Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans
Scrub typhus is a febrile disease caused by <em>Orientia tsutsugamushi</em>, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of <em>O. tsutsugamushi</em> in chiggers, small mammals and humans remains poorly un...
| Main Authors: | , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Elsevier
2021
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| _version_ | 1826311846074777600 |
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| author | Elliott, I Thangnimitchok, N de Cesare, M Linsuwanon, P Paris, D Day, NPJ Newton, P Bowden, R Batty, E |
| author_facet | Elliott, I Thangnimitchok, N de Cesare, M Linsuwanon, P Paris, D Day, NPJ Newton, P Bowden, R Batty, E |
| author_sort | Elliott, I |
| collection | OXFORD |
| description | Scrub typhus is a febrile disease caused by <em>Orientia tsutsugamushi</em>, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of <em>O. tsutsugamushi</em> in chiggers, small mammals and humans remains poorly understood. To combat the limitations imposed by the low relative quantities of pathogen DNA in typical <em>O. tsutsugamushi</em> clinical and ecological samples, along with the technical, safety and cost limitations of cell culture, a novel probe-based target enrichment sequencing protocol was developed. The method was designed to capture variation among conserved genes and facilitate phylogenomic analysis at the scale of population samples. A whole-genome amplification step was incorporated to enhance the efficiency of sequencing by reducing duplication rates. This resulted in on-target capture rates of up to 93% for a diverse set of human, chigger, and rodent samples, with the greatest success rate in samples with real-time PCR Ct values below 35. Analysis of the best-performing samples revealed phylogeographic clustering at local, provincial and international scales. Applying the methodology to a comprehensive set of samples could yield a more complete understanding of the ecology, genomic evolution and population structure of <em>O. tsutsugamushi</em> and other similarly challenging organisms, with potential benefits in the development of diagnostic tests and vaccines. |
| first_indexed | 2024-03-07T08:15:46Z |
| format | Journal article |
| id | oxford-uuid:81aaa6cd-73c5-497c-b392-ea6b17cbcb5c |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:15:46Z |
| publishDate | 2021 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | oxford-uuid:81aaa6cd-73c5-497c-b392-ea6b17cbcb5c2024-01-04T14:35:44ZTargeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humansJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:81aaa6cd-73c5-497c-b392-ea6b17cbcb5cEnglishSymplectic ElementsElsevier2021Elliott, IThangnimitchok, Nde Cesare, MLinsuwanon, PParis, DDay, NPJNewton, PBowden, RBatty, EScrub typhus is a febrile disease caused by <em>Orientia tsutsugamushi</em>, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of <em>O. tsutsugamushi</em> in chiggers, small mammals and humans remains poorly understood. To combat the limitations imposed by the low relative quantities of pathogen DNA in typical <em>O. tsutsugamushi</em> clinical and ecological samples, along with the technical, safety and cost limitations of cell culture, a novel probe-based target enrichment sequencing protocol was developed. The method was designed to capture variation among conserved genes and facilitate phylogenomic analysis at the scale of population samples. A whole-genome amplification step was incorporated to enhance the efficiency of sequencing by reducing duplication rates. This resulted in on-target capture rates of up to 93% for a diverse set of human, chigger, and rodent samples, with the greatest success rate in samples with real-time PCR Ct values below 35. Analysis of the best-performing samples revealed phylogeographic clustering at local, provincial and international scales. Applying the methodology to a comprehensive set of samples could yield a more complete understanding of the ecology, genomic evolution and population structure of <em>O. tsutsugamushi</em> and other similarly challenging organisms, with potential benefits in the development of diagnostic tests and vaccines. |
| spellingShingle | Elliott, I Thangnimitchok, N de Cesare, M Linsuwanon, P Paris, D Day, NPJ Newton, P Bowden, R Batty, E Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans |
| title | Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans |
| title_full | Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans |
| title_fullStr | Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans |
| title_full_unstemmed | Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans |
| title_short | Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans |
| title_sort | targeted capture and sequencing of orientia tsutsugamushi genomes from chiggers and humans |
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