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 () and Celia C. Carlos ()
Additional contact information
Silvia Argimón: Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
Melissa A. L. Masim: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
June M. Gayeta: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Marietta L. Lagrada: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Polle K. V. Macaranas: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Victoria Cohen: Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
Marilyn T. Limas: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Holly O. Espiritu: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Janziel C. Palarca: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Jeremiah Chilam: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Manuel C. Jamoralin: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Alfred S. Villamin: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Janice B. Borlasa: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Agnettah M. Olorosa: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Lara F. T. Hernandez: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Karis D. Boehme: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Benjamin Jeffrey: Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
Khalil Abudahab: Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
Charmian M. Hufano: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
Sonia B. Sia: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine
John Stelling: Brigham and Women’s Hospital
Matthew T. G. Holden: University of St Andrews School of Medicine
David M. Aanensen: Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
Celia C. Carlos: Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16322-5

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