{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T21:05:41Z","timestamp":1763499941289,"version":"3.37.3"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,3,28]],"date-time":"2024-03-28T00:00:00Z","timestamp":1711584000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2021A1515012255, 2023A1515012021","2021B1212030014"],"award-info":[{"award-number":["2021A1515012255, 2023A1515012021","2021B1212030014"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011478","name":"Foshan Science and Technology Bureau","doi-asserted-by":"publisher","award":["2220001004153"],"award-info":[{"award-number":["2220001004153"]}],"id":[{"id":"10.13039\/501100011478","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Foshan Municipal Health Bureau","award":["20220311"],"award-info":[{"award-number":["20220311"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,10,16]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n Chlamydia trachomatis is the causative agent of the most prevalent bacterial sexually transmitted infections globally. Whole genome sequencing is essential for molecular Chlamydia surveillance; however, its application is hampered by the pathogen's low abundance in clinical specimens and the expensive labor-intensive nature of existing enrichment methodologies for Chlamydia.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n We developed a targeted whole genome amplification tool termed SWITCH by integrating phi29 DNA polymerase-mediated amplification with meticulously designed primer sets to enrich the C trachomatis genome, followed by whole genome sequencing. This method underwent evaluation through testing synthetic and clinical specimens.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n SWITCH demonstrated robust ability to achieve up to 98.3% genomic coverage of C trachomatis from as few as 26.4 genomic copies present in synthetic specimens, and it exhibited excellent performance across diverse C trachomatis serovars. Utilizing SWITCH, we directly generated 21 Chlamydia genomes from 26 clinical samples, enabling us to gain insights into the genetic relationships and phylogeny of current Chlamydia strains circulating in the country. Remarkably, this study marked the first instance of generating Chinese Chlamydia genomes directly from clinical samples.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n SWITCH represents a practical cost-efficient approach to enrich the Chlamydia genome directly from clinical specimens, offering an efficient avenue for molecular surveillance of Chlamydia.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/infdis\/jiae163","type":"journal-article","created":{"date-parts":[[2024,3,28]],"date-time":"2024-03-28T21:13:14Z","timestamp":1711660394000},"page":"857-867","source":"Crossref","is-referenced-by-count":1,"title":["Revealing the Genetic Diversity of Chinese Chlamydia trachomatis<\/i> Strains Directly From Clinical Samples Through Selective Whole Genome Amplification"],"prefix":"10.1093","volume":"230","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4062-3865","authenticated-orcid":false,"given":"Wentao","family":"Chen","sequence":"first","affiliation":[{"name":"BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China"},{"name":"Dermatology Hospital, Southern Medical University , Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuchan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Maoming People's Hospital, Southern Medical University , Maoming, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine) , Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaona","family":"Yin","sequence":"additional","affiliation":[{"name":"Dermatology Hospital, Southern Medical University , Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weixi","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Foshan Women and Children Hospital, Foshan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuncai","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Lecong Hospital of Shunde , Foshan ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Zhao","sequence":"additional","affiliation":[{"name":"BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,3,28]]},"reference":[{"key":"2024101612583611000_jiae163-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1093\/infdis\/jis644","article-title":"Chlamydia public health programs and the epidemiology of pelvic inflammatory disease and ectopic pregnancy","volume":"207","author":"Rekart","year":"2013","journal-title":"J Infect Dis"},{"author":"World Health Organization","key":"2024101612583611000_jiae163-B2"},{"key":"2024101612583611000_jiae163-B3","first-page":"596","article-title":"Epidemiologic features of genital Chlamydia trachomatis infection at national sexually transmitted disease surveillance sites in China, 2015\u20132019","volume":"53","author":"Yue","year":"2020","journal-title":"Chin J Dermatol"},{"key":"2024101612583611000_jiae163-B4","doi-asserted-by":"crossref","first-page":"e1197","DOI":"10.1016\/S2214-109X(19)30279-7","article-title":"Epidemiology of Chlamydia trachomatis in the Middle East and North Africa: a systematic review, meta-analysis, and meta-regression","volume":"7","author":"Smolak","year":"2019","journal-title":"Lancet Glob Health"},{"key":"2024101612583611000_jiae163-B5","first-page":"100143","article-title":"Spatiotemporal analysis of 11 years of Chlamydia trachomatis data from southern