{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T16:42:15Z","timestamp":1784824935017,"version":"3.55.0"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82002193"],"award-info":[{"award-number":["82002193"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["3332019092"],"award-info":[{"award-number":["3332019092"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences","award":["2016-I2M-3-021"],"award-info":[{"award-number":["2016-I2M-3-021"]}]},{"name":"Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences","award":["2019PT310029"],"award-info":[{"award-number":["2019PT310029"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Antimicrobial resistance (AMR) of Neisseria gonorrhoeae has spread worldwide. Rapid and comprehensive methods are needed to describe N. gonorrhoeae AMR profiles accurately. A method based on multiplex amplicon sequencing was developed to simultaneously sequence 13 genes related to AMR in N. gonorrhoeae directly from clinical samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Nine N. gonorrhoeae strains were used for the establishment and validation of the method. Eleven urethral swabs and their corresponding cultured isolates were matched as pairs to determine the accuracy of the method. Mock samples with different dilutions were prepared to determine the sensitivity of the method. Five nongonococcal Neisseria strains and 24\u2009N. gonorrhoeae negative clinical samples were used to evaluate the cross-reactivity. Finally, the method was applied to 64 clinical samples to assess its performance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Using Sanger sequencing as a reference method, sequences recovered from amplicon sequencing had a base accuracy of over 99.5% and the AMR sites were correctly identified. The limit of detection (LOD) was lower than 31 copies\/reaction. No significant cross-reactivity was observed. Furthermore, target genes were successfully recovered from 64 clinical samples including 9 urines, demonstrating this method could be used in different types of samples. For clinical samples, the results can be obtained within a time frame of 7\u2009h 40\u2009min to 10\u2009h 40\u2009min, while for isolates, the turnaround time was approximately 2\u2009h shorter.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This method can serve as a versatile and convenient culture-free diagnostic method with the advantages of high sensitivity and accuracy.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/clinchem\/hvaa306","type":"journal-article","created":{"date-parts":[[2020,11,20]],"date-time":"2020-11-20T13:18:24Z","timestamp":1605878304000},"page":"610-620","source":"Crossref","is-referenced-by-count":32,"title":["Multiplex PCR and Nanopore Sequencing of Genes Associated with Antimicrobial Resistance in <i>Neisseria gonorrhoeae<\/i> Directly from Clinical Samples"],"prefix":"10.1093","volume":"67","author":[{"given":"Chi","family":"Zhang","sequence":"first","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"},{"name":"Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leshan","family":"Xiu","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"},{"name":"Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yamei","family":"Li","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"},{"name":"Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liying","family":"Sun","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"},{"name":"Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yizhun","family":"Li","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaling","family":"Zeng","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Wang","sequence":"additional","affiliation":[{"name":"Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7959-5286","authenticated-orcid":false,"given":"Junping","family":"Peng","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"},{"name":"Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"2021033116261437100_hvaa306-B1","doi-asserted-by":"crossref","first-page":"1800323","DOI":"10.2807\/1560-7917.ES.2018.23.27.1800323","article-title":"Gonorrhoea treatment failure caused by a Neisseria gonorrhoeae strain with combined ceftriaxone and high-level azithromycin resistance, England, February 2018","volume":"23","author":"Eyre","year":"2018","journal-title":"Euro Surveill"},{"key":"2021033116261437100_hvaa306-B2","doi-asserted-by":"crossref","first-page":"1800617","DOI":"10.2807\/1560-7917.ES.2018.23.47.1800617","article-title":"Multidrug-resistant Neisseria gonorrhoeae isolate, belonging to the internationally spreading Japanese FC428 clone, with ceftriaxone resistance and intermediate resistance to azithromycin, Ireland, August 2018","volume":"23","author":"Golparian","year":"2018","journal-title":"Euro 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