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

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.

Citation

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 , Sia , S B , Stelling , J , Holden , M T G , Aanensen , D M & Carlos , C C 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

Publication

Nature Communications

Status

Peer reviewed

DOI

https://doi.org/10.1038/s41467-020-16322-5

ISSN

2041-1723

Type

Journal article

Rights

Copyright © The Author(s) 2020. 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, visithttp://creativecommons.org/licenses/by/4.0/.

Description

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).

Collections

University of St Andrews Research

URI

http://hdl.handle.net/10023/20060

St Andrews Research Repository