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  • 1.
    Hadfield, James
    et al.
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
    Harris, Simon R
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
    Seth-Smith, Helena M B
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Clinical Microbiology, University Hospital Basel, Basel, Switzerland.
    Parmar, Surendra
    Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
    Andersson, Patiyan
    Menzies School of Health Research, Darwin NT, Australia.
    Giffard, Philip M.
    Menzies School of Health Research, Darwin NT, Australia; School of Psychological and Clinical Sciences, Charles Darwin University, Darwin, Australia.
    Schachter, Julius
    Department of Laboratory Medicine, University of California, San Francisco CA, USA.
    Moncada, Jeanne
    Department of Laboratory Medicine, University of Californiao, San Francisco CA, USA.
    Ellison, Louise
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
    Vaulet, María Lucía Gallo
    Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Microbiología Clínica, Universidad de Buenos Aires, Buenos Aires, Argentina.
    Fermepin, Marcelo Rodríguez
    Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Microbiología Clínica, Universidad de Buenos Aires, Buenos Aires, Argentina.
    Radebe, Frans
    Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
    Mendoza, Suyapa
    Jefe Laboratorio de ITS, Laboratorio Nacional de Vigilancia, Honduras.
    Ouburg, Sander
    Department of Medical Microbiology and Infection Control, Laboratory of Immunogenetics, Vrije University Medical Center, Amsterdam, The Netherlands.
    Morré, Servaas A
    Department of Medical Microbiology and Infection Control, Laboratory of Immunogenetics, Vrije University Medical Center, Amsterdam, The Netherlands; Department of Genetics and Cell Biology, Institute of Public Health Genomics, School for Oncology & Developmental Biology (GROW), Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, The Netherlands.
    Sachse, Konrad
    Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany.
    Puolakkainen, Mirja
    Department of Virology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.
    Korhonen, Suvi J
    Department of Virology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.
    Sonnex, Chris
    Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
    Wiggins, Rebecca
    Department of Biology, University of York, York, United Kingdom.
    Jalal, Hamid
    Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
    Brunelli, Tamara
    Clinical Chemistry and Microbiology Laboratory, Santo Stefano Hospital, Prato, Italy.
    Casprini, Patrizia
    Clinical Chemistry and Microbiology Laboratory, Santo Stefano Hospital, Prato, Italy.
    Pitt, Rachel
    Sexually Transmitted Bacteria Reference Unit, Microbiological Services, Public Health England, London, United Kingdom.
    Ison, Cathy
    Sexually Transmitted Bacteria Reference Unit, Microbiological Services, Public Health England, London, United Kingdom.
    Savicheva, Alevtina
    Laboratory of Microbiology, D.O. Ott Research Institute of Obstetrics and Gynecology, St. Petersburg, Russia.
    Shipitsyna, Elena
    Laboratory of Microbiology, D.O. Ott Research Institute of Obstetrics and Gynecology, St. Petersburg, Russia; WHO Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden.
    Hadad, Ronza
    Örebro University, School of Science and Technology. WHO Collaborating Centre for Gonorrhoea and other STIs, Örebro University Hospital, Örebro, Sweden.
    Kari, Laszlo
    Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton Montana, USA.
    Burton, Matthew J
    Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.
    Mabey, David
    Centre for Infectious Diseases and Microbiology, Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Clinical School, University of Sydney, Sydney, Australia.
    Solomon, Anthony W
    Centre for Infectious Diseases and Microbiology, Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Clinical School, University of Sydney, Sydney, Australia.
    Lewis, David
    Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Centre for Infectious Diseases and Microbiology, Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Clinical School, University of Sydney, Sydney, Australia.
    Marsh, Peter
    Public Health England, Public Health Laboratory Southampton, Southampton General Hospital, Southampton, United Kingdom.
    Unemo, Magnus
    Örebro University, School of Medical Sciences; WHO Collaborating Centre for Gonorrhoea and other STIs, Örebro University Hospital, Örebro, Sweden.
    Clarke, Ian N
    Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, United Kingdom.
    Parkhill, Julian
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
    Thomson, Nicholas R.
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom; Department of Pathogen Molecular Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom.
    Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion2017In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 7, p. 1220-1229Article in journal (Refereed)
    Abstract [en]

    Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.

  • 2.
    Seth-Smith, Helena M. B.
    et al.
    Wellcome Trust Sanger Inst, Hinxton, England.
    Harris, Simon R.
    Wellcome Trust Sanger Inst, Hinxton, England.
    Skilton, Rachel J.
    Fac Med, Mol Microbiol Grp, Southampton Gen Hosp, Univ Southampton, Southampton, England.
    Radebe, Frans M.
    Natl Inst Communicable Dis, Ctr HIV & Sexually Transmitted Infect, National Health Laboratory Service, Johannesburg, South Africa.
    Golparian, Daniel
    Natl Reference Lab Pathogen Neisseria, WHO Collaborating Ctr Gonorrhoea & Other STIs, Örebro University Hospital, Örebro, Sweden.
    Shipitsyna, Elena
    Lab Microbiol, DO Ott Res Inst Obstet & Gynaecol, St Petersburg, Russia.
    Duy, Pham Thanh
    Scott, Paul
    Wellcome Trust Sanger Inst, Hinxton, England.
    Cutcliffe, Lesley T.
    Fac Med, Mol Microbiol Grp, Southampton Gen Hosp, Univ Southampton, Southampton, England.
    O'Neill, Colette
    Fac Med, Mol Microbiol Grp, Southampton Gen Hosp, Univ Southampton, Southampton, England.
    Parmar, Surendra
    Hlth Protect Agcy, Clin Microbiol & Publ Hlth Lab, Addenbrookes Hosp, Cambridge, England.
    Pitt, Rachel
    Sexually Transmitted Bacteria Reference Lab, Health Protection Agency, London, England.
    Baker, Stephen
    Clin Res Unit, Wellcome Trust Major Overseas List, Hosp Trop Dis, Univ Oxford, Ho Chi Minh City, Vietnam.
    Ison, Catherine A.
    Sexually Transmitted Bacteria Reference Lab, Health Protection AgencyLondon NW9 5HT, England..
    Marsh, Peter
    Publ Hlth Lab Southampton, Health Protection Agency, Southampton Gen Hosp, Southampton, England.
    Jalal, Hamid
    Health Protection Agency, Clin Microbiol & Publ Hlth Lab, Addenbrookes Hosp, Cambridge, England.
    Lewis, David A.
    Natl Inst Communicable Dis, Ctr HIV & Sexually Transmitted Infect, National Health Laboratory ServiceJohannesburg, South Africa; Fac Hlth Sci, Dept Internal Med, Univ Witwatersrand, Johannesburg, South Africa.
    Unemo, Magnus
    Örebro University Hospital. Natl Reference Lab Pathogen Neisseria, WHO Collaborating Ctr Gonorrhoea & Other STIs, Örebro University Hospital, Örebro, Sweden.
    Clarke, Ian N.
    Fac Med, Mol Microbiol Grp, Southampton Gen Hosp, Univ Southampton, Southampton, England.
    Parkhill, Julian
    Wellcome Trust Sanger Inst, Hinxton, England.
    Thomson, Nicholas R.
    Wellcome Trust Sanger Inst, Hinxton, England.
    Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture2013In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 23, no 5, p. 855-866Article in journal (Refereed)
    Abstract [en]

    The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA ill conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern.

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