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Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, ge...

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Autores principales: Argimón, Silvia, Masim, Melissa A. L., Gayeta, June M., Lagrada, Marietta L., Macaranas, Polle K. V., Cohen, Victoria, Limas, Marilyn T., Espiritu, Holly O., Palarca, Janziel C., Chilam, Jeremiah, Jamoralin, Manuel C., Villamin, Alfred S., Borlasa, Janice B., Olorosa, Agnettah M., Hernandez, Lara F. T., Boehme, Karis D., Jeffrey, Benjamin, Abudahab, Khalil, Hufano, Charmian M., Sia, Sonia B., Stelling, John, Holden, Matthew T. G., Aanensen, David M., Carlos, Celia C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264328/
https://www.ncbi.nlm.nih.gov/pubmed/32483195
http://dx.doi.org/10.1038/s41467-020-16322-5
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author Argimón, Silvia
Masim, Melissa A. L.
Gayeta, June M.
Lagrada, Marietta L.
Macaranas, Polle K. V.
Cohen, Victoria
Limas, Marilyn T.
Espiritu, Holly O.
Palarca, Janziel C.
Chilam, Jeremiah
Jamoralin, Manuel C.
Villamin, Alfred S.
Borlasa, Janice B.
Olorosa, Agnettah M.
Hernandez, Lara F. T.
Boehme, Karis D.
Jeffrey, Benjamin
Abudahab, Khalil
Hufano, Charmian M.
Sia, Sonia B.
Stelling, John
Holden, Matthew T. G.
Aanensen, David M.
Carlos, Celia C.
author_facet Argimón, Silvia
Masim, Melissa A. L.
Gayeta, June M.
Lagrada, Marietta L.
Macaranas, Polle K. V.
Cohen, Victoria
Limas, Marilyn T.
Espiritu, Holly O.
Palarca, Janziel C.
Chilam, Jeremiah
Jamoralin, Manuel C.
Villamin, Alfred S.
Borlasa, Janice B.
Olorosa, Agnettah M.
Hernandez, Lara F. T.
Boehme, Karis D.
Jeffrey, Benjamin
Abudahab, Khalil
Hufano, Charmian M.
Sia, Sonia B.
Stelling, John
Holden, Matthew T. G.
Aanensen, David M.
Carlos, Celia C.
author_sort Argimón, Silvia
collection PubMed
description National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.
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spelling pubmed-72643282020-06-12 Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines Argimón, Silvia Masim, Melissa A. L. Gayeta, June M. Lagrada, Marietta L. Macaranas, Polle K. V. Cohen, Victoria Limas, Marilyn T. Espiritu, Holly O. Palarca, Janziel C. Chilam, Jeremiah Jamoralin, Manuel C. Villamin, Alfred S. Borlasa, Janice B. Olorosa, Agnettah M. Hernandez, Lara F. T. Boehme, Karis D. Jeffrey, Benjamin Abudahab, Khalil Hufano, Charmian M. Sia, Sonia B. Stelling, John Holden, Matthew T. G. Aanensen, David M. Carlos, Celia C. Nat Commun Article National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance. Nature Publishing Group UK 2020-06-01 /pmc/articles/PMC7264328/ /pubmed/32483195 http://dx.doi.org/10.1038/s41467-020-16322-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Argimón, Silvia
Masim, Melissa A. L.
Gayeta, June M.
Lagrada, Marietta L.
Macaranas, Polle K. V.
Cohen, Victoria
Limas, Marilyn T.
Espiritu, Holly O.
Palarca, Janziel C.
Chilam, Jeremiah
Jamoralin, Manuel C.
Villamin, Alfred S.
Borlasa, Janice B.
Olorosa, Agnettah M.
Hernandez, Lara F. T.
Boehme, Karis D.
Jeffrey, Benjamin
Abudahab, Khalil
Hufano, Charmian M.
Sia, Sonia B.
Stelling, John
Holden, Matthew T. G.
Aanensen, David M.
Carlos, Celia C.
Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
title Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
title_full Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
title_fullStr Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
title_full_unstemmed Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
title_short Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines
title_sort integrating whole-genome sequencing within the national antimicrobial resistance surveillance program in the philippines
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264328/
https://www.ncbi.nlm.nih.gov/pubmed/32483195
http://dx.doi.org/10.1038/s41467-020-16322-5
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