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

Anti-Bacterial Agents / pharmacology Bacteria / drug effects Bacterial Infections / epidemiology Drug Resistance, Bacterial / genetics Genome, Bacterial / genetics Genomics / methods Humans Microbial Sensitivity Tests / methods Philippines / epidemiology Surveys and Questionnaires Whole Genome Sequencing / methods

Journal

Nature communications

ISSN: 2041-1723

Titre abrégé: Nat Commun

Pays: England

ID NLM: 101528555

Informations de publication

Date de publication:
01 06 2020

Historique:

received: 06 03 2020

accepted: 25 04 2020

entrez: 3 6 2020

pubmed: 3 6 2020

medline: 18 8 2020

Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-020-16322-5 PMID: 32483195 PMC: PMC7264328

pubmed: 32483195

doi: 10.1038/s41467-020-16322-5

pii: 10.1038/s41467-020-16322-5

pmc: PMC7264328

doi:

Substances chimiques

Anti-Bacterial Agents 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

2719

Subventions

Organisme : NCRR NIH HHS

ID : R01 RR025040

Pays : United States

Organisme : NCI NIH HHS

ID : U01 CA207167

Pays : United States

Organisme : Medical Research Council

ID : MR/N019296/1

Pays : United Kingdom

Organisme : Department of Health

ID : 16_136_111

Pays : United Kingdom

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