A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate charact...
| Main Authors: | , , , , |
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| פורמט: | Journal article |
| יצא לאור: |
American Association for Microbiology
2017
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| _version_ | 1826278846756814848 |
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| author | Cody, A Bray, J Jolley, K McCarthy, N Maiden, M |
| author_facet | Cody, A Bray, J Jolley, K McCarthy, N Maiden, M |
| author_sort | Cody, A |
| collection | OXFORD |
| description | Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterisation methods. Whole genome sequencing (WGS) data enables the improvement of sequence-based typing approaches, such as multi locus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high-resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a sub-set of the 1,643 loci identified in the re-annotation of the genome sequence of C. jejuni isolate NTCT 1168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates comprising 2,207 (89.3%) C. jejuni and 265 (10.7%) C. coli. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak. |
| first_indexed | 2024-03-06T23:50:04Z |
| format | Journal article |
| id | oxford-uuid:724c6f3e-1439-422d-b5a8-68a62af474ec |
| institution | University of Oxford |
| last_indexed | 2024-03-06T23:50:04Z |
| publishDate | 2017 |
| publisher | American Association for Microbiology |
| record_format | dspace |
| spelling | oxford-uuid:724c6f3e-1439-422d-b5a8-68a62af474ec2022-03-26T19:49:10ZA core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolatesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:724c6f3e-1439-422d-b5a8-68a62af474ecSymplectic Elements at OxfordAmerican Association for Microbiology2017Cody, ABray, JJolley, KMcCarthy, NMaiden, MHuman campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterisation methods. Whole genome sequencing (WGS) data enables the improvement of sequence-based typing approaches, such as multi locus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high-resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a sub-set of the 1,643 loci identified in the re-annotation of the genome sequence of C. jejuni isolate NTCT 1168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates comprising 2,207 (89.3%) C. jejuni and 265 (10.7%) C. coli. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak. |
| spellingShingle | Cody, A Bray, J Jolley, K McCarthy, N Maiden, M A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates |
| title | A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates |
| title_full | A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates |
| title_fullStr | A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates |
| title_full_unstemmed | A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates |
| title_short | A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates |
| title_sort | core genome multi locus sequence typing scheme for stable comparative analyses of campylobacter jejuni and c coli human disease isolates |
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