOING SEQUENCING PROJECTS

Aedes aegypti Rexville University of Notre Dame
U01 AI50936 		 
Anopheles gambiae PEST University of Notre Dame
U01AI48846 		http://konops.imbb.forth.gr/AnoDB

 
Aspergillus fumigatus Af293 Victoria University of Manchester
U01 AI48830 		http://www.sanger.ac.uk/Projects/A_fumigatus

http://www.tigr.org/tdb/fungal

 
Bacillus anthracis   The Institute for Genomic Research
NIAID Contract 		 
Bacillus cereus G9241 The Institute for Genomic Research (TIGR)
NIAID Contract 		 
Brugia malayi NIAID/TRS The Institute for Genomic Research (TIGR)
U01AI50903 		http://www.tigr.org/tdb/e2k1/bma1

 
Burkholderia thailandensis E264 The Institute for Genomic Research
U01 AI49037 		 
Clostridium perfringens SM101 The Institute for Genomic Research
U01 AI49921 		 
Coccidioides immitis C735 The Institute for Genomic Research (TIGR)
U01AI50910 		http://www.tigr.org/tdb/ufmg

 
Cryptosporidum parvum Human isolate Virginia Commonwealth University
U01 AI46418 		http://www.parvum.mic.vcu.edu

 
Ehrlichia spp.   Ohio State University
R01AI47885 		http://riki-lb1.vet.ohio-state.edu/ehrlichia

 
Entamoeba histolytica HM1:IMSS The Institute for Genomic Research (TIGR)
R01AI46516 		http://www.tigr.org/tdb/e2k1/eha1

 
Giardia lamblia WB5 chromosomes Marine Biological Laboratory
U01AI43273 		http://hermes.mbl.edu/baypaul/Giardia-HTML/index2.html

 
Histoplasma capsulatum G217B Washington University, St Louis
U01AI50934 		http://genome.wustl.edu/projects/hcapsulatum

 
Legionella pneumophila Philadelphia 1 Columbia University
U01AI44371 		http://genome3.cpmc.columbia.edu/~legion/

 
Mycobacterium smegmatis MC2155 The Institute for Genomic Research (TIGR)
U01 AI46517 		http://www.tigr.org/tdb/mdb/mdbinprogress.html

 
Plasmodium vivax Salvador I The Institute for Genomic Research (TIGR)
U01 AI42243 		 
Pneumocystis carinii Rat and human isolates University of Cincinnati
R01AI44651 		http://pneumocystis.uc.edu

 
Schistosoma mansoni Puerto Rican Strain The Institute for Genomic Research (TIGR)
U01AI48828 		http://www.tigr.org/tdb/e2k1/sma1

 
Streptococcus pneumonia serotype 6 University of Alabama, Birmingham
R01AI40645 		http://genome.microbio.uab.edu//strep/

 
Toxoplasma gondii ME49 The Institute for Genomic Research (TIGR)
U01AI50930 		http://toxodb.org

 
Trichomonas vaginalis G3 The Institute for Genomic Research
U01AI050913 		 
Trypanosoma brucei TREU 927/4 The Institute for Genomic Research (TIGR)
R01AI43062 		http://www.genedb.org/genedb/tryp/index.jsp

http://www.tigr.org/tdb/e2k1/tba1

 

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