{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T13:56:43Z","timestamp":1775570203973,"version":"3.50.1"},"reference-count":39,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Tuberculosis (TB) control in Nepal faces persistent challenges due to underdiagnosis and increasing drug resistance. This study assessed the diagnostic performance of the Xpert MTB\/RIF assay compared with conventional smear microscopy and estimated the prevalence of rifampicin-resistant TB (RR-TB) in Biratnagar, a high-burden urban center. Between March and September 2023, 509 clinical specimens from TB suspects were analyzed by Ziehl-Neelsen (ZN) staining, fluorescence microscopy (FM), and Xpert MTB\/RIF. Using Xpert as the operational reference, ZN and FM exhibited overall sensitivities of 55.9% (89\/159) and 68.5% (109\/159), respectively. In paired sputum-only analyses (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 446; sputum Xpert positives = 145), ZN and FM sensitivities were 60.0% (87\/145) and 70.3% (102\/145), respectively; sputum specificity was 100% for both methods. Xpert detected 31.2% (159\/509) positive cases\u201478.7% more than ZN and 45.9% more than FM. Rifampicin resistance was identified in 5.03% (8\/159) of Xpert-positive samples and was strongly associated with prior treatment (\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      &lt; 0.001); RR-TB occurred in 66.7% (6\/9) of retreatment cases vs 1.3% (2\/150) of new cases. Xpert increased detection in paucibacillary and extrapulmonary specimens. These findings support expanded use of rapid molecular testing, but results should be interpreted cautiously because culture\/speciation was not performed.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>The spread of drug-resistant tuberculosis (TB) is a growing public health threat in Nepal. Using a rapid molecular test in Biratnagar, we simultaneously diagnosed TB and identified rifampicin resistance. We found rifampicin-resistant TB in &gt;5% of Xpert-positive patients, higher than national averages for new cases, and a markedly elevated risk among previously treated patients. Rapid detection of resistance permits earlier initiation of appropriate therapy and can reduce onward transmission.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.02460-25","type":"journal-article","created":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T13:31:31Z","timestamp":1773235891000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Comparative evaluation of sputum microscopy and Xpert MTB\/RIF assay for tuberculosis detection and rifampicin resistance surveillance in Biratnagar, Nepal"],"prefix":"10.1128","volume":"14","author":[{"given":"Shristy","family":"Ojha","sequence":"first","affiliation":[{"name":"Department of Microbiology, Central Campus of Technology","place":["Dharan, Nepal"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akash","family":"Adhikari","sequence":"additional","affiliation":[{"name":"Institute of Agriculture and Animal Science, Paklihawa Campus","place":["Bhairahawa, Nepal"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6097-9486","authenticated-orcid":true,"given":"Sujan","family":"Adhikari","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University","place":["Chitwan, Nepal"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2568-5119","authenticated-orcid":false,"given":"Swagat","family":"Khanal","sequence":"additional","affiliation":[{"name":"Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University","place":["Chitwan, Nepal"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chandan Sah","family":"Kalwar","sequence":"additional","affiliation":[{"name":"Sam Higginbottom University of Agriculture, Technology and Sciences","place":["Prayagraj, India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Om Prakash","family":"Panta","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Central Campus of Technology","place":["Dharan, Nepal"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","unstructured":"Tuberculosis resurges as top infectious disease killer. Available from: https:\/\/www.who.int\/news\/item\/29-10-2024-tuberculosis-resurges-as-top-infectious-disease-killer. Retrieved 7 Oct 2025."},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.15212\/ZOONOSES-2024-0061"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.54394\/CJQU6666"},{"key":"e_1_3_3_5_2","series-title":"Factsheet","volume-title":"Tuberculosis profile: World TB Day, March 24, 2025","author":"National Tuberculosis Control Center (NTCC)","year":"2025","unstructured":"National Tuberculosis Control Center (NTCC). 2025. Tuberculosis profile: World TB Day, March 24, 2025. Factsheet. National Tuberculosis Control Center, Nepal."},{"key":"e_1_3_3_6_2","volume-title":"Annual report 2078\/79 (2021\/2022)","author":"Department of Health Services","year":"2022","unstructured":"Department of Health Services. 2022. Annual report 2078\/79 (2021\/2022). 28th. 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Government of Nepal"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.4103\/lungindia.lungindia_98_17"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.943545"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1097\/MCP.0000000000001070"},{"key":"e_1_3_3_14_2","first-page":"442","article-title":"Sputum smear microscopy in tuberculosis: is it still relevant?","volume":"137","author":"Desikan P","year":"2013","unstructured":"Desikan P. 2013. Sputum smear microscopy in tuberculosis: is it still relevant? Indian J Med Res 137:442\u2013444.","journal-title":"Indian J Med Res"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1002\/ila2.11"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccm.2023.08.012"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.imj.2025.100203"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.11.84"},{"key":"e_1_3_3_19_2","unstructured":"World Health Organization. 2013. Automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance: Xpert MTB\/RIF assay for the diagnosis of pulmonary and extrapulmonary TB in adults and children: policy update. World Health Organization Geneva. Available from: https:\/\/iris.who.int\/handle\/10665\/112472. Retrieved 30 Jul 2025."},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2018.04.005"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgph.0004676"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0201731"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511543470"},{"key":"e_1_3_3_24_2","unstructured":"National TB Control Centre. 2020. Nepal National TB prevalence survey brief: TB burden in Nepal. Policy Brief. 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Advances in TB testing, p 33\u201362. In Advances in clinical chemistry. Elsevier."},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00007814"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-024-09566-9"},{"key":"e_1_3_3_38_2","unstructured":"WHO consolidated guidelines on tuberculosis: module 3: Diagnosis \u2013 rapid diagnostics for tuberculosis detection. 2024. World Health Organization."},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01891-2015"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-14-2"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02460-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.02460-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T13:06:07Z","timestamp":1775567167000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.02460-25"}},"subtitle":[],"editor":[{"given":"Cheryl P.","family":"Andam","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,7]]},"references-count":39,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4,7]]}},"alternative-id":["10.1128\/spectrum.02460-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.02460-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,7]]},"assertion":[{"value":"2025-08-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-03-11","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02460-25"}}