Pathogen Genomics aims to sequence the genomes of organisms relevant to human and animal health. We have a large portfolio of projects ranging from bacterial plasmids and phage, through bacterial genomes and protist parasites to helminths and insect vectors. The projects themselves range from EST sequencing through comparative genomic sequencing, to fully finished genomes.

Pathogen Genome Sequencing

Bacteria:

All data from these projects are immediately and freely available.

Protozoa:

All data from these projects are immediately and freely available.

Fungi:

All data from these projects are immediately and freely available.

Parasitic Helminths:

All data from these projects are immediately and freely available.

Plasmids:

All data from these projects are immediately and freely available.

Vectors:

All data from these projects are immediately and freely available.

Bacteriophage:

All data from these projects are immediately and freely available.

Viruses:

All data from these projects are immediately and freely available.

Analysis tools

ACT:

DNA Sequence Comparison Viewer

Artemis:

DNA sequence viewer and annotation tool

Pathogen Genomics

New proposals

Pathogen Genomics has core Wellcome Trust funding for pathogen sequencing and informatics. We have a large number of sequencing projects in progress; including some 45 bacteria and 20 protozoa. We are able to take on new sequencing projects either using our existing core funding or through external funding agencies.

We have an advisory group, the Pathogen Sequencing Advisory Group (PSAG) that provides advice on new sequencing projects that would use our core funding, and on other activities of the unit. Suggestions for sequencing can be made to Pathogen Genomics and if appropriate an application to PSAG or to an appropriate funding agency can be drawn up. A PDF file containing the criteria for the assesment of proposals PSAG, and the data required, is available here.

Scientists intending to submit a proposal should first contact Pathogen Sequencing. Please note that the Pathogen Genomics is not a funding agency, and no funding is available per se.

Data release

Data from all sequencing projects are made immediately available under conditions described in our data release policy and guidelines and conditions on use of data.

Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP.

Annotation from a growing number of organisms is available from our web database GeneDB.

Data Release Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale.

History

In 1995 the Wellcome Trust took the decision to set up a Pathogen Genomics group at what was then the Sanger Centre, to sequence the genomes of organisms relevant to human and animal health. It was initially funded through individual grants and later through the Wellcome Trust Beowulf Genomics Panel. The Beowulf panel no longer operates, and the PSU is now funded through the Sanger Institute Wellcome Trust envelope funding. The PSU has now been renamed to Pathogen Genomics.

The teams were based on those that were involved in the sequencing of the yeast genome and in addition to pathogen sequencing we still maintain an interest in sequencing the genomes of model organisms.

In 2006, Julian Parkhill took over the running of the PSU from Bart Barrell, who continues to work on sequence analysis within the group.

Published sequencing projects [Full publication list]

