Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species

Abstract

BackgroundChlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species.ResultsWe performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes).ConclusionsWe have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.

Evidence for horizontal gene transfer betweenChlamydophila pneumoniaeand Chlamydia phage

“…13,15 PRIP from the 4 human-infecting strains is 100% identical at the DNA sequence level, while the one found in the koala-infecting LPCoLN strain is slightly different. It is thought DNA sequences shared between related organisms but absent in close relatives are likely acquired via horizontal gene transfer.…”

“…26), is found in the LPCoLN strain. 13 This gene CPK_ORF00730 (nucleotides 580833-581277) is annotated in GenBank as "scaffolding protein, authentic frameshift." This region shows homology to the Chlamydia phage VP3 gene, but is missing 2 nucleotides, resulting in the frameshift (Fig.…”

“…12), but the LPCoLN genome is larger and includes a number of additional genes not found in the human-infecting strains. 13 Six different Chlamydia-infecting bacteriophages have also been sequenced (fChp1 [refs. [14][15][16] 23 specifically the sub-group infecting obligate intracellular parasites, the Gokushovirinae, 24,25 these single-stranded DNA phages are distantly related to fX-174.…”

“…27 Previous reports called attention to the fact that orthologs of Chlamydia phage genes are found in C. pneumoniae. 13,15,28 With the availability of additional phage and bacterial sequences, we evaluated the extent to which horizontal gene transfer between Chlamydia bacteriophages and Chlamydia species might have occurred. Here we report findings from our bioinformatics analysis, which are consistent with the hypothesis that first, genes could have been acquired by C. pneumoniae from the phage; and second, that this transfer event may have occurred in the ancestor of the existing C. pneumoniae strains, since we find no evidence for the phage sequences in other Chlamydia or Chlamydophila species, however from this analysis we can't rule out the possibility that the bacterial and the phage PRIP sequences evolved independently.…”

Mutational Analysis of the Chlamydia muridarum Plasticity Zone

“…Thus, if unrelated background mutations were not responsible for the very similar GT phenotypes, our results suggest C. muridarum could encode an additional cryptic GMP synthase enzyme or that C. muridarum purine salvage acts noncanonically. The guaBA-add cluster has been retained by several chlamydial species, including those that cause respiratory illness, such as Chlamydia psittaci, Chlamydia felis, and human isolates of C. pneumoniae, but it is unknown if they are functional (33,46,47). guaA and guaB are known virulence deter- (48,49).…”