China","volume":"11","author":"Smith","year":"2021","journal-title":"Lancet Reg Health West Pac"},{"key":"2024101612583611000_jiae163-B6","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1098\/rsif.2011.0131","article-title":"Transmission of Chlamydia trachomatis through sexual partnerships: a comparison between three individual-based models and empirical data","volume":"9","author":"Althaus","year":"2012","journal-title":"J R Soc Interface"},{"key":"2024101612583611000_jiae163-B7","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1093\/aje\/kwy272","article-title":"The impact of screening and partner notification on Chlamydia prevalence and numbers of infections averted in the United States, 2000\u20132015: evaluation of epidemiologic trends using a pair-formation transmission model","volume":"188","author":"R\u00f6nn","year":"2019","journal-title":"Am J Epidemiol"},{"key":"2024101612583611000_jiae163-B8","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1136\/sextrans-2013-051381","article-title":"The sexual health of female sex workers compared with other women in England: analysis of cross-sectional data from genitourinary medicine clinics","volume":"90","author":"McGrath-Lone","year":"2014","journal-title":"Sex Transm Infect"},{"key":"2024101612583611000_jiae163-B9","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1136\/sti.2010.042770","article-title":"Sexually transmitted infections among female sex workers in Tunisia: high prevalence of Chlamydia trachomatis","volume":"86","author":"Znazen","year":"2010","journal-title":"Sex Transm Infect"},{"key":"2024101612583611000_jiae163-B10","doi-asserted-by":"crossref","first-page":"e0001782","DOI":"10.1371\/journal.pgph.0001782","article-title":"Sexually transmitted infections amongst men who have sex with men (MSM) in South Africa","volume":"3","author":"Mashingaidze","year":"2023","journal-title":"PLOS Glob Public Health"},{"key":"2024101612583611000_jiae163-B11","doi-asserted-by":"crossref","first-page":"21270","DOI":"10.7448\/IAS.19.1.21270","article-title":"High prevalence of HIV, chlamydia and gonorrhoea among men who have sex with men and transgender women attending trusted community centres in Abuja and Lagos, Nigeria","volume":"19","author":"Keshinro","year":"2016","journal-title":"J Int AIDS Soc"},{"key":"2024101612583611000_jiae163-B12","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1056\/NEJMoa2211934","article-title":"Postexposure doxycycline to prevent bacterial sexually transmitted infections","volume":"388","author":"Luetkemeyer","year":"2023","journal-title":"N Engl J Med"},{"key":"2024101612583611000_jiae163-B13","doi-asserted-by":"crossref","first-page":"1036264","DOI":"10.3389\/fpubh.2022.1036264","article-title":"Distribution of Chlamydia trachomatis ompA genotypes and its association with abnormal cervical cytology among women of reproductive age in Shenzhen, China","volume":"10","author":"Liu","year":"2022","journal-title":"Front Public Health"},{"key":"2024101612583611000_jiae163-B14","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1128\/JCM.00249-15","article-title":"Global multilocus sequence type analysis of Chlamydia trachomatis strains from 16 countries","volume":"53","author":"Herrmann","year":"2015","journal-title":"J Clin Microbiol"},{"key":"2024101612583611000_jiae163-B15","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.3201\/eid1509.090272","article-title":"Predicting phenotype and emerging strains among Chlamydia trachomatis infections","volume":"15","author":"Dean","year":"2009","journal-title":"Emerg Infect Dis"},{"key":"2024101612583611000_jiae163-B16","doi-asserted-by":"crossref","first-page":"e0159658","DOI":"10.1371\/journal.pone.0159658","article-title":"Prevalence of Chlamydia trachomatis genotypes in men who have sex with men and men who have sex with women using multilocus VNTR analysis-ompA typing in Guangzhou, China","volume":"11","author":"Qin","year":"2016","journal-title":"PLoS One"},{"key":"2024101612583611000_jiae163-B17","doi-asserted-by":"crossref","first-page":"10688","DOI":"10.1038\/ncomms10688","article-title":"Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages","volume":"7","author":"Andersson","year":"2016","journal-title":"Nat Commun"},{"key":"2024101612583611000_jiae163-B18","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/ng.2214","article-title":"Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing","volume":"44","author":"Harris","year":"2012","journal-title":"Nat Genet"},{"key":"2024101612583611000_jiae163-B19","doi-asserted-by":"crossref","first-page":"2109","DOI":"10.1099\/mic.0.070029-0","article-title":"Culture-independent sequence analysis of Chlamydia trachomatis in urogenital specimens identifies regions of recombination and in-patient sequence mutations","volume":"159","author":"Putman","year":"2013","journal-title":"Microbiology"},{"key":"2024101612583611000_jiae163-B20","doi-asserted-by":"crossref","first-page":"e99290","DOI":"10.1371\/journal.pone.0099290","article-title":"Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples","volume":"9","author":"Joseph","year":"2014","journal-title":"PLoS One"},{"key":"2024101612583611000_jiae163-B21","first-page":"6","article-title":"Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from patient clinical vaginal and rectal