A proposed core genome scheme for analyses of the Salmonella genus
The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were no...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Elsevier
2019
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| _version_ | 1797061198058881024 |
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| author | Pearce, M Chattaway, M Grant, K Maiden, M |
| author_facet | Pearce, M Chattaway, M Grant, K Maiden, M |
| author_sort | Pearce, M |
| collection | OXFORD |
| description | The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations. |
| first_indexed | 2024-03-06T20:27:38Z |
| format | Journal article |
| id | oxford-uuid:2fec9596-9509-41f5-9a79-c0dbbddfb727 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T20:27:38Z |
| publishDate | 2019 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | oxford-uuid:2fec9596-9509-41f5-9a79-c0dbbddfb7272022-03-26T12:58:25ZA proposed core genome scheme for analyses of the Salmonella genusJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:2fec9596-9509-41f5-9a79-c0dbbddfb727EnglishSymplectic Elements at OxfordElsevier2019Pearce, MChattaway, MGrant, KMaiden, MThe salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations. |
| spellingShingle | Pearce, M Chattaway, M Grant, K Maiden, M A proposed core genome scheme for analyses of the Salmonella genus |
| title | A proposed core genome scheme for analyses of the Salmonella genus |
| title_full | A proposed core genome scheme for analyses of the Salmonella genus |
| title_fullStr | A proposed core genome scheme for analyses of the Salmonella genus |
| title_full_unstemmed | A proposed core genome scheme for analyses of the Salmonella genus |
| title_short | A proposed core genome scheme for analyses of the Salmonella genus |
| title_sort | proposed core genome scheme for analyses of the salmonella genus |
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