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

Author

Listed:
  • 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
    St. Luke’s Medical Center—Global City)

  • 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
    Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford)

  • Celia C. Carlos

    (Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine)

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.

Suggested Citation

  • 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 & Man, 2020. "Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16322-5
    DOI: 10.1038/s41467-020-16322-5
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    Cited by:

    1. Shizuo Kayama & Koji Yahara & Yo Sugawara & Sayoko Kawakami & Kohei Kondo & Hui Zuo & Shoko Kutsuno & Norikazu Kitamura & Aki Hirabayashi & Toshiki Kajihara & Hitomi Kurosu & Liansheng Yu & Masato Suz, 2023. "National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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