Organism	Disease	Reference	Funding
Citrobacter rodentium	mouse pathogen	Petty et al., J. Bacteriol., epublication (2009)	Wellcome Trust
Candida dubliniensis	nosocomial infection	Jackson et al., Genome Res., epublication	Wellcome Trust
Schistosoma mansoni	schistosomiasis / bilharzia	Berriman et al., Nature, 460, 352-8 (2009)	Wellcome Trust
Candida parapsilosis	nosocomial infection	Butler et al., Nature, 459, 657-62 (2009)	Wellcome Trust
Chlamydia trachomatis Jali		Seth-Smith et al., BMC Genomics, 10, 59 (2009)	Wellcome Trust
Chlamydia trachomatis serovar B		Seth-Smith et al., BMC Genomics, 10, 59 (2009)	Wellcome Trust
Chlamydia trachomatis serovar A		Seth-Smith et al., BMC Genomics, 10, 59 (2009)	Wellcome Trust
Pseudomonas fluorescens	a plant-growth promoting bacterium	Silby et al., Genome Biology, 10, r51 (2009)	BBSRC
Streptococcus uberis	bovine mastitis	Ward et al., BMC Genomics, 10, 54 (2009)	Wellcome Trust
Streptococcus pneumoniae 23F		Croucher et al., J. Bacteriol., 191, 1480-9 (2009)	Wellcome Trust
Pseudomonas aeruginosa	a cause of lung infections in Cystic Fibrosis patients	Winstanley et al., Genome Res., 19, 12-23 (2009)	Wellcome Trust
Salmonella paratyphi A	a cause of Typhoid fever	Holt et al., J. Bacteriol., 191, 347-354 (2009)	Wellcome Trust
Escherichia coli E2348/969		Iguchi et al., J Bacteriol., 191, 347-354 (2009)	Wellcome Trust
Alivibrio salmonicida	cold-water vibriosis in Atlantic salmon	Hjerde et al., BMC Genomics, 9, 616 (2008)	Wellcome Trust
Plasmodium knowlesi (H strain)	monkey malaria	Pain et al., Nature, 455, 799-803 (2008)	Wellcome Trust
Proteus mirabilis	urinary tract infection	Pearson et al., Genome Research, epublication (2008)	Wellcome Trust
Salmonella enterica Enteritidis PT4	human food poisoning	Thomson et al., J. Bacteriol., 190, 4027-37 (2008)	Wellcome Trust
Salmonella enterica gallinarum	avian typhoid	Thomson et al., Genome Research, epublication (2008)	Wellcome Trust
Mycobacterium marinum	tuberculosis-like disease in cold-blooded animals and peripheral granulomatous disease in humans	Stinear et al., Genome Research, epublication (2008)	Wellcome Trust
Clavibacter michiganensis	potato ring rot	Bentley et al., Journal of Bacteriology, epublication (2008)	USDA
Vi Bacteriophage of Salmonella typhi		Pickard et al., Journal of Bacteriology, epublication (2008)	Wellcome Trust
Chlamydia trachomatis L2	infectious blindness, sexually transmitted disease	Thomson et al., Genome research, 18 161-171 (2008)	Wellcome Trust
Leishmania infantum Leishmania braziliensis	Leishmaniasis	Peacock et al., Nature Genetics, 39 839-847 (2007)	Wellcome Trust
Clostridium botulinum	Botulism	Sebaihia et al., Genome research 17 1082-1092 (2007)	Beowulf Genomics
Mycobaterium bovis BCG	The vaccine strain of tuberculosis	Brosch et al., P.N.A.S., 104 5596-5601 (2007)	DEFRA/Beowulf Genomics
Neisseria meningitidis serogroup C strain FAM18	Meningitis	Bentley et al., PloS Genetics 3, e23 (2007)	Beowulf Genomics
Eimeria tenella chromosome 1	Coccidiosis in poultry	Ling et al., Genome Research 17 311-319 (2007)	Beowulf Genomics
Plasmodium falciparum Ghanaian isolate	Malaria	Jeffares et al., Nature Genetics 39, 120-125 (2007)	Beowulf Genomics
Yersinia enterocolitica	a cause of gastroenteritis	Thomson et al., PLoS Genetics 2, e206 (2006)	Beowulf Genomics
Streptococcus pyogenes	streptococcal toxic-shock syndrome, acute rheumatic fever, scarlet fever	Holden et al., Journal of Bacteriology 188, epublication (2006)	Beowulf Genomics
Bordetella avium	cause of disease in turkeys	Sebaihia et al., Journal of Bacteriology 188, 6002-6015 (2006)	USDA
Clostridium difficile	major nosocomial pathogen	Sebaihia et al., Nature Genetics 38, 779-786 (2006)	Wellcome Trust
Rhizobium leguminosarum	nitrogen-fixing plant symbiont	Young et al., Genome Biology 7, r34 (2006)	BBSRC
