Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved]
<i>Chlamydia trachomatis</i> (<i>C. trachomatis</i>) is a common sexually transmitted infection (STI). In 2019, the World Health Organization reported about 131 million infections. The majority of infected patients are asymptomatic with cases remaining undetected. It is likely that missed <i>C. trac...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
F1000 Research Ltd
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/144164 |
| _version_ | 1855532280229920768 |
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| author | Shiluli, C. Kamath, S. Kanoi, B.N. Kimani, R. Maina, M. Waweru, H. Kamita, M. Ndirangu, I. Abkallo, Hussein M. Oduor, Bernard Pamme, N. Dupaty, J. Klapperich, C.M. Lolabattu, S.R. Gitaka, J. |
| author_browse | Abkallo, Hussein M. Dupaty, J. Gitaka, J. Kamath, S. Kamita, M. Kanoi, B.N. Kimani, R. Klapperich, C.M. Lolabattu, S.R. Maina, M. Ndirangu, I. Oduor, Bernard Pamme, N. Shiluli, C. Waweru, H. |
| author_facet | Shiluli, C. Kamath, S. Kanoi, B.N. Kimani, R. Maina, M. Waweru, H. Kamita, M. Ndirangu, I. Abkallo, Hussein M. Oduor, Bernard Pamme, N. Dupaty, J. Klapperich, C.M. Lolabattu, S.R. Gitaka, J. |
| author_sort | Shiluli, C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | <i>Chlamydia trachomatis</i> (<i>C. trachomatis</i>) is a common sexually transmitted infection (STI). In 2019, the World Health Organization reported about 131 million infections. The majority of infected patients are asymptomatic with cases remaining undetected. It is likely that missed <i>C. trachomatis</i> infections contribute to preventable adverse health outcomes in women and children. Consequently, there is an urgent need of developing efficient diagnostic methods. In this study, genome-mining approaches to identify identical multi-repeat sequences (IMRS) distributed throughout the <i>C. trachomatis</i> genome were used to design a primer pair that would target regions in the genome. Genomic DNA was 10-fold serially diluted (100pg/μL to 1×10<sup>-3</sup>pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and products were resolved on agarose gel. The novel assay, <i>C. trachomatis</i> IMRS-PCR, had an analytical sensitivity of 4.31 pg/µL, representing better sensitivity compared with 16S rRNA PCR (9.5 fg/µL). Our experimental data demonstrate the successful development of lateral flow and isothermal assays for detecting <i>C. trachomatis</i> DNA with potential use in field settings. There is a potential to implement this concept in miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for reliable point-of-care testing. |
| format | Journal Article |
| id | CGSpace144164 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | F1000 Research Ltd |
| publisherStr | F1000 Research Ltd |
| record_format | dspace |
| spelling | CGSpace1441642024-06-26T09:37:22Z Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] Shiluli, C. Kamath, S. Kanoi, B.N. Kimani, R. Maina, M. Waweru, H. Kamita, M. Ndirangu, I. Abkallo, Hussein M. Oduor, Bernard Pamme, N. Dupaty, J. Klapperich, C.M. Lolabattu, S.R. Gitaka, J. health genomics diagnosis <i>Chlamydia trachomatis</i> (<i>C. trachomatis</i>) is a common sexually transmitted infection (STI). In 2019, the World Health Organization reported about 131 million infections. The majority of infected patients are asymptomatic with cases remaining undetected. It is likely that missed <i>C. trachomatis</i> infections contribute to preventable adverse health outcomes in women and children. Consequently, there is an urgent need of developing efficient diagnostic methods. In this study, genome-mining approaches to identify identical multi-repeat sequences (IMRS) distributed throughout the <i>C. trachomatis</i> genome were used to design a primer pair that would target regions in the genome. Genomic DNA was 10-fold serially diluted (100pg/μL to 1×10<sup>-3</sup>pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and products were resolved on agarose gel. The novel assay, <i>C. trachomatis</i> IMRS-PCR, had an analytical sensitivity of 4.31 pg/µL, representing better sensitivity compared with 16S rRNA PCR (9.5 fg/µL). Our experimental data demonstrate the successful development of lateral flow and isothermal assays for detecting <i>C. trachomatis</i> DNA with potential use in field settings. There is a potential to implement this concept in miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for reliable point-of-care testing. 2024-05-09 2024-05-30T14:20:56Z 2024-05-30T14:20:56Z Journal Article https://hdl.handle.net/10568/144164 en Open Access F1000 Research Ltd Shiluli, C., Kamath, S., Kanoi, B.N., Kimani, R., Maina, M., Waweru, H., Kamita, M., Ndirangu, I., Abkallo, H.M., Oduor, B., Pamme, N., Dupaty, J., Klapperich, C.M., Lolabattu, S.R. and Gitaka, J. 2024. Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of <i>Chlamydia trachomatis</i> [version 2; peer review: 2 approved]. <i>Open Research Africa</i> 7: 2. |
| spellingShingle | health genomics diagnosis Shiluli, C. Kamath, S. Kanoi, B.N. Kimani, R. Maina, M. Waweru, H. Kamita, M. Ndirangu, I. Abkallo, Hussein M. Oduor, Bernard Pamme, N. Dupaty, J. Klapperich, C.M. Lolabattu, S.R. Gitaka, J. Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] |
| title | Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] |
| title_full | Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] |
| title_fullStr | Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] |
| title_full_unstemmed | Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] |
| title_short | Multi-repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of Chlamydia trachomatis [version 2; peer review: 2 approved] |
| title_sort | multi repeat sequences identification using genome mining techniques for developing highly sensitive molecular diagnostic assay for the detection of chlamydia trachomatis version 2 peer review 2 approved |
| topic | health genomics diagnosis |
| url | https://hdl.handle.net/10568/144164 |
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