{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T18:11:58Z","timestamp":1789668718236,"version":"4.0.1"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T00:00:00Z","timestamp":1718064000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010751","name":"Fondo Nacional de Desarrollo Cient\u00edfico, Tecnol\u00f3gico y de Innovaci\u00f3n Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["029-2021-PROCIENCIA"],"award-info":[{"award-number":["029-2021-PROCIENCIA"]}],"id":[{"id":"10.13039\/501100010751","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Direcci\u00f3n de Investigaci\u00f3n de la Universidad Peruana de Ciencias Aplicadas","award":["A-053-2021-2"],"award-info":[{"award-number":["A-053-2021-2"]}]},{"DOI":"10.13039\/100010897","name":"Newton Fund","doi-asserted-by":"publisher","award":["414591184 Moore PER"],"award-info":[{"award-number":["414591184 Moore PER"]}],"id":[{"id":"10.13039\/100010897","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Whole Genome Sequencing (WGS) is a promising tool in the global fight against tuberculosis (TB). The aim of this study was to evaluate the use of WGS in routine conditions for detection of drug resistance markers and transmission clusters in a multidrug-resistant TB <jats:italic>hot-spot<\/jats:italic> area in Peru. For this, 140 drug-resistant <jats:italic>Mycobacterium tuberculosis<\/jats:italic> strains from Lima and Callao were prospectively selected and processed through routine (GenoType MTBDR<jats:italic>sl<\/jats:italic> and BACTEC MGIT) and WGS workflows, simultaneously. Resistance was determined in accordance with the World Health Organization mutation catalogue. Agreements between WGS and BACTEC results were calculated for rifampicin, isoniazid, pyrazinamide, moxifloxacin, levofloxacin, amikacin and capreomycin. Transmission clusters were determined using different cut-off values of Single Nucleotide Polymorphism differences. 100% (140\/140) of strains had valid WGS results for 13 anti-TB drugs. However, the availability of final, definitive phenotypic BACTEC MGIT results varied by drug with 10\u201317% of invalid results for the seven compared drugs. The median time to obtain results of WGS for the complete set of drugs was 11.5 days, compared to 28.6\u201352.6 days for the routine workflow. Overall categorical agreement by WGS and BACTEC MGIT for the compared drugs was 96.5%. Kappa index was good (0.65\u2264k\u22641.00), except for moxifloxacin, but the sensitivity and specificity values were high for all cases. 97.9% (137\/140) of strains were characterized with only one sublineage (134 belonging to \u201clineage 4\u201d and 3 to \u201clineage 2\u201d), and 2.1% (3\/140) were mixed strains presenting two different sublineages. Clustering rates of 3.6% (5\/140), 17.9% (25\/140) and 22.1% (31\/140) were obtained for 5, 10 and 12 SNP cut-off values, respectively. In conclusion, routine WGS has a high diagnostic accuracy to detect resistance against key current anti-TB drugs, allowing results to be obtained through a single analysis and helping to cut quickly the chain of transmission of drug-resistant TB in Peru.<\/jats:p>","DOI":"10.1371\/journal.pone.0304130","type":"journal-article","created":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T18:17:31Z","timestamp":1718129851000},"page":"e0304130","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Whole Genome Sequencing of Mycobacterium tuberculosis under routine conditions in a high-burden area of multidrug-resistant tuberculosis in Peru"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5068-0986","authenticated-orcid":true,"given":"Zully M.","family":"Puy\u00e9n","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Santos-L\u00e1zaro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiko N.","family":"Vigo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidia V.","family":"Cotrina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaly","family":"Ruiz-Nizama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam J.","family":"Alarc\u00f3n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Belisa","family":"Asto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Huam\u00e1n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3748-0154","authenticated-orcid":true,"given":"David A. J.","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,6,11]]},"reference":[{"key":"pone.0304130.ref001","unstructured":"World Health Organization. Global Tuberculosis Report 2022. 2022 [cited 28 Dec 2022]. Available: https:\/\/www.who.int\/teams\/global-tuberculosis-programme\/tb-reports\/global-tuberculosis-report-2022"},{"key":"pone.0304130.ref002","unstructured":"World Health Organization. Global Tuberculosis Report 2023. 2023. Available: https:\/\/www.who.int\/publications-detail-redirect\/9789240083851"},{"key":"pone.0304130.ref003","unstructured":"Ministerio de Salud. Direcci\u00f3n de Prevenci\u00f3n y Control de la Tuberculosis \u2010 Portal de Informaci\u00f3n peruano. 2022 [cited 2 Feb 2022]. Available: http:\/\/www.tuberculosis.minsa.gob.pe\/DashboardDPCTB\/MapasTB.aspx"},{"key":"pone.0304130.ref004","unstructured":"World Health Organization. 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Available: https:\/\/www.gov.uk\/government\/news\/england-world-leaders-in-the-use-of-whole-genome-sequencing-to-diagnose-tb"},{"key":"pone.0304130.ref040","doi-asserted-by":"crossref","first-page":"15333","DOI":"10.1038\/s41598-021-94297-z","article-title":"Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country","volume":"11","author":"M Vogel","year":"2021","journal-title":"Sci Rep"},{"key":"pone.0304130.ref041","first-page":"100556","article-title":"Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020","volume":"28","author":"K Dale","year":"2022","journal-title":"Lancet Reg Health West Pac"},{"key":"pone.0304130.ref042","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1080\/17843286.2021.1999588","article-title":"Retrospective evaluation of routine whole genome sequencing of Mycobacterium tuberculosis at the Belgian National Reference Center, 2019","volume":"77","author":"K Soetaert","year":"2022","journal-title":"Acta Clin Belg"},{"key":"pone.0304130.ref043","doi-asserted-by":"crossref","first-page":"1800387","DOI":"10.1183\/13993003.00387-2018","article-title":"Countrywide implementation of whole genome sequencing: an opportunity to improve tuberculosis management, surveillance and contact tracing in low incidence countries","volume":"51","author":"AM Cabibbe","year":"2018","journal-title":"Eur Respir J"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0304130","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T18:18:05Z","timestamp":1718129885000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0304130"}},"subtitle":[],"editor":[{"given":"Shahriar","family":"Ahmed","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,6,11]]},"references-count":43,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,6,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0304130","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,11]]}}}