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

Sait, Michelle; Livingstone, Morag; Clark, Ewan M; Wheelhouse, Nick; Spalding, Lucy; Markey, Bryan; Magnino, Simone; Lainson, Frederick A; Myers, Garry S A; Longbottom, David

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.

Citation

Sait, M., Livingstone, M., Clark, E. M., Wheelhouse, N., Spalding, L., Markey, B., Magnino, S., Lainson, F. A., Myers, G. S. A., & Longbottom, D. (2014). Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes. BMC Genomics, 15, 23. https://doi.org/10.1186/1471-2164-15-23

• Journal Article Type: Article
• Acceptance Date: Jan 6, 2014
• Online Publication Date: Jan 14, 2014
• Publication Date: 2014
• Deposit Date: Jul 21, 2016
• Publicly Available Date: Jul 25, 2016
• Journal: BMC Genomics
• Electronic ISSN: 1471-2164
• Publisher: BMC
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Pages: 23
• DOI: https://doi.org/10.1186/1471-2164-15-23
• Keywords: Chlamydia pecorum , Genome sequence, Polymorphic membrane proteins, Plasticity zone, Tryptophan metabolism, Folate biosynthesis, Clustered tandem repeats
• Public URL: http://researchrepository.napier.ac.uk/Output/304735
• Related Public URLs: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932018/pdf/12864_2013_Article_7002.pdf
• Contract Date: Jul 25, 2016