title: Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.
abstract: Chlamydia trachomatis causes sexually transmitted infections and the blinding disease trachoma. Current data on C. trachomatis 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 C. trachomatis 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 C. trachomatis phylogenetic tree. The Australian trachoma isolates appear to be recombinants with UGT C. trachomatis genome backbones, in which loci that encode immunodominant surface proteins (ompA and pmpEFGH) have been replaced by those characteristic of classical ocular isolates.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 ompA and pmpEFGH.
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.
authors.forename: Patiyan
authors.initials: P
authors.lastname: Andersson
authors.affiliation: Pathogen Variation Programme, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Pathogen Variation Programme, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.|Functional Genomics Centre Zürich, University of Zurich, Zurich CH-8057, Switzerland.|Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich CH-8057, Switzerland.
authors.forename: Helena M B Seth
authors.initials: HMBS
authors.lastname: Smith
authors.affiliation: Pathogen Variation Programme, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
authors.forename: James
authors.initials: J
authors.lastname: Hadfield
authors.affiliation: Department of Clinical and Experimental Science, Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, UK.
authors.forename: Colette
authors.initials: C
authors.lastname: O'Neill
authors.affiliation: Department of Clinical and Experimental Science, Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, UK.
authors.forename: Lesley T
authors.initials: LT
authors.lastname: Cutcliffe
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.
authors.forename: Fiona P
authors.initials: FP
authors.lastname: Douglas
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.
authors.forename: L Valerie
authors.initials: LV
authors.lastname: Asche
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.|School of Population and Global Health, University of Melbourne, Melbourne, Victoria 3010, Australia.
authors.forename: John D
authors.initials: JD
authors.lastname: Mathews
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.
authors.forename: Susan I
authors.initials: SI
authors.lastname: Hutton
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.
authors.forename: Derek S
authors.initials: DS
authors.lastname: Sarovich
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.
authors.forename: Steven Y C
authors.initials: SYC
authors.lastname: Tong
authors.affiliation: Department of Clinical and Experimental Science, Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, UK.
authors.forename: Ian N
authors.initials: IN
authors.lastname: Clarke
authors.affiliation: Pathogen Variation Programme, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.|Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina, Northern Territory 0811, Australia.|School of Psychological and Clinical Sciences, Charles Darwin University, Casuarina, Northern Territory 0811, Australia.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Giffard
mesh_terms: D000328:Adult; D001315:Australia / Q000453:epidemiology; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics*; D002648:Child; D002692:Chlamydia trachomatis / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic; D019353:Endemic Diseases; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D012703:Serotyping; D014141:Trachoma / Q000208:ethnology / Q000382:microbiology*
chemical_list: D001425:Bacterial Outer Membrane Proteins; C410161:PmpG protein, Chlamydia trachomatis; C410162:PmpH protein, Chlamydia trachomatis; C078167:OMPA outer membrane proteins