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

Silvia Argimón; Melissa A L Masim; June M Gayeta; Marietta L Lagrada; Polle K V Macaranas; Victoria Cohen; Marilyn T Limas; Holly O Espiritu; Janziel C Palarca; Jeremiah Chilam; Manuel C Jamoralin; Alfred S Villamin; Janice B Borlasa; Agnettah M Olorosa; Lara F T Hernandez; Karis D Boehme; Benjamin Jeffrey; Khalil Abudahab; Charmian M Hufano; Sonia B Sia; John Stelling; Matthew T G Holden; David M Aanensen; Celia C Carlos

doi:10.1038/s41467-020-16322-5

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

Silvia Argimón, Melissa A L Masim, June M Gayeta, Marietta L Lagrada, Polle K V Macaranas, Victoria Cohen, Marilyn T Limas, Holly O Espiritu, Janziel C Palarca, Jeremiah Chilam, Manuel C Jamoralin, Alfred S Villamin, Janice B Borlasa, Agnettah M Olorosa, Lara F T Hernandez, Karis D Boehme, Benjamin Jeffrey, Khalil Abudahab, Charmian M Hufano, Sonia B SiaJohn Stelling, Matthew T G Holden, David M Aanensen, Celia C Carlos

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Article number	2719
Number of pages	15
Journal	Nature Communications
Volume	11
DOIs	https://doi.org/10.1038/s41467-020-16322-5
Publication status	Published - 1 Jun 2020

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Matthew Holden
- mtghst-andrews.acuk
- School of Medicine - Director of Impact, Professor
- Biomedical Sciences Research Complex
- St Andrews Bioinformatics Unit
- Infection and Global Health Division
Person: Academic

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Argimón, S., Masim, M. A. L., Gayeta, J. M., Lagrada, M. L., Macaranas, P. K. V., Cohen, V., Limas, M. T., Espiritu, H. O., Palarca, J. C., Chilam, J., Jamoralin, M. C., Villamin, A. S., Borlasa, J. B., Olorosa, A. M., Hernandez, L. F. T., Boehme, K. D., Jeffrey, B., Abudahab, K., Hufano, C. M., ... Carlos, C. C. (2020). Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines. Nature Communications, 11, Article 2719. https://doi.org/10.1038/s41467-020-16322-5

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title = "Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines",

abstract = "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.",

author = "Silvia Argim{\'o}n and Masim, {Melissa A L} and Gayeta, {June M} and Lagrada, {Marietta L} and Macaranas, {Polle K V} and Victoria Cohen and Limas, {Marilyn T} and Espiritu, {Holly O} and Palarca, {Janziel C} and Jeremiah Chilam and Jamoralin, {Manuel C} and Villamin, {Alfred S} and Borlasa, {Janice B} and Olorosa, {Agnettah M} and Hernandez, {Lara F T} and Boehme, {Karis D} and Benjamin Jeffrey and Khalil Abudahab and Hufano, {Charmian M} and Sia, {Sonia B} and John Stelling and Holden, {Matthew T G} and Aanensen, {David M} and Carlos, {Celia C}",

note = "Funding: This work was funded by the Newton Fund, Medical Research Council (UK) grant MR/N019296/1, Philippine Council for Health Research and Development project number FP160007. J.S. was partially supported by research grants RR025040 and U01CA207167 from the National Institutes of Health (NIH). S.A. and D.M.A. were additionally supported by the National Institute for Health Research (UK) Global Health Research Unit on genomic Surveillance of AMR(16_136_111) and by the Centre for Genomic Pathogen Surveillance (http://pathogensurveillance.net).",

year = "2020",

month = jun,

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doi = "10.1038/s41467-020-16322-5",

language = "English",

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Argimón, S, Masim, MAL, Gayeta, JM, Lagrada, ML, Macaranas, PKV, Cohen, V, Limas, MT, Espiritu, HO, Palarca, JC, Chilam, J, Jamoralin, MC, Villamin, AS, Borlasa, JB, Olorosa, AM, Hernandez, LFT, Boehme, KD, Jeffrey, B, Abudahab, K, Hufano, CM, Sia, SB, Stelling, J, Holden, MTG, Aanensen, DM & Carlos, CC 2020, 'Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines', Nature Communications, vol. 11, 2719. https://doi.org/10.1038/s41467-020-16322-5

TY - JOUR

T1 - Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

AU - Argimón, Silvia

AU - Masim, Melissa A L

AU - Gayeta, June M

AU - Lagrada, Marietta L

AU - Macaranas, Polle K V

AU - Cohen, Victoria

AU - Limas, Marilyn T

AU - Espiritu, Holly O

AU - Palarca, Janziel C

AU - Chilam, Jeremiah

AU - Jamoralin, Manuel C

AU - Villamin, Alfred S

AU - Borlasa, Janice B

AU - Olorosa, Agnettah M

AU - Hernandez, Lara F T

AU - Boehme, Karis D

AU - Jeffrey, Benjamin

AU - Abudahab, Khalil

AU - Hufano, Charmian M

AU - Sia, Sonia B

AU - Stelling, John

AU - Holden, Matthew T G

AU - Aanensen, David M

AU - Carlos, Celia C

N1 - Funding: This work was funded by the Newton Fund, Medical Research Council (UK) grant MR/N019296/1, Philippine Council for Health Research and Development project number FP160007. J.S. was partially supported by research grants RR025040 and U01CA207167 from the National Institutes of Health (NIH). S.A. and D.M.A. were additionally supported by the National Institute for Health Research (UK) Global Health Research Unit on genomic Surveillance of AMR(16_136_111) and by the Centre for Genomic Pathogen Surveillance (http://pathogensurveillance.net).

PY - 2020/6/1

Y1 - 2020/6/1

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-020-16322-5

DO - 10.1038/s41467-020-16322-5

M3 - Article

C2 - 32483195

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

M1 - 2719

ER -

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

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