{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T05:31:07Z","timestamp":1770442267012,"version":"3.49.0"},"reference-count":30,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2016,3,1]],"date-time":"2016-03-01T00:00:00Z","timestamp":1456790400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Scottish Government Rural and Environmental Science and Analytical Services Division"},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["SFRH\/BD\/62469\/2009"],"award-info":[{"award-number":["SFRH\/BD\/62469\/2009"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2016,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Typing of\n            <jats:named-content content-type=\"genus-species\">Mycobacterium avium<\/jats:named-content>\n            subspecies\n            <jats:named-content content-type=\"genus-species\">paratuberculosis<\/jats:named-content>\n            strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of\n            <jats:named-content content-type=\"genus-species\">Mycobacterium avium<\/jats:named-content>\n            subspecies\n            <jats:named-content content-type=\"genus-species\">paratuberculosis<\/jats:named-content>\n            , and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133\n            <jats:named-content content-type=\"genus-species\">Mycobacterium avium<\/jats:named-content>\n            subspecies\n            <jats:named-content content-type=\"genus-species\">paratuberculosis<\/jats:named-content>\n            isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs\n            <jats:named-content content-type=\"genus-species\">Mycobacterium avium<\/jats:named-content>\n            subspecies\n            <jats:named-content content-type=\"genus-species\">paratuberculosis<\/jats:named-content>\n            isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit\u2013variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of\n            <jats:named-content content-type=\"genus-species\">Mycobacterium avium<\/jats:named-content>\n            subspecies\n            <jats:named-content content-type=\"genus-species\">paratuberculosis<\/jats:named-content>\n            isolates.\n          <\/jats:p>","DOI":"10.1128\/jcm.01958-15","type":"journal-article","created":{"date-parts":[[2015,12,17]],"date-time":"2015-12-17T04:35:44Z","timestamp":1450326944000},"page":"556-564","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":20,"title":["Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis"],"prefix":"10.1128","volume":"54","author":[{"given":"C\u00e9lia","family":"Le\u00e3o","sequence":"first","affiliation":[{"name":"Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom"},{"name":"Unidade Estrat\u00e9gica de Investiga\u00e7\u00e3o e Servi\u00e7os em Produ\u00e7\u00e3o e Sa\u00fade Animal, Instituto Nacional de Investiga\u00e7\u00e3o Agr\u00e1ria e Veterin\u00e1ria, I.P. (INIAV, I.P.), Lisbon, Portugal"}]},{"given":"Robert J.","family":"Goldstone","sequence":"additional","affiliation":[{"name":"Institute of Infection, Inflammation, and Immunity, University of Glasgow, Glasgow, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0149-5768","authenticated-orcid":false,"given":"Josephine","family":"Bryant","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, University College London, London, United Kingdom"}]},{"given":"Joyce","family":"McLuckie","sequence":"additional","affiliation":[{"name":"Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7367-5007","authenticated-orcid":false,"given":"Jo\u00e3o","family":"In\u00e1cio","sequence":"additional","affiliation":[{"name":"Unidade de Microbiologia M\u00e9dica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal"},{"name":"School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom"}]},{"given":"David G. E.","family":"Smith","sequence":"additional","affiliation":[{"name":"Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom"},{"name":"Institute of Infection, Inflammation, and Immunity, University of Glasgow, Glasgow, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0270-9550","authenticated-orcid":false,"given":"Karen","family":"Stevenson","sequence":"additional","affiliation":[{"name":"Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v20.i23.7403"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.62.081307.162832"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-7012(99)00091-3"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.5.1798-1804.2002"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.41.5.2015-2026.2003"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1135(00)00358-8"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00476-07"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-8-204"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-9-212"},{"key":"e_1_3_2_11_2","volume-title":"BMC Genomics","author":"Bryant JM","unstructured":"Bryant JM, Thibault VC, Smith DGE, McLuckie J, Heron I, Sevilla IA, Biet F, Harris SR, Maskell DJ, Bentley SD, Parkhill J, Stevenson K. 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