{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T03:02:33Z","timestamp":1785207753497,"version":"3.55.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:00:00Z","timestamp":1760140800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:00:00Z","timestamp":1760140800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Ganzhou Science and Technology Plan Project (grant number","award":["GZ2023ZSF339"],"award-info":[{"award-number":["GZ2023ZSF339"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Curr Microbiol"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s00284-025-04530-5","type":"journal-article","created":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:38:39Z","timestamp":1760197119000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Accuracy of SAM-TB Platform as a Diagnostic Assay for Detection of Mycobacterium tuberculosis Drug Resistance Versus TB-Proflier, PhyResSE, and Mykrobe: A Head-to-Head Comparison"],"prefix":"10.1007","volume":"82","author":[{"given":"Juexin","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoling","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuchu","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jielian","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Liao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Lei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2865-2441","authenticated-orcid":false,"given":"Zhenbo","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,11]]},"reference":[{"key":"4530_CR1","unstructured":"Global tuberculosis report 2024 (2024)"},{"key":"4530_CR2","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/1471-2334-9-91","volume":"9","author":"CT Sreeramareddy","year":"2009","unstructured":"Sreeramareddy CT et al (2009) Time delays in diagnosis of pulmonary tuberculosis: a systematic review of literature. BMC Infect Dis 9:91. https:\/\/doi.org\/10.1186\/1471-2334-9-91","journal-title":"BMC Infect Dis"},{"key":"4530_CR3","doi-asserted-by":"publisher","first-page":"4188","DOI":"10.1128\/JCM.02283-12","volume":"50","author":"GE Pfyffer","year":"2012","unstructured":"Pfyffer GE et al (2012) Incubation time of mycobacterial cultures: how long is long enough to issue a final negative report to the clinician? J Clin Microbiol 50:4188\u20134189. https:\/\/doi.org\/10.1128\/JCM.02283-12","journal-title":"J Clin Microbiol"},{"key":"4530_CR4","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.5588\/ijtld.15.0389","volume":"19","author":"Y Zhang","year":"2015","unstructured":"Zhang Y et al (2015) Mechanisms of drug resistance in Mycobacterium tuberculosis: update 2015. Int J Tuberc Lung Dis 19:1276\u20131289. https:\/\/doi.org\/10.5588\/ijtld.15.0389","journal-title":"Int J Tuberc Lung Dis"},{"key":"4530_CR5","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1016\/j.cmi.2018.03.041","volume":"25","author":"J Beek","year":"2019","unstructured":"Beek J et al (2019) Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis. Clin Microbiol Infec 25:82\u201386. https:\/\/doi.org\/10.1016\/j.cmi.2018.03.041","journal-title":"Clin Microbiol Infec"},{"key":"4530_CR6","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.ijmyco.2016.09.021","volume":"5","author":"DL Dolinger","year":"2016","unstructured":"Dolinger DL et al (2016) Next-generation sequencing-based user-friendly platforms for drug-resistant tuberculosis diagnosis: a promise for the near future. Int J Mycobacteriol 5:27\u201328. https:\/\/doi.org\/10.1016\/j.ijmyco.2016.09.021","journal-title":"Int J Mycobacteriol"},{"key":"4530_CR7","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/s13073-015-0164-0","volume":"7","author":"F Coll","year":"2015","unstructured":"Coll F et al (2015) Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 7:51. https:\/\/doi.org\/10.1186\/s13073-015-0164-0","journal-title":"Genome Med"},{"key":"4530_CR8","doi-asserted-by":"publisher","first-page":"1908","DOI":"10.1128\/jcm.00025-15","volume":"53","author":"S Feuerriegel","year":"2015","unstructured":"Feuerriegel S et al (2015) PhyResSE:a web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data. J Clin Microbiol 53:1908\u20131914. https:\/\/doi.org\/10.1128\/jcm.00025-15","journal-title":"J Clin Microbiol"},{"key":"4530_CR9","doi-asserted-by":"publisher","first-page":"10063","DOI":"10.1038\/ncomms10063","volume":"6","author":"P Bradley","year":"2015","unstructured":"Bradley P et al (2015) Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 6:10063. https:\/\/doi.org\/10.1038\/ncomms10063","journal-title":"Nat Commun"},{"key":"4530_CR10","doi-asserted-by":"publisher","first-page":"3ba0","DOI":"10.1093\/bib\/bbac030","volume":"23","author":"TT Yang","year":"2022","unstructured":"Yang TT et al (2022) SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission. Brief Bioinform 23:3ba0. https:\/\/doi.org\/10.1093\/bib\/bbac030","journal-title":"Brief Bioinform"},{"key":"4530_CR11","unstructured":"Word Health Organization. (2018) Technical manual for drug susceptibility testing of medicines used in the treatment of tuberculosis. WHO\/CDS\/TB\/2018. 