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Current data on <jats:italic>C. trachomatis<\/jats:italic> phylogeny show that there is only a single trachoma-causing clade, which is distinct from the lineages causing urogenital tract (UGT) and lymphogranuloma venerum diseases. Here we report the whole-genome sequences of ocular <jats:italic>C. trachomatis<\/jats:italic> isolates obtained from young children with clinical signs of trachoma in a trachoma endemic region of northern Australia. The isolates form two lineages that fall outside the classical trachoma lineage, instead being placed within UGT clades of the <jats:italic>C. trachomatis<\/jats:italic> phylogenetic tree. The Australian trachoma isolates appear to be recombinants with UGT <jats:italic>C. trachomatis<\/jats:italic> genome backbones, in which loci that encode immunodominant surface proteins (<jats:italic>ompA<\/jats:italic> and <jats:italic>pmpEFGH<\/jats:italic>) have been replaced by those characteristic of classical ocular isolates. This suggests that ocular tropism and association with trachoma are functionally associated with some sequence variants of <jats:italic>ompA<\/jats:italic> and <jats:italic>pmpEFGH<\/jats:italic>.<\/jats:p>","DOI":"10.1038\/ncomms10688","type":"journal-article","created":{"date-parts":[[2016,2,25]],"date-time":"2016-02-25T10:24:24Z","timestamp":1456395864000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages"],"prefix":"10.1038","volume":"7","author":[{"given":"Patiyan","family":"Andersson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon R.","family":"Harris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena M. B. 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