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

被引：69

作者：

Argimon, Silvia ^{[1
]}

Masim, Melissa A. L. ^{[2
]}

Gayeta, June M. ^{[2
]}

Lagrada, Marietta L. ^{[2
]}

Macaranas, Polle K., V ^{[2
]}

Cohen, Victoria ^{[1
]}

Limas, Marilyn T. ^{[2
]}

Espiritu, Holly O. ^{[2
]}

Palarca, Janziel C. ^{[2
]}

Chilam, Jeremiah ^{[2
]}

Jamoralin Jr, Manuel C. ^{[2
]}

Villamin, Alfred S. ^{[2
]}

Borlasa, Janice B. ^{[2
]}

Olorosa, Agnettah M. ^{[2
]}

Hernandez, Lara F. T. ^{[2
]}

Boehme, Karis D. ^{[2
]}

Jeffrey, Benjamin ^{[1
]}

Abudahab, Khalil ^{[1
]}

Hufano, Charmian M. ^{[2
,6
]}

Sia, Sonia B. ^{[2
]}

Stelling, John ^{[3
]}

Holden, Matthew T. G. ^{[4
]}

Aanensen, David M. ^{[1
,5
]}

Carlos, Celia C. ^{[2
]}

机构：

[1] Wellcome Genome Campus, Ctr Genom Pathogen Surveillance, Hinxton, England

[2] Res Inst Trop Med, Antimicrobial Resistance Surveillance Reference L, Muntinlupa, Philippines

[3] Brigham & Womens Hosp, 75 Francis St, Boston, MA 02115 USA

[4] Univ St Andrews, Sch Med, St Andrews, Fife, Scotland

[5] Univ Oxford, Li Ka Shing Ctr Hlth Informat & Discovery, Big Data Inst, Oxford, England

[6] St Lukes Med Ctr Global City, Taguig, Metro Manila, Philippines

来源：

NATURE COMMUNICATIONS | 2020年 / 11卷 / 01期

基金：

英国医学研究理事会; 美国国家卫生研究院;

关键词：

OXA-181-PRODUCING ESCHERICHIA-COLI; PUBLIC-HEALTH SURVEILLANCE; CARBAPENEMASE GENES; BETA-LACTAMASE; TYPING SCHEME; 1ST REPORT; ENTEROBACTERIACEAE; IDENTIFICATION; SALMONELLA; EMERGENCE;

D O I：

10.1038/s41467-020-16322-5

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：15

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