24. Geneva: Word Health Organization."},{"key":"4530_CR12","unstructured":"Babraham Bioinformatics et al. (2020) FastQC: a quality control tool for high through put sequence data.Soil.5,47\u201381.https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/"},{"key":"4530_CR13","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM et al (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114\u20132120. https:\/\/doi.org\/10.1093\/bioinformatics\/btu170","journal-title":"Bioinformatics"},{"key":"4530_CR14","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754\u20131760. https:\/\/doi.org\/10.1093\/bioinformatics\/btp324","journal-title":"Bioinformatics"},{"key":"4530_CR15","unstructured":"World Health Organization (2023) Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance.2nd ed. https:\/\/iris.who.int\/handle\/10665\/374061."},{"key":"4530_CR16","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/s2213-2600(15)00510-x","volume":"4","author":"C Colijn","year":"2016","unstructured":"Colijn C et al (2016) Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond. Lancet Respir Med 4:6\u20138. https:\/\/doi.org\/10.1016\/s2213-2600(15)00510-x","journal-title":"Lancet Respir Med"},{"key":"4530_CR17","doi-asserted-by":"publisher","first-page":"5783","DOI":"10.2147\/idr.S423955","volume":"16","author":"JY Wang","year":"2023","unstructured":"Wang JY et al (2023) Analysis of drug-resistance characteristics and genetic diversity of multidrug-resistant tuberculosis based on whole-genome sequencing on the Hainan island, China. Infect Drug Resist 16:5783\u20135798. https:\/\/doi.org\/10.2147\/idr.S423955","journal-title":"Infect Drug Resist"},{"key":"4530_CR18","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1186\/s13073-021-00953-4","volume":"13","author":"MI Groschel","year":"2021","unstructured":"Groschel MI et al (2021) Gentb: a user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome Med 13:138. https:\/\/doi.org\/10.1186\/s13073-021-00953-4","journal-title":"Genome Med"},{"key":"4530_CR19","doi-asserted-by":"publisher","first-page":"116","DOI":"10.69854\/jcq.2024.0016","volume":"3","author":"N Horita","year":"2024","unstructured":"Horita N et al (2024) Minimal clinically important difference (MCID) of effect sizes other than mean difference. J Clin Questons. 3:116\u2013127. https:\/\/doi.org\/10.69854\/jcq.2024.0016","journal-title":"J Clin Questons."},{"key":"4530_CR20","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.3390\/antibiotics12081257","volume":"12","author":"MW Zhang","year":"2023","unstructured":"Zhang MW et al (2023) Whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance: a retrospective observational study in eastern China. Antibiotics 12:1257. https:\/\/doi.org\/10.3390\/antibiotics12081257","journal-title":"Antibiotics"},{"key":"4530_CR21","doi-asserted-by":"publisher","first-page":"11826","DOI":"10.1038\/s41598-019-48401-z","volume":"9","author":"G Torrea","year":"2019","unstructured":"Torrea G et al (2019) Variable ability of rapid tests to detect Mycobacterium tuberculosis ropb mutations conferring phenotypically occult rifampicin resistance. Sci Rep 9:11826. https:\/\/doi.org\/10.1038\/s41598-019-48401-z","journal-title":"Sci Rep"},{"key":"4530_CR22","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.ijid.2021.03.033","volume":"113","author":"C Lam","year":"2021","unstructured":"Lam C et al (2021) Value of routine whole genome sequencing for Mycobacterium tuberculosis drug resistance detection. Int J Infect Dis 113:48\u201354. https:\/\/doi.org\/10.1016\/j.ijid.2021.03.033","journal-title":"Int J Infect Dis"},{"key":"4530_CR23","doi-asserted-by":"publisher","DOI":"10.1016\/s2666-5247(23)00007-1","volume":"4","author":"YW Chen","year":"2023","unstructured":"Chen YW et al (2023) Phenotypic instability of Mycobacterium tuberculosis strains harbouring clinically prevalent drug-resistant mutations. Lancet Microbe 4:e292. https:\/\/doi.org\/10.1016\/s2666-5247(23)00007-1","journal-title":"Lancet Microbe"},{"key":"4530_CR24","doi-asserted-by":"publisher","first-page":"2551","DOI":"10.1007\/s10096-021-04316-0","volume":"40","author":"JMW Pinhata","year":"2021","unstructured":"Pinhata JMW et al (2021) Correlating genetic mutations with isoniazid phenotypic levels of resistance in Mycobacterium tuberculosis isolates from patients with drug-resistant tuberculosis in a high burden setting. Eur J Clin Microbiol Infect Dis 40:2551\u20132561. https:\/\/doi.org\/10.1007\/s10096-021-04316-0","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"4530_CR25","doi-asserted-by":"publisher","first-page":"4119","DOI":"10.2147\/IDR.S333433","volume":"14","author":"MC Li","year":"2021","unstructured":"Li MC et al (2021) ropB mutations and effects on rifampin resistance in Mycobacterium tuberculosis. Infect Drug Resist 