{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T12:45:00Z","timestamp":1774529100486,"version":"3.50.1"},"reference-count":44,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["UM1AI104681"],"award-info":[{"award-number":["UM1AI104681"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2023,10,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Tuberculosis (TB) originating from expatriates that hail from high TB-burden countries is hypothesized to play a role in continued TB transmission in Oman. Here, we used whole-genome sequencing (WGS) to assess national TB transmission dynamics. The annual incidence per 100,000 population per year was calculated for nationals and expatriates. A convenience sample of\n            <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n            (MTB) isolates from 2018 to 2019 was sequenced and analyzed with publicly available TB sequences from Bangladesh, Tanzania, the Philippines, India, and Pakistan. Relatedness was assessed by generating core-genome single nucleotide polymorphism (SNP) distances. The incidence of TB was five cases per 100,000 persons in 2018 and seven cases per 100,000 persons in 2020 (\n            <jats:italic>\n              R\n              <jats:sup>2<\/jats:sup>\n            <\/jats:italic>\n            = 0.34,\n            <jats:italic>P<\/jats:italic>\n            = 0.60). Incidence among nationals was 3.9 per 100,000 persons in 2018 and 3.5 per 100,000 persons in 2020 (\n            <jats:italic>\n              R\n              <jats:sup>2<\/jats:sup>\n            <\/jats:italic>\n            = 0.20\n            <jats:italic>, P<\/jats:italic>\n            = 0.70), and incidence among expatriates was 7.2 per 100,000 persons in 2018 and 12.7 per 100,000 persons in 2020 (\n            <jats:italic>\n              R\n              <jats:sup>2<\/jats:sup>\n            <\/jats:italic>\n            = 0.74,\n            <jats:italic>P<\/jats:italic>\n            = 0.34). Sixty-eight local MTB isolates were sequenced and analyzed with 393 global isolates. Isolates belonged to nine distinct spoligotypes. Two isolates, originating from an expatriate and an Omani national, were grouped into a WGS-based cluster (SNP distance &lt; 12), which was corroborated by an epidemiological investigation. Relatedness of local and global isolates (SNP distance &lt; 100) was also seen. The relatedness between MTB strains in Oman and those in expatriate countries of origin can aid inform TB control policy. Our results provide evidence that WGS can complement epidemiological analysis to achieve the End TB strategy goal in Oman.\n          <\/jats:p>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              Tuberculosis (TB) incidence in Oman remains above national program control targets. TB transmission originating from expatriates from high TB-burden countries has been hypothesized to play a role. We used whole-genome sequencing (WGS) to assess TB transmission dynamics between expatriates and Omani nationals to inform TB control efforts. Available\n              <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n              isolates from 2018 to 2019 underwent WGS and analysis with publicly available TB sequences from Bangladesh, the Philippines, India, and Pakistan to assess for genetic relatedness. Our analysis revealed evidence of previously unrecognized transmission between an expatriate and an Omani national, which was corroborated by epidemiological investigation. Analysis of local and global isolates revealed evidence of distant relatedness between local and global isolates. Our results provide evidence that WGS can complement classic public health surveillance to inform targeted interventions to achieve the End TB strategy goal in Oman.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.02420-23","type":"journal-article","created":{"date-parts":[[2023,9,28]],"date-time":"2023-09-28T13:08:55Z","timestamp":1695906535000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":6,"title":["<i>Mycobacterium tuberculosis<\/i>\n            epidemiology in Oman: whole-genome sequencing uncovers transmission pathways"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0007-7513","authenticated-orcid":false,"given":"Hamza A","family":"Babiker","sequence":"first","affiliation":[{"name":"Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University , Muscat, Oman"},{"name":"Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh , Edinburgh, United Kingdom"}]},{"given":"Amina","family":"Al-Jardani","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health , Muscat, Oman"}]},{"given":"Saleh","family":"Al-Azri","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health , Muscat, Oman"}]},{"suffix":"III","given":"Robert A.","family":"Petit","sequence":"additional","affiliation":[{"name":"Wyoming Department of Health, Wyoming Public Health Laboratory , Cheyenne, Wyoming, USA"}]},{"given":"Eltaib","family":"Saad","sequence":"additional","affiliation":[{"name":"Department of Medicine, Ascension Saint Francis Hospital , Evanston, Illinois, USA"}]},{"given":"Sarah","family":"Al-Mahrouqi","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health , Muscat, Oman"}]},{"given":"Reham A.H.","family":"Mohamed","sequence":"additional","affiliation":[{"name":"Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University , Muscat, Oman"}]},{"given":"Salama","family":"Al-Hamidhi","sequence":"additional","affiliation":[{"name":"Biochemistry Department, College of Medicine and Health Sciences, Sultan Qaboos University , Muscat, Oman"}]},{"given":"Abdullah A.","family":"Balkhair","sequence":"additional","affiliation":[{"name":"Department of Medicine, College of Medicine and Health Sciences, Sultan Qaboos University , Muscat, Oman"}]},{"given":"Najma","family":"Al Kharusi","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health , Muscat, Oman"}]},{"given":"Laila","family":"Al Balushi","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health , Muscat, Oman"}]},{"given":"Samiya","family":"Al Zadjali","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratories, National Tuberculosis Reference Laboratory, Directorate General for Disease Surveillance and Control, Ministry of Health , Muscat, Oman"}]},{"given":"Luc\u00eda","family":"P\u00e9rez-Pardal","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Labora\u00ad t\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto, Vair\u00e3o, Portugal , Vair\u00e3o, Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vair\u00e3o , Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1607-7382","authenticated-orcid":false,"given":"Albano","family":"Beja-Pereira","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Labora\u00ad t\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto, Vair\u00e3o, Portugal , Vair\u00e3o, Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vair\u00e3o , Vair\u00e3o, Portugal"},{"name":"DGAOT, Faculty of Sciences, Universidade do Porto , Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0578-4871","authenticated-orcid":false,"given":"Ahmed","family":"Babiker","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine , Atlanta, Georgia, 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