Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis
Objective: This study aimed to standardize a quantitative polymerase chain reaction (qPCR)-based test to identify and quantify the uncultivable bacteria associated with periodontitis. Methods: The standardization of qPCR, the curves for the quantification of Eubacterium saphenum, Eubacterium brachy,...
- Autores:
-
Castillo, Yormaris
Delgadillo, Nathaly Andrea
Neuta, Yineth
Iniesta, Margarita
Sanz, Mariano
Herrera, David
Pianeta, Roquelina
Lafaurie, Gloria Inés
Castillo, Diana Marcela
- Tipo de recurso:
- Article of journal
- Fecha de publicación:
- 2023
- Institución:
- Universidad El Bosque
- Repositorio:
- Repositorio U. El Bosque
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.unbosque.edu.co:20.500.12495/11082
- Acceso en línea:
- http://hdl.handle.net/20.500.12495/11082
https://doi.org/10.1016/j.archoralbio.2023.105758
- Palabra clave:
- Eficacia de la PCR
QPCR
Número de copias
Bacterias orales
Periodontitis
PCR efficiency
QPCR
Copy number
Oral bacteria
Periodontitis
- Rights
- openAccess
- License
- Attribution-NonCommercial-NoDerivatives 4.0 Internacional
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dc.title.spa.fl_str_mv |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
dc.title.translated.spa.fl_str_mv |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
title |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
spellingShingle |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis Eficacia de la PCR QPCR Número de copias Bacterias orales Periodontitis PCR efficiency QPCR Copy number Oral bacteria Periodontitis |
title_short |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
title_full |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
title_fullStr |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
title_full_unstemmed |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
title_sort |
Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis |
dc.creator.fl_str_mv |
Castillo, Yormaris Delgadillo, Nathaly Andrea Neuta, Yineth Iniesta, Margarita Sanz, Mariano Herrera, David Pianeta, Roquelina Lafaurie, Gloria Inés Castillo, Diana Marcela |
dc.contributor.author.none.fl_str_mv |
Castillo, Yormaris Delgadillo, Nathaly Andrea Neuta, Yineth Iniesta, Margarita Sanz, Mariano Herrera, David Pianeta, Roquelina Lafaurie, Gloria Inés Castillo, Diana Marcela |
dc.contributor.orcid.none.fl_str_mv |
Castillo, Yormaris [0000-0002-8673-8449] Delgadillo, Nathaly Andrea [0000-0001-8842-549X] Neuta, Yineth [0000-0001-9350-0941] Iniesta, Margarita [0000-0001-7557-4023] |
dc.subject.spa.fl_str_mv |
Eficacia de la PCR QPCR Número de copias Bacterias orales Periodontitis |
topic |
Eficacia de la PCR QPCR Número de copias Bacterias orales Periodontitis PCR efficiency QPCR Copy number Oral bacteria Periodontitis |
dc.subject.keywords.spa.fl_str_mv |
PCR efficiency QPCR Copy number Oral bacteria Periodontitis |
description |
Objective: This study aimed to standardize a quantitative polymerase chain reaction (qPCR)-based test to identify and quantify the uncultivable bacteria associated with periodontitis. Methods: The standardization of qPCR, the curves for the quantification of Eubacterium saphenum, Eubacterium brachy, Desulfobulbus oralis, and Filifactor alocis were developed by cloning the 16 S rRNA target gene fragment, using the GEMTEasy vector. The qPCRs were validated in 55 subgingival biofilm clinical samples, from different stages of periodontitis and from periodontally healthy/gingivitis individuals, which were previously evaluated by next-generation sequencing (NGS). The results obtained by the two methods were compared by the concordance of Cohen's Kappa index, and sensitivity, specificity, receiver operating characteristic (ROC) curve, and predictive values were established. Results: obtained by the two methods were compared using the concordance of Cohen's Kappa index, and