14:4119\u20134128. https:\/\/doi.org\/10.2147\/IDR.S333433","journal-title":"Infect Drug Resist"},{"key":"4530_CR26","doi-asserted-by":"publisher","first-page":"781","DOI":"10.3389\/fmicb.2020.00781","volume":"11","author":"MC Li","year":"2020","unstructured":"Li MC et al (2020) Detecting ethambutol resistance in Mycobacterium tuberculosis isolates in China: a comparison between phenotypic drug susceptibility testing methods and DNA sequencing of embAB. Front Microbiol 11:781. https:\/\/doi.org\/10.3389\/fmicb.2020.00781","journal-title":"Front Microbiol"},{"key":"4530_CR27","first-page":"2713","volume":"12","author":"YL Wang","year":"2019","unstructured":"Wang YL et al (2019) The roles of rpsL, rrs, and gidB mutations in predicting streptomycin-resistant drugs used in clinical Mycobacterium tuberculosis isolates from Hebei Province. China Int J Clin Exp Pathol 12:2713\u20132721","journal-title":"China Int J Clin Exp Pathol"},{"key":"4530_CR28","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1186\/s12879-023-08629-7","volume":"23","author":"A Viksna","year":"2023","unstructured":"Viksna A et al (2023) Genotypic and phenotypic comparison of drug resistance profiles of clinical multidrug-resistant Mycobacterium tuberculosis isolates using whole genome sequencing in Latvia. BMC Infect Dis 23:638. https:\/\/doi.org\/10.1186\/s12879-023-08629-7","journal-title":"BMC Infect Dis"},{"key":"4530_CR29","doi-asserted-by":"publisher","first-page":"2200166","DOI":"10.1183\/13993003.00166-2022","volume":"59","author":"Antimycobacterial Susceptibility Testing Group","year":"2022","unstructured":"Antimycobacterial Susceptibility Testing Group (2022) Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment. Eur Respir J 59:2200166. https:\/\/doi.org\/10.1183\/13993003.00166-2022","journal-title":"Eur Respir J"},{"key":"4530_CR30","doi-asserted-by":"publisher","first-page":"1900","DOI":"10.1128\/AAC.50.5.1900-1902.2006","volume":"50","author":"C Plinke","year":"2006","unstructured":"Plinke C et al (2006) Significance of mutations in embB codon 306 for prediction of ethambutol resistance in clinical Mycobacterium tuberculosis isolates. Antimicrob Agents Chemother 50:1900\u20131902. https:\/\/doi.org\/10.1128\/AAC.50.5.1900-1902.2006","journal-title":"Antimicrob Agents Chemother"},{"key":"4530_CR31","doi-asserted-by":"publisher","first-page":"3810","DOI":"10.1128\/JCM.40.10.3810-3813.2002","volume":"40","author":"I Mokrousov","year":"2002","unstructured":"Mokrousov I et al (2002) Detection of embB306 mutations in ethambutol-susceptible clinical isolates of Mycobacterium tuberculosis from Northwestern Russia: implications for genotypic resistance testing. J Clin Microbiol 40:3810\u20133813. https:\/\/doi.org\/10.1128\/JCM.40.10.3810-3813.2002","journal-title":"J Clin Microbiol"},{"key":"4530_CR32","doi-asserted-by":"publisher","first-page":"46327","DOI":"10.1038\/srep46327","volume":"7","author":"V Schleusener","year":"2017","unstructured":"Schleusener V et al (2017) Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools. Sci Rep 7:46327. https:\/\/doi.org\/10.1038\/srep46327","journal-title":"Sci Rep"},{"key":"4530_CR33","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1146\/annurev-pharmtox-010617-052438","volume":"58","author":"LH Brake","year":"2018","unstructured":"Brake LH et al (2018) The role of efflux pumps in tuberculosis treatment and their promise as a target in drug development: unraveling the black box. Annu Rev Pharmacol Toxicol 58:271\u2013291. https:\/\/doi.org\/10.1146\/annurev-pharmtox-010617-052438","journal-title":"Annu Rev Pharmacol Toxicol"}],"container-title":["Current Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00284-025-04530-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00284-025-04530-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00284-025-04530-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T16:04:31Z","timestamp":1763222671000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00284-025-04530-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,11]]},"references-count":33,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["4530"],"URL":"https:\/\/doi.org\/10.1007\/s00284-025-04530-5","relation":{},"ISSN":["0343-8651","1432-0991"],"issn-type":[{"value":"0343-8651","type":"print"},{"value":"1432-0991","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,11]]},"assertion":[{"value":"3 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"The study was approved by the Ethics Review Committee of Ganzhou Centers for Disease Control and Prevention. Informed consent of the patients was not required because our study used isolates from a collection.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical Approval"}},{"value":"Not applicable.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to Participate"}},{"value":"Not applicable.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for Publication"}}],"article-number":"547"}}