{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:49:39Z","timestamp":1787010579711,"version":"build-2736575974"},"reference-count":36,"publisher":"Microbiology Society","issue":"11","license":[{"start":{"date-parts":[[2023,11,27]],"date-time":"2023-11-27T00:00:00Z","timestamp":1701043200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,27]]},"abstract":"<jats:p>\n                    The National Tuberculosis Programme (NTBP) monitors the occurrence and spread of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) in Singapore. Since 2020, whole-genome sequencing (WGS) of\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.10886\" xlink:type=\"simple\">Mycobacterium tuberculosis<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    isolates has been performed at the National Public Health Laboratory (NPHL) for genomic surveillance, replacing spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeats analysis (MIRU-VNTR). Four thousand three hundred and seven\u2009samples were sequenced from 2014 to January 2023, initially as research projects and later developed into a comprehensive public health surveillance programme. Currently, all newly diagnosed culture-positive cases of TB in Singapore are prospectively sent for WGS, which is used to perform lineage classification, predict drug resistance profiles and infer genetic relationships between TB isolates. This paper describes NPHL\u2019s operational and technical experiences with implementing the WGS service in an urban TB-endemic setting, focusing on cluster detection and genomic drug susceptibility testing (DST). Cluster detection: WGS has been used to guide contact tracing by detecting clusters and discovering unknown transmission networks. Examples have been clusters in a daycare centre, housing apartment blocks and a horse-racing betting centre. Genomic DST: genomic DST prediction (gDST) identifies mutations in core genes known to be associated with TB drug resistance catalogued in the TBProfiler drug resistance mutation database. Mutations are reported with confidence scores according to a standardized approach referencing NPHL\u2019s internal gDST confidence database, which is adapted from the World Health Organization (WHO) TB drug mutation catalogue. Phenotypic\u2013genomic concordance was observed for the first-line drugs ranging from 2959\/2998 (98.7\u200a%) (ethambutol) to 2983\/2996 (99.6\u200a%) (rifampicin). Aspects of internal database management, reporting standards and caveats in results interpretation are discussed.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001139","type":"journal-article","created":{"date-parts":[[2023,11,27]],"date-time":"2023-11-27T11:19:18Z","timestamp":1701083958000},"source":"Crossref","is-referenced-by-count":3,"title":["Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019\u20142022"],"prefix":"10.1099","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-1094-6238","authenticated-orcid":false,"given":"Ansel Yi Herh","family":"Lim","sequence":"first","affiliation":[{"name":"National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle L.T.","family":"Ang","sequence":"additional","affiliation":[{"name":"National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharol S. L.","family":"Cho","sequence":"additional","affiliation":[{"name":"National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah H. L.","family":"Ng","sequence":"additional","affiliation":[{"name":"National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffery","family":"Cutter","sequence":"additional","affiliation":[{"name":"National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raymond T. 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