swabs","author":"Bowden","year":"2021","journal-title":"mSphere"},{"key":"2024101612583611000_jiae163-B22","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1186\/s12879-014-0591-3","article-title":"Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples","volume":"14","author":"Christiansen","year":"2014","journal-title":"BMC Infect Dis"},{"key":"2024101612583611000_jiae163-B23","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1101\/gr.150037.112","article-title":"Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture","volume":"23","author":"Seth-Smith","year":"2013","journal-title":"Genome Res"},{"key":"2024101612583611000_jiae163-B24","doi-asserted-by":"crossref","first-page":"e0000922","DOI":"10.1128\/msphere.00009-22","article-title":"Selective whole-genome amplification as a tool to enrich specimens with low Treponema pallidum genomic DNA copies for whole-genome sequencing","volume":"7","author":"Thurlow","year":"2022","journal-title":"mSphere"},{"key":"2024101612583611000_jiae163-B25","doi-asserted-by":"crossref","first-page":"e1011230","DOI":"10.1371\/journal.ppat.1011230","article-title":"Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies","volume":"19","author":"Pilling","year":"2023","journal-title":"PLoS Pathog"},{"key":"2024101612583611000_jiae163-B26","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1471-2334-8-56","article-title":"Rapid detection of Chlamydia trachomatis and typing of the Lymphogranuloma venereum associated L-serovars by TaqMan PCR","volume":"8","author":"Schaeffer","year":"2008","journal-title":"BMC Infect Dis"},{"key":"2024101612583611000_jiae163-B27","doi-asserted-by":"crossref","first-page":"e1010137","DOI":"10.1371\/journal.pcbi.1010137","article-title":"A fast machine-learning-guided primer design pipeline for selective whole genome amplification","volume":"19","author":"Dwivedi-Yu","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2024101612583611000_jiae163-B28","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1038\/s41564-021-01000-z","article-title":"Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis","volume":"6","author":"Beale","year":"2021","journal-title":"Nat Microbiol"},{"key":"2024101612583611000_jiae163-B29","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol"},{"key":"2024101612583611000_jiae163-B30","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2024101612583611000_jiae163-B31","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.12688\/f1000research.15931.1","article-title":"FastQ Screen: a tool for multi-genome mapping and quality control","volume":"7","author":"Wingett","year":"2018","journal-title":"F1000Res"},{"key":"2024101612583611000_jiae163-B32","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/bioinformatics\/bty630","article-title":"Simulating Illlumina metagenomic data with InSilicoSeq","volume":"35","author":"Gourl\u00e9","year":"2019","journal-title":"Bioinformatics"},{"year":"2013","author":"Li","key":"2024101612583611000_jiae163-B33"},{"key":"2024101612583611000_jiae163-B34","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2024101612583611000_jiae163-B35","doi-asserted-by":"crossref","first-page":"2678","DOI":"10.1093\/bioinformatics\/bts503","article-title":"Qualimap: evaluating next-generation sequencing alignment data","volume":"28","author":"Garc\u00eda-Alcalde","year":"2012","journal-title":"Bioinformatics"},{"key":"2024101612583611000_jiae163-B36","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2024101612583611000_jiae163-B37","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024101612583611000_jiae163-B38","doi-asserted-by":"crossref","first-page":"e96","DOI":"10.1002\/cpbi.96","article-title":"Using ggtree to visualize data on tree-like structures","volume":"69","author":"Yu","year":"2020","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024101612583611000_jiae163-B39","first-page":"e000056","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"Page","year":"2016","journal-title":"Microb Genom"},{"key":"2024101612583611000_jiae163-B40","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res"},{"key":"2024101612583611000_jiae163-B41","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024101612583611000_jiae163-B42","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nrmicro.2016.30","article-title":"Chlamydia cell biology and pathogenesis","volume":"14","author":"Elwell","year":"2016","journal-title":"Nat Rev Microbiol"}],"container-title":["The Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jid\/advance-article-pdf\/doi\/10.1093\/infdis\/jiae163\/57350859\/jiae163.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jid\/article-pdf\/230\/4\/857\/59789964\/jiae163.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jid\/article-pdf\/230\/4\/857\/59789964\/jiae163.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,16]],"date-time":"2024-10-16T12:59:01Z","timestamp":1729083541000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jid\/article\/230\/4\/857\/7637135"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,28]]},"references-count":42,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2024,3,28]]},"published-print":{"date-parts":[[2024,10,16]]}},"URL":"https:\/\/doi.org\/10.1093\/infdis\/jiae163","relation":{},"ISSN":["0022-1899","1537-6613"],"issn-type":[{"type":"print","value":"0022-1899"},{"type":"electronic","value":"1537-6613"}],"subject":[],"published-other":{"date-parts":[[2024,10,15]]},"published":{"date-parts":[[2024,3,28]]}}}