sensitivity, specificity, predictive values, and ROC curves were generated. The qPCR test was standardized with efficiencies between 90% and 100% and R2: 0.997–0.999. Concordance between the qPCR and NSG was moderate to F. alocis (agreement 78.2%; kappa 0.56, p < 0.05) and fair to the other microorganisms (agreement 67.27%−72.73; kappa 0.37–0.38, p < 0.05). qPCR exhibited a high sensitivity (82.2–100%) and specificity (100%) for E. brachy, E. saphenum, and F. alocis. Sensitivity was lower to D. oralis. Conversely, qPCR demonstrated higher sensitivity to E. saphenum than NSG (100 vs. 68.1). Conclusions: The uncultivable microorganisms associated with periodontitis, D. oralis, E. brachy, E. saphenum, and F. alocis can be detected and quantified with the newly developed and validates qPCR test. |
publishDate |
2023 |
dc.date.accessioned.none.fl_str_mv |
2023-07-19T16:32:13Z |
dc.date.available.none.fl_str_mv |
2023-07-19T16:32:13Z |
dc.date.issued.none.fl_str_mv |
2023 |
dc.type.coar.fl_str_mv |
http://purl.org/coar/resource_type/c_2df8fbb1 |
dc.type.local.none.fl_str_mv |
Artículo de revista |
dc.type.hasversion.none.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.coar.none.fl_str_mv |
http://purl.org/coar/resource_type/c_6501 |
dc.type.driver.none.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.coarversion.none.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
format |
http://purl.org/coar/resource_type/c_6501 |
status_str |
publishedVersion |
dc.identifier.issn.none.fl_str_mv |
0003-9969 |
dc.identifier.uri.none.fl_str_mv |
http://hdl.handle.net/20.500.12495/11082 |
dc.identifier.doi.none.fl_str_mv |
https://doi.org/10.1016/j.archoralbio.2023.105758 |
dc.identifier.instname.spa.fl_str_mv |
instname:Universidad El Bosque |
dc.identifier.reponame.spa.fl_str_mv |
reponame:Repositorio Institucional Universidad El Bosque |
dc.identifier.repourl.none.fl_str_mv |
repourl:https://repositorio.unbosque.edu.co |
identifier_str_mv |
0003-9969 instname:Universidad El Bosque reponame:Repositorio Institucional Universidad El Bosque repourl:https://repositorio.unbosque.edu.co |
url |
http://hdl.handle.net/20.500.12495/11082 https://doi.org/10.1016/j.archoralbio.2023.105758 |
dc.language.iso.none.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofseries.spa.fl_str_mv |
Archives of Oral Biology, 0003-9969, 154, 2023, 1 - 8 |
dc.relation.uri.none.fl_str_mv |
https://www.sciencedirect.com/science/article/pii/S0003996923001462?pes=vor |
dc.rights.*.fl_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 Internacional |
dc.rights.uri.*.fl_str_mv |
http://creativecommons.org/licenses/by-nc-nd/4.0/ |
dc.rights.local.spa.fl_str_mv |
Acceso abierto |
dc.rights.accessrights.none.fl_str_mv |
info:eu-repo/semantics/openAccess http://purl.org/coar/access_right/c_abf2 |
rights_invalid_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ Acceso abierto http://purl.org/coar/access_right/c_abf2 |
eu_rights_str_mv |
openAccess |
dc.format.mimetype.none.fl_str_mv |
application/pdf |
dc.publisher.spa.fl_str_mv |
Elsevier |
dc.publisher.journal.spa.fl_str_mv |
Archives of Oral Biology |
institution |
Universidad El Bosque |
bitstream.url.fl_str_mv |
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spelling |
Castillo, YormarisDelgadillo, Nathaly AndreaNeuta, YinethIniesta, MargaritaSanz, MarianoHerrera, DavidPianeta, RoquelinaLafaurie, Gloria InésCastillo, Diana MarcelaCastillo, Yormaris [0000-0002-8673-8449]Delgadillo, Nathaly Andrea [0000-0001-8842-549X]Neuta, Yineth [0000-0001-9350-0941]Iniesta, Margarita [0000-0001-7557-4023]2023-07-19T16:32:13Z2023-07-19T16:32:13Z20230003-9969http://hdl.handle.net/20.500.12495/11082https://doi.org/10.1016/j.archoralbio.2023.105758instname:Universidad El Bosquereponame:Repositorio Institucional Universidad El Bosquerepourl:https://repositorio.unbosque.edu.coapplication/pdfengElsevierArchives of Oral BiologyArchives of Oral Biology, 0003-9969, 154, 