ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2021
Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- Towards accurate genomic detection of fungal antimicrobial resistance: progress in fungal resistance databases and bioinformatic tools.Microbial genomics · 2026Review
- Bundled management improves clinical outcome and reduces healthcare cost in multidrug-resistant bacterial infections: a retrospective study.American journal of translational research · 2026Article
- Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.Frontiers in public health · 2026Article
- Antimicrobial resistance interventions in Latin America and the Caribbean: a scoping review of reported interventions between 2018-2024.Antimicrobial resistance and infection control · 2025Article
- Bacterial Genomics for National Antimicrobial Resistance Surveillance in Cambodia.The Journal of infectious diseases · 2025Article
- A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens.The Lancet. Infectious diseases · 2025Review
- Advances in genotypic antimicrobialresistance testing: a comprehensive review.Science China. Life sciences · 2025Review
- Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings.Frontiers in microbiology · 2025Article
- Enhancing clinical microbiology for genomic surveillance of antimicrobial resistance implementation in Africa.Antimicrobial resistance and infection control · 2024Review
- Genomic epidemiology of ceftriaxone-resistant non-typhoidal Salmonella enterica strain in China.BMC genomics · 2024Article
- The Prevalence of Multidrug-ResistantIndian journal of microbiology · 2024Article
- National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales.Nature communications · 2023Article
- Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology.Antibiotics (Basel, Switzerland) · 2023Review
- Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.The Journal of hospital infection · 2023Article
- Whole-genome sequencing for surveillance of antimicrobial resistance in Ecuador: present and future implications.Revista panamericana de salud publica = Pan American journal of public health · 2023Article
- Circulation of Third-Generation Cephalosporin Resistant Salmonella Typhi in Mumbai, India.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Whole genome sequencing and prediction of antimicrobial susceptibilities in non-tuberculous mycobacteria.Frontiers in microbiology · 2022Review
- Towards Equitable Access to Public Health Pathogen Genomics in the Western Pacific.The Lancet regional health. Western Pacific · 2022Review
- Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antimicrobial resistance (AMR) is considered a global threat, and novel drug discovery needs to be complemented with systematic and standardized epidemiological surveillance. Surveillance data are currently generated using phenotypic characterization. However, due to poor scalability, this approach does little for true epidemiological investigations. There is a strong case for whole-genome sequencing (WGS) to enhance the phenotypic data. To establish global AMR surveillance using WGS, we developed a laboratory implementation approach that we applied within the NIHR Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance. In this paper, we outline the laboratory implementation at 4 units: Colombia, India, Nigeria, and the Philippines. The journey to embedding WGS capacity was split into 4 phases: Assessment, Assembly, Optimization, and Reassessment. We show that on-boarding WGS capabilities can greatly enhance the real-time processing power within regional and national AMR surveillance initiatives, despite the high initial investment in laboratory infrastructure and maintenance. Countries looking to introduce WGS as a surveillance tool could begin by sequencing select Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens that can demonstrate the standardization and impact genome sequencing has in tackling AMR.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.