Chlamydia pneumoniae Is Genetically Diverse in Animals and Appears to Have Crossed the Host Barrier to Humans on (At Least) Two Occasions

Abstract

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of diseases. Since the first isolation of C. pneumoniae TWAR in 1965, all human isolates have been essentially clonal, providing little evolutionary insight. To address this gap, we investigated the genetic diversity of 30 isolates from diverse geographical locations, from both human and animal origin (amphibian, reptilian, equine and marsupial). Based on the level of variation that we observed at 23 discreet gene loci, it was clearly evident that the animal isolates were more diverse than the isolates of human origin. Furthermore, we show that C. pneumoniae isolates could be grouped into five major genotypes, A-E, with A, B, D and E genotypes linked by geographical location, whereas genotype C was found across multiple continents. Our evidence strongly supports two separate animal-to-human cross species transfer events in the evolutionary history of this pathogen. The C. pneumoniae human genotype identified in the USA, Canada, Taiwan, Iran, Japan, Korea and Australia (non-Indigenous) most likely originated from a single amphibian or reptilian lineage, which appears to have been previously geographically widespread. We identified a separate human lineage present in two Australian Indigenous isolates (independent geographical locations). This lineage is distinct and is present in Australian amphibians as well as a range of Australian marsupials.

Characterisation of Chlamydia pneumoniae and other novel chlamydial infections in captive snakes

“…Due to a lack of full length chlamydial 16S rRNA sequences from reptiles, no further comparisons are able to be made within this host range. Nevertheless, phylogenetically, these novel genotypes form a clade separate from animal and human C. pneumoniae strains, supporting previous suggestions that human C. pneumoniae isolates have diverged from reptilian and amphibian C. pneumoniae isolates (Mitchell et al, 2010). The full length 16S rRNA gene of a novel genotype (genotype 4), is 96.9% and 96.8% identical to C. pneumoniae strains LPCoLN and TW-183, respectively, placing it as a novel species within the Chlamydiaceae (Everett et al, 1999).…”

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“…Nevertheless, phylogenetically, these novel genotypes form a clade separate from animal and human C. pneumoniae strains, supporting previous suggestions that human C. pneumoniae isolates have diverged from reptilian and amphibian C. pneumoniae isolates (Mitchell et al, 2010). Seven genotypes were found among six collections in Switzerland.…”

Candidatus Syngnamydia Venezia, a Novel Member of the Phylum Chlamydiae from the Broad Nosed Pipefish, Syngnathus typhle

“…Although molecular clock approaches have not been applied to the study of chlamydial evolution, the rate of genetic change in this group appears to be slow, given a high degree of synteny between different human strains of the species Chlamydia trachomatis or Chlamydia pneumoniae [1], [2], [3]. The evolutionary origins of the phylum Chlamydiae are old, associated with the rise of the cyanobacteria and plant life.…”