ArticleGenome medicine2021
An implementation science approach to evaluating pathogen whole genome sequencing in public health.
Article in Genome medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Whole genome sequencing analysis of antibiotic resistant genes of Shigella species: A systematic review and meta-analysis.PloS one · 2025Pooled it
- Novel surveillance design exploiting network analysis for efficient, rapid detection of emerging Clostridioides difficile strains.Nature communications · 2026Article
- Current Perspectives onInternational journal of molecular sciences · 2026Review
- Interregional outbreak ofEpidemiology and infection · 2026Article
- High acceptability of a national platform for public health genomic data sharing and surveillance in Australia: a mixed methods study.BMC global and public health · 2026Article
- Whole genome sequencing for Mycobacterium tuberculosis in public health responses: a review of current practice and enablers in select low-incidence jurisdictions.BMC public health · 2026Review
- Implementation of a SARS-CoV-2 genomic surveillance network as a strategy to face other health challenges in Peru.Revista peruana de medicina experimental y salud publica · 2026Article
- Evaluating the use of whole-genome sequencing and SangerJournal of medical microbiology · 2026Article
- 8,266 SARS-CoV-2 Genomic Assemblies from Asymptomatic Carriers in Japan.Scientific data · 2026Article
- The public health utility of whole genome sequencing: Insights from a tuberculosis outbreak in Australia and perspectives of public health professionals.PLOS global public health · 2026Article
- Review
- Beyond presence and frequency: a determinant-level framework for interpreting AMR dissemination in One Health surveillance.Frontiers in bioinformatics · 2026Article
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Prospects of pathogen whole-genome sequencing in outbreak tracing and antimicrobial resistance surveillance of spinal infections.Frontiers in cellular and infection microbiology · 2026Review
- Describing the outcomes and factors of using pathogen genomic results in public health.Frontiers in public health · 2026Article
- Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.Microbiology spectrum · 2025Article
- Phenotypic and genotypic relationships between Shigella species and Escherichia coli O37:H10 isolates in Addis Ababa, Ethiopia.BMC research notes · 2025Article
- A case report ofASM case reports · 2025Article
- Large-scale screening of SARS-CoV-2 variants in Tokyo, Japan: A 3-year and 9-month longitudinal survey.Global health & medicine · 2025Article
- Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.Antibiotics (Basel, Switzerland) · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
backgroundPathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease surveillance, outbreak investigation and infection prevention and control. However, to date, there are limited data regarding (i) the optimal models for integration of genomic data into epidemiological investigations and (ii) how to quantify and evaluate public health impacts resulting from genomic epidemiological investigations.
methodsWe developed the Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework to guide examination of the use of WGS in public health surveillance and disease control. We illustrate the use of this framework with three pathogens as case studies: Listeria monocytogenes, Mycobacterium tuberculosis and SARS-CoV-2.
resultsThe framework utilises an adaptable whole-of-system approach towards understanding how interconnected elements in the public health application of pathogen genomics contribute to public health processes and outcomes. The three phases of the PG-PHASE Framework are designed to support understanding of WGS laboratory processes, analysis, reporting and data sharing, and how genomic data are utilised in public health practice across all stages, from the decision to send an isolate or sample for sequencing to the use of sequence data in public health surveillance, investigation and decision-making. Importantly, the phases can be used separately or in conjunction, depending on the need of the evaluator. Subsequent to conducting evaluation underpinned by the framework, avenues may be developed for strategic investment or interventions to improve utilisation of whole genome sequencing.
conclusionsComprehensive evaluation is critical to support health departments, public health laboratories and other stakeholders to successfully incorporate microbial genomics into public health practice. The PG-PHASE Framework aims to assist public health laboratories, health departments and authorities who are either considering transitioning to whole genome sequencing or intending to assess the integration of WGS in public health practice, including the capacity to detect and respond to outbreaks and associated costs, challenges and facilitators in the utilisation of microbial genomics and public health impacts.
Indexed as
Identifiers
What OpenQuestion holds
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.