Streptococcus pneumoniae capsular loci	Various	Bentley et al., PLoS Genetics 2(3), e31 (2006)	W.H.O.
Aspergillus fumigatus	Pathogenic fungus	Nierman et al., Nature 438, 1151-1156 (2005)	Beowulf Genomics
Emiliania huxleyi virus 86	double stranded DNA virus of a marine phytoplankton	Wilson et al., Science 309, 1090-1092 (2005)	The Marine Biological Association
Leishmania major	Leishmaniasis	Ivens et al., Science 309, 436-442 (2005)	Beowulf Genomics/European Commission
Trypanosoma brucei	African sleeping sickness	Berriman et al., Science 309, 416-422 (2005)	Beowulf Genomics
Leishmania major Trypanosoma brucei Trypanosoma cruzi	Comparative Genomics of Trypanosomatid Parasitic Protozoa	El-Sayed et al., Science 309, 404-409 (2005)	Beowulf Genomics
Theileria annulata	Tick borne cattle disease	Pain et al, Science 309, 131-133 (2005)	Beowulf Genomics
Chlamydophila abortus S26/3	Ovine and human abortion	Thomson et al., Genome Research 15, 629-640	The Scottish Executive
Dictyostelium discoideum	Social amoeba	Eichinger et al., Nature 435, 43-57 (2005)	MRC/European Commission
Entamoeba histolytica	Amoebic dysentry	Loftus et al., Nature 433, 865-868 (2005)	Beowulf Genomics
Bacteroides fragilis NCTC9343	Gut commensal / opportunistic pathogen	Cerdeño-Tárraga et al., Science 307, 1463-1465 (2005)	Beowulf Genomics
Plasmodium berghei Plasmodium chabaudi	Rodent malaria	Hall et al., Science 307, 82-86 (2005)	Beowulf Genomics
Nematode ESTs	Various	Parkinson et al., Nature Genetics 36, 1259-1267 (2004)	Beowulf Genomics
Burkholderia pseudomallei	Melioidosis	Holden et al., P.N.A.S. 101, 14240-14245 (doi/10.1073/pnas.0403302101) (2004)	Beowulf Genomics
Erwinia carotovora subsp. atroseptica	Potato pathogen	Bell et al. PNAS 101(30): 11105-11110 (2004)	The Scottish Executive
Staphylococcus aureus (MRSA252)	Various	Holden et al. PNAS 101(26): 9786-9791 (2004)	Beowulf Genomics
Staphylococcus aureus (MSSA476)	Various	Holden et al. PNAS 101(26): 9786-9791 (2004)	Beowulf Genomics
Corynebacterium diphtheriae	Diphtheria	Cerdeño-Tárraga et al., Nucleic Acids Research 31(22), 6516-6523 (2003)	Beowulf Genomics
Trypanosoma brucei chr I	Sleeping sickness	Hall et al. Nuc. Acids. Res. 31 4864-4873 (2003)	Beowulf Genomics
Bordetella bronchiseptica	Veterinary respiratory infections	Parkhill et al. Nature Genetics 35 32-40 (2003)	Beowulf Genomics
Bordetella parapertussis	Whooping cough	Parkhill et al. Nature Genetics 35 32-40 (2003)	Beowulf Genomics
Bordetella pertussis	Whooping cough	Parkhill et al. Nature Genetics 35 32-40 (2003)	Beowulf Genomics
Mycobacterium bovis	Bovine tuberculosis	Garnier et al., P.N.A.S. (2003)	DEFRA/ Beowulf Genomics
Tropheryma whipplei	Whipple's disease	Bentley et al., Lancet 361 637-644 (2003)	Beowulf Genomics
Plasmodium falciparum	Malaria	Hall et al., Nature 419, 498-511 (2002)	Wellcome Trust
Streptomyces coelicolor	Antibiotic producer	Bentley et al., Nature 417, 141-147 (2002)	BBSRC / Beowulf Genomics
Schizosaccharomyces pombe	Model organism	Wood et al., Nature 415, 871-880 (2002)	Wellcome Trust / European Commission
Salmonella typhi	Typhoid fever	Parkhill et al., Nature 413, 848-852 (2001)	Beowulf Genomics
Yersinia pestis	Plague	Parkhill et al., Nature 413, 523-527 (2001)	Beowulf Genomics
Mycobacterium leprae	Leprosy	Cole et al., Nature 409, 1007-1011 (2001)	Heiser/ Follereau
Neisseria meningitidis Serogroup A strain Z2491	Bacterial meningitis	Parkhill et al., Nature 404 502-506 (2000)	Wellcome Trust
Campylobacter jejuni	Food poisoning	Parkhill et al., Nature 403, 665-668 (2000)	Beowulf Genomics
Mycobacterium tuberculosis	Tuberculosis	Cole et al., Nature 393, 537-544 (1998)	Wellcome Trust
Saccharomyces cerevisiae	Model organism	Nature 387, 6632 Suppl (1997)	Wellcome Trust

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