Evidence that human Chlamydia pneumoniae was zoonotically acquired

Abstract

Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species of Chlamydia, C. pecorum and C. pneumoniae. Transmission of C. pneumoniae between animals and humans has not been reported; however, two other chlamydial species, C. psittaci and C. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.

FIG. 1.

Circular representation of C. pneumoniae genomes and comparative analyses. For each genome, data are from outermost circle to innermost. In circles 1 and 2, tick marks represent predicted CDSs on the plus strand of C. pneumoniae AR39 and minus strand, respectively, colored by cellular role as follows: amino acid biosynthesis, violet; biosynthesis of cofactors, prosthetic groups, and carriers, light blue; cell envelope, light green; cellular processes, red; central intermediary metabolism, brown; DNA metabolism, gold; energy metabolism, light gray; fatty acid and phospholipid metabolism, magenta; protein synthesis and fate, pink; biosynthesis of purines, pyrimidines, nucleosides, and nucleotides, orange; regulatory functions and signal transduction, olive; transcription, dark green; transport and binding proteins, blue-green; other categories, salmon; unknown function, gray; conserved hypothetical proteins, blue; hypothetical proteins, black. Circles 3 and 4 show a histogram of cumulative SNP density on the plus and minus strands, respectively, of the LPCoLN genome compared to AR39, using a 5,000-bp window. Histogram coloring: <30 SNPs, red; 20 to 29 SNPs, orange; 10 to 19 SNPs, yellow; 0 to 9 SNPs, light blue. In circles 5 and 6, tick marks represent SNP locations on the plus (green) and minus (red) strands, respectively, of the LPCoLN genome. In circles 7 to 12, tick marks represent SNP locations on the plus (green) and minus (red) strands of the TW183 (circles 7 and 8), J138 (circles 9 and 10), and CWL-029 (circles 11 and 12) genomes. Ten regions of high SNP accumulation in the LPCoLN genome versus AR39 are marked with light blue radial sections and numbered. The top and bottom panels show detail of high SNP accumulation in regions III and VI, with SNP location and type (synonymous, green; nonsynonymous, red) within PMP clusters ([left to right] LPCoLN gene region, ORF00989 to ORF00956; AR39 gene region, CP_0280 to CP_0309) and the PZ (LPCoLN gene region, ORF00689 to ORF00665; AR39 gene region, CP_0585 to CP_0622), respectively. Grey highlighting shows SNP-associated CDS fragmentation.

FIG. 2.

sSNP phylogenetic tree using all sequenced C. pneumoniae genomes. The number of separating sSNPs is give on each branch.

FIG. 3.

Phylogeny of all animal chlamydiae and C. pneumoniae, using 111 highly conserved gene clusters. The host range for each species is noted in parentheses; the known chlamydial zoonotic agents are boxed. The bootstrap value at each branch point is 100% unless otherwise indicated.

FIG. 4.

Annotated detail of additional regions shown in Fig. 1 with high SNP accumulation, showing SNP location and type (synonymous, green; nonsynonymous, red). Colors are used to distinguish notable annotated genes in each region. Gray highlighting shows SNP-associated CDS fragmentation. The icon to the left of each region denotes the approximate location of each region in Fig. 1.

FIG. 4.

Annotated detail of additional regions shown in Fig. 1 with high SNP accumulation, showing SNP location and type (synonymous, green; nonsynonymous, red). Colors are used to distinguish notable annotated genes in each region. Gray highlighting shows SNP-associated CDS fragmentation. The icon to the left of each region denotes the approximate location of each region in Fig. 1.