Open Access Research article

Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

Michelle Sait15, Morag Livingstone1, Ewan M Clark16, Nick Wheelhouse1, Lucy Spalding1, Bryan Markey2, Simone Magnino3, Frederick A Lainson1, Garry SA Myers4 and David Longbottom1*

Author Affiliations

1 Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK

2 School of Veterinary Medicine, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland

3 Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna “Bruno Ubertini”, National Reference Laboratory for Animal Chlamydioses, Sezione Diagnostica di Pavia, Strada Campeggi 61, 27100 Pavia, Italy

4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

5 Current address: Microbiological Diagnostic Unit, The University of Melbourne, Parkville, Victoria 3010, Australia

6 Current address: BigDNA Ltd, Wallace Building, Roslin BioCentre, Roslin, Midlothian EH25 9PP, UK

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BMC Genomics 2014, 15:23  doi:10.1186/1471-2164-15-23

Published: 14 January 2014



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.


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.


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.

Chlamydia pecorum; Genome sequence; Polymorphic membrane proteins; Plasticity zone; Tryptophan metabolism; Folate biosynthesis; Clustered tandem repeats