{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:32:15Z","timestamp":1785407535827,"version":"3.56.0"},"reference-count":58,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hangzhou Science and Technology Commission","award":["No. 20220919Y060"],"award-info":[{"award-number":["No. 20220919Y060"]}]},{"award":["No. 20220919Y060"],"award-info":[{"award-number":["No. 20220919Y060"]}],"id":[{"id":"https:\/\/ror.org\/04gvkax77","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diagnostics"],"abstract":"<jats:p>Background\/Objectives: Nanopore sequencing is increasingly used in mycobacterial diagnostics, where clinical microbiologists and diagnostic laboratories must decide when broad metagenomic next-generation sequencing (mNGS) or focused targeted next-generation sequencing (tNGS) is most appropriate. This review examined reported clinical and laboratory roles of nanopore mNGS and tNGS in tuberculosis (TB) and nontuberculous mycobacterial (NTM) settings. Methods: Targeted searches of PubMed\/MEDLINE, Embase, Web of Science Core Collection, and Scopus were refreshed on 4 April 2026. Thirty-five records spanning original clinical studies, evidence syntheses, and guideline-context documents were included. Results: Nanopore mNGS is most useful for broad organism detection and diagnostic rescue in unresolved pulmonary and extrapulmonary presentations, particularly when first-line testing is negative, discordant, low-yield, or when mixed infection is suspected. Nanopore tNGS appears better aligned with predefined TB confirmation and resistance-focused workflows because targeted regions allow more standardized interpretation. Agreement is strongest for rifampicin- and isoniazid-related resistance targets. In NTM settings, evidence is stronger for detection and species identification than for disease-level diagnosis. Common implementation constraints include pre-analytical variation, contamination control, host-background interference, inconsistent bioinformatics, and limited workforce capacity. Conclusions: A practical tiered approach is supported in which mNGS is positioned mainly for diagnostic rescue and discovery, whereas tNGS is considered for predefined workflows requiring standardized target interrogation and resistance-associated mutation reporting under local validation and quality systems.<\/jats:p>","DOI":"10.3390\/diagnostics16121850","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T15:00:48Z","timestamp":1781535648000},"page":"1850","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Nanopore Sequencing in Mycobacterial Diagnostics: Clinical and Laboratory Roles of mNGS and tNGS"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-5356-2225","authenticated-orcid":false,"given":"Meng","family":"Wang","sequence":"first","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institute), Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.ijid.2020.11.165","article-title":"Clinical efficacy of metagenomic next-generation sequencing for rapid detection of Mycobacterium tuberculosis in smear-negative extrapulmonary specimens in a high tuberculosis burden area","volume":"103","author":"Sun","year":"2021","journal-title":"Int. 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