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Background    Chlamydia abortus  (formerly  Chlamydophila abortus ) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on  C. abortus . Our aim was to investigate a broad collection of European isolates of  C. abortus , using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics.    Results  Whole genome sequencing was performed on our collection of 57  C. abortus  isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the  C. abortus  species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for  C. trachomatis  and  C. psittaci . No recombination was identified within  C. abortus , and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied.    Conclusions  The diversity within  C. abortus  appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of  Chlamydia  may demonstrate different evolutionary dynamics, and that the genome of  C. abortus  is highly stable.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3657-y) contains supplementary material, which is available to authorized users.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures