SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex
The clinical phenotype of zoonotic tuberculosis and its contribution to the global burden of disease are poorly understood and probably underestimated. This shortcoming is partly because of the inability of currently available laboratory and in silico tools to accurately identify all subspecies of t...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Centers for Disease Control and Prevention
2019-03-01
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| Series: | Emerging Infectious Diseases |
| Subjects: | |
| Online Access: | https://wwwnc.cdc.gov/eid/article/25/3/18-0894_article |
| _version_ | 1818549887439994880 |
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| author | Samuel Lipworth Rana Jajou Albert de Neeling Phelim Bradley Wim van der Hoek Gugu Maphalala Maryline Bonnet Elizabeth Sanchez-Padilla Roland Diel Stefan Niemann Zamin Iqbal Grace Smith Tim Peto Derrick Crook Timothy Walker Dick van Soolingen |
| author_facet | Samuel Lipworth Rana Jajou Albert de Neeling Phelim Bradley Wim van der Hoek Gugu Maphalala Maryline Bonnet Elizabeth Sanchez-Padilla Roland Diel Stefan Niemann Zamin Iqbal Grace Smith Tim Peto Derrick Crook Timothy Walker Dick van Soolingen |
| author_sort | Samuel Lipworth |
| collection | DOAJ |
| description | The clinical phenotype of zoonotic tuberculosis and its contribution to the global burden of disease are poorly understood and probably underestimated. This shortcoming is partly because of the inability of currently available laboratory and in silico tools to accurately identify all subspecies of the Mycobacterium tuberculosis complex (MTBC). We present SNPs to Identify TB (SNP-IT), a single-nucleotide polymorphism–based tool to identify all members of MTBC, including animal clades. By applying SNP-IT to a collection of clinical genomes from a UK reference laboratory, we detected an unexpectedly high number of M. orygis isolates. M. orygis is seen at a similar rate to M. bovis, yet M. orygis cases have not been previously described in the United Kingdom. From an international perspective, it is possible that M. orygis is an underestimated zoonosis. Accurate identification will enable study of the clinical phenotype, host range, and transmission mechanisms of all subspecies of MTBC in greater detail. |
| first_indexed | 2024-12-12T08:39:07Z |
| format | Article |
| id | doaj.art-cf25db1983234d508292be3cbb217810 |
| institution | Directory Open Access Journal |
| issn | 1080-6040 1080-6059 |
| language | English |
| last_indexed | 2024-12-12T08:39:07Z |
| publishDate | 2019-03-01 |
| publisher | Centers for Disease Control and Prevention |
| record_format | Article |
| series | Emerging Infectious Diseases |
| spelling | doaj.art-cf25db1983234d508292be3cbb2178102022-12-22T00:30:51ZengCenters for Disease Control and PreventionEmerging Infectious Diseases1080-60401080-60592019-03-0125348248810.3201/eid2503.180894SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis ComplexSamuel LipworthRana JajouAlbert de NeelingPhelim BradleyWim van der HoekGugu MaphalalaMaryline BonnetElizabeth Sanchez-PadillaRoland DielStefan NiemannZamin IqbalGrace SmithTim PetoDerrick CrookTimothy WalkerDick van SoolingenThe clinical phenotype of zoonotic tuberculosis and its contribution to the global burden of disease are poorly understood and probably underestimated. This shortcoming is partly because of the inability of currently available laboratory and in silico tools to accurately identify all subspecies of the Mycobacterium tuberculosis complex (MTBC). We present SNPs to Identify TB (SNP-IT), a single-nucleotide polymorphism–based tool to identify all members of MTBC, including animal clades. By applying SNP-IT to a collection of clinical genomes from a UK reference laboratory, we detected an unexpectedly high number of M. orygis isolates. M. orygis is seen at a similar rate to M. bovis, yet M. orygis cases have not been previously described in the United Kingdom. From an international perspective, it is possible that M. orygis is an underestimated zoonosis. Accurate identification will enable study of the clinical phenotype, host range, and transmission mechanisms of all subspecies of MTBC in greater detail.https://wwwnc.cdc.gov/eid/article/25/3/18-0894_articletuberculosiswhole genome sequencingzoonosesphylogenysingle nucleotide polymorphismSNP-IT |
| spellingShingle | Samuel Lipworth Rana Jajou Albert de Neeling Phelim Bradley Wim van der Hoek Gugu Maphalala Maryline Bonnet Elizabeth Sanchez-Padilla Roland Diel Stefan Niemann Zamin Iqbal Grace Smith Tim Peto Derrick Crook Timothy Walker Dick van Soolingen SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex Emerging Infectious Diseases tuberculosis whole genome sequencing zoonoses phylogeny single nucleotide polymorphism SNP-IT |
| title | SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex |
| title_full | SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex |
| title_fullStr | SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex |
| title_full_unstemmed | SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex |
| title_short | SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex |
| title_sort | snp it tool for identifying subspecies and associated lineages of mycobacterium tuberculosis complex |
| topic | tuberculosis whole genome sequencing zoonoses phylogeny single nucleotide polymorphism SNP-IT |
| url | https://wwwnc.cdc.gov/eid/article/25/3/18-0894_article |
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