Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture Full article

Journal

Genome Research
ISSN: 1088-9051 , E-ISSN: 1549-5469

Output data

Year: 2013, Volume: 23, Number: 5, Pages: 855-866 Pages count : 12 DOI: 10.1101/gr.150037.112

Authors

Seth-Smith Helena M.B. ¹ , Harris Simon R. ¹ , Skilton Rachel J. ² , Radebe Frans M. ³ , Golparian Daniel ⁴ , Shipitsyna Elena ⁵ , Duy Pham Thanh ⁶ , Scott Paul ¹ , Cutcliffe Lesley T. ² , O’Neill Colette ² , Parmar Surendra ⁷ , Pitt Rachel ⁸ , Baker Stephen ⁶ , Ison Catherine A. ⁸ , Marsh Peter ⁹ , Jalal Hamid ⁷ , Lewis David A. ^10,3 , Unemo Magnus ⁴ , Clarke Ian N. ² , Parkhill Julian ¹ , Thomson Nicholas R. ¹

Affiliations

1	1Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;
2	2Molecular Microbiology Group, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, United Kingdom;
3	3Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa;
4	4WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for Pathogenic Neisseria, Örebro University Hospital, Örebro SE-701 85, Sweden;
5	5Laboratory of Microbiology, D.O. Ott Research Institute of Obstetrics and Gynaecology, 199034, St. Petersburg, Russia;
6	6Oxford University Clinical Research Unit, Wellcome Trust Major Overseas List, The Hospital for Tropical Diseases, Ho Chi Minh City, Q5, Vietnam;
7	7Clinical Microbiology and Public Health Laboratory, Health Protection Agency, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom;
8	8Sexually Transmitted Bacteria Reference Laboratory, Health Protection Agency, Colindale, London NW9 5HT, United Kingdom;
9	9Health Protection Agency, Public Health Laboratory Southampton, Southampton General Hospital, Southampton SO16 6YD, United Kingdom;
10	10Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa

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 in 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.

Seth-Smith H.M.B. , Harris S.R. , Skilton R.J. , Radebe F.M. , Golparian D. , Shipitsyna E. , Duy P.T. , Scott P. , Cutcliffe L.T. , O’Neill C. , Parmar S. , Pitt R. , Baker S. , Ison C.A. , Marsh P. , Jalal H. , Lewis D.A. , Unemo M. , Clarke I.N. , Parkhill J. , Thomson N.R.
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
Genome Research. 2013. V.23. N5. P.855-866. DOI: 10.1101/gr.150037.112 WOS Scopus РИНЦ OpenAlex

Published online:

Feb 12, 2013

Web of science:	WOS:000318202400010
Scopus:	eid_2-s2.0-84877118112
Elibrary:	20443365
OpenAlex:	W2158378925

DB	Citing
OpenAlex	123
Web of science	102