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The obligate intracellular bacterial pathogen  Chlamydophila abortus  strain S26/3 (formerly the abortion subtype of  Chlamydia psittaci ) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other  Chlamydiaceae . The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of  Chlamydophila caviae  and  Chlamydophila pneumoniae . Within this conserved  Cp. abortus  core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly,  Cp. abortus  lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging ( guaB  is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species.

The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation