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Background   Chlamydia abortus  and  Chlamydia psittaci  are important pathogens of livestock and avian species, respectively. While  C. abortus  is recognized as descended from  C. psittaci  species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of  C. abortus . Such strains include  C. psittaci  strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both  C. abortus  and  C. psittaci .    Results  In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with  C. abortus  species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to  C. abortus  in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with  C. abortus  strains. The analysis also suggested a closer evolutionary relationship between this strain and the major  C. abortus  clade, than to two other intermediary avian  C. abortus  strains or  C. psittaci  strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced  C. abortus  genomes as well as similar features to both  C. abortus  and  C. psittaci  species. The strain also possesses an extrachromosomal plasmid, as found in most  C. psittaci  species but absent from all sequenced classical  C. abortus  strains.    Conclusion  Overall, the results show that  C. psittaci  strain 84/2334 clusters very closely with  C. abortus  strains, and are consistent with the strain being a recent  C. abortus  ancestral species. This suggests that the strain should be reclassified as  C. abortus . Furthermore, the identification of a  C. abortus  strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from  C. abortus  infection.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07477-6.

bmc genomics

Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species