2023, 1 - 8https://www.sciencedirect.com/science/article/pii/S0003996923001462?pes=vorAttribution-NonCommercial-NoDerivatives 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/Acceso abiertoinfo:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Eficacia de la PCRQPCRNúmero de copiasBacterias oralesPeriodontitisPCR efficiencyQPCRCopy numberOral bacteriaPeriodontitisDesign and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitisDesign and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitisArtículo de revistainfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1info:eu-repo/semantics/articlehttp://purl.org/coar/version/c_970fb48d4fbd8a85Objective: This study aimed to standardize a quantitative polymerase chain reaction (qPCR)-based test to identify and quantify the uncultivable bacteria associated with periodontitis. Methods: The standardization of qPCR, the curves for the quantification of Eubacterium saphenum, Eubacterium brachy, Desulfobulbus oralis, and Filifactor alocis were developed by cloning the 16 S rRNA target gene fragment, using the GEMTEasy vector. The qPCRs were validated in 55 subgingival biofilm clinical samples, from different stages of periodontitis and from periodontally healthy/gingivitis individuals, which were previously evaluated by next-generation sequencing (NGS). The results obtained by the two methods were compared by the concordance of Cohen's Kappa index, and sensitivity, specificity, receiver operating characteristic (ROC) curve, and predictive values were established. Results: obtained by the two methods were compared using the concordance of Cohen's Kappa index, and sensitivity, specificity, predictive values, and ROC curves were generated. The qPCR test was standardized with efficiencies between 90% and 100% and R2: 0.997–0.999. Concordance between the qPCR and NSG was moderate to F. alocis (agreement 78.2%; kappa 0.56, p < 0.05) and fair to the other microorganisms (agreement 67.27%−72.73; kappa 0.37–0.38, p < 0.05). qPCR exhibited a high sensitivity (82.2–100%) and specificity (100%) for E. brachy, E. saphenum, and F. alocis. Sensitivity was lower to D. oralis. Conversely, qPCR demonstrated higher sensitivity to E. saphenum than NSG (100 vs. 68.1). Conclusions: The uncultivable microorganisms associated with periodontitis, D. oralis, E. brachy, E. saphenum, and F. alocis can be detected and quantified with the newly developed and validates qPCR test.ORIGINAL1-s2.0-S0003996923001462-main.pdf1-s2.0-S0003996923001462-main.pdfDesign and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitisapplication/pdf2994222https://repositorio.unbosque.edu.co/bitstreams/7b0eb293-5fe8-48da-afa3-1333803c0ec4/downloadc0b584a202fb262095b0a590ffdb7de5MD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8908https://repositorio.unbosque.edu.co/bitstreams/974b9aa6-1668-497c-91a8-79e918457fa0/download0175ea4a2d4caec4bbcc37e300941108MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-82000https://repositorio.unbosque.edu.co/bitstreams/1b361c0b-3d26-42d7-bb42-1968548304c8/download17cc15b951e7cc6b3728a574117320f9MD53THUMBNAIL1-s2.0-S0003996923001462-main.pdf.jpg1-s2.0-S0003996923001462-main.pdf.jpgIM Thumbnailimage/jpeg10064https://repositorio.unbosque.edu.co/bitstreams/5d942738-acd9-42b8-a3ad-b45f8137158f/downloadcf0d4d5306632d89a9b77a8064adb748MD54TEXT1-s2.0-S0003996923001462-main.pdf.txt1-s2.0-S0003996923001462-main.pdf.txtExtracted texttext/plain49856https://repositorio.unbosque.edu.co/bitstreams/4c0bb448-473c-419f-9396-d5bb06cb159d/downloadc4ddfe82e25580e3b754619c737af738MD5520.500.12495/11082oai:repositorio.unbosque.edu.co:20.500.12495/110822024-02-07 07:44:21.896http://creativecommons.org/licenses/by-nc-nd/4.0/Attribution-NonCommercial-NoDerivatives 4.0 Internacionalopen.accesshttps://repositorio.unbosque.edu.coRepositorio Institucional Universidad El Bosquebibliotecas@biteca.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 |