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

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

doi:10.1186/1471-2164-15-23

Abstract

BackgroundChlamydia 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.ResultsGene 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.ConclusionsGenome 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-23) contains supplementary material, which is available to authorized users.

Highlights

Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds
We present the complete genome sequences of three C. pecorum strains isolated from animals exhibiting different disease manifestations and use comparative genomics to provide insights into the biology of C. pecorum and to identify both genus- and species-specific virulence factors
There are 38 tRNA genes corresponding to all the amino acids except selenocysteine and pyrrolysine, one rRNA operon, and 3 small non-coding RNAs (sRNA) molecules corresponding to SsrA, RNaseP and ffs (Additional file 1: Table S1) present in each chromosome

Summary

Introduction

Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. 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. Chlamydia pecorum infects a broad host range, including small and large ruminants, swine, birds and marsupials. Seroprevalence and PCR-based studies suggest that infection or exposure to C. pecorum induced in vitro by antibiotic exposure [7], amino acid[8] or iron- [9] deficiencies and exposure to IFN-γ [10] and it is likely that C. pecorum causes a persistent, subclinical infection in the host. C. pecorum can cause clinical disease including encephalomyelitis, vaginitis, endometritis, mastitis, conjunctivitis, polyarthritis, pneumonia, enteritis, orchitis, pleuritis, infertility or pericarditis [6]

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