title: Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes.
abstract: BACKGROUND
  Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined using Illumina/Solexa and Roche 454 genome sequencing.
  
  
  RESULTS
  Gene order and synteny was almost identical between C. pecorum strains and C. psittaci. Differences between C. pecorum and other chlamydiae occurred at a number of loci, including the plasticity zone, which contained a MAC/perforin domain protein, two copies of a >3400 amino acid putative cytotoxin gene and four (PV3056/3) or five (P787 and W73) genes encoding phospholipase D. Chlamydia pecorum contains an almost intact tryptophan biosynthesis operon encoding trpABCDFR and has the ability to sequester kynurenine from its host, however it lacks the genes folA, folKP and folB required for folate metabolism found in other chlamydiae. A total of 15 polymorphic membrane proteins were identified, belonging to six pmp families. Strains possess an intact type III secretion system composed of 18 structural genes and accessory proteins, however a number of putative inc effector proteins widely distributed in chlamydiae are absent from C. pecorum. Two genes encoding the hypothetical protein ORF663 and IncA contain variable numbers of repeat sequences that could be associated with persistence of infection.
  
  
  CONCLUSIONS
  Genome sequencing of three C. pecorum strains, originating from animals with different disease manifestations, has identified differences in ORF663 and pseudogene content between strains and has identified genes and metabolic traits that may influence intracellular survival, pathogenicity and evasion of the host immune system.
authors.forename: Michelle
authors.initials: M
authors.lastname: Sait
authors.forename: Morag
authors.initials: M
authors.lastname: Livingstone
authors.forename: Ewan M
authors.initials: EM
authors.lastname: Clark
authors.forename: Nick
authors.initials: N
authors.lastname: Wheelhouse
authors.forename: Lucy
authors.initials: L
authors.lastname: Spalding
authors.forename: Bryan
authors.initials: B
authors.lastname: Markey
authors.forename: Simone
authors.initials: S
authors.lastname: Magnino
authors.forename: Frederick A
authors.initials: FA
authors.lastname: Lainson
authors.forename: Garry S A
authors.initials: GS
authors.lastname: Myers
authors.affiliation: Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK. david.longbottom@moredun.ac.uk.
authors.forename: David
authors.initials: D
authors.lastname: Longbottom
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D018938:Caco-2 Cells; D002417:Cattle; D002689:Chlamydia / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D003603:Cytotoxins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005243:Feces / Q000382:microbiology; D005492:Folic Acid / Q000378:metabolism; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008565:Membrane Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012756:Sheep; D013582:Synovial Fluid / Q000382:microbiology; D020080:Tandem Repeat Sequences / Q000235:genetics; D014364:Tryptophan / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D003603:Cytotoxins; D008565:Membrane Proteins; D014364:Tryptophan; D005492:Folic Acid