ReviewGenes2018
The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain.
Review in Genes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 79 papers, 2 of them syntheses 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
79 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Predicting Antibiotic Resistance inInternational journal of molecular sciences · 2025Pooled it
- Whole genome sequencing analysis of antibiotic resistant genes of Shigella species: A systematic review and meta-analysis.PloS one · 2025Pooled it
- Reimagining antimicrobial resistance: AI-driven predictive epidemiology and the C-AMRE framework for next-generation antibiotic discovery.The Journal of antibiotics · 2026Review
- Clinical and Epidemiological Landscape of Antimicrobial Resistance and Virulence inAntibiotics (Basel, Switzerland) · 2026Review
- Clinical and Genomic Characterization of High-Risk Multidrug-ResistantMicroorganisms · 2026Article
- Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.Diagnostics (Basel, Switzerland) · 2026Review
- Methicillin-ResistantInternational journal of molecular sciences · 2026Review
- Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Whole-Genome Analysis of Multidrug-Resistant Escherichia coli from Bloodstream Infections in Iraqi Cancer Patients.Asian Pacific journal of cancer prevention : APJCP · 2026Article
- Food-borne bacterial pathogens: emerging approaches in detection and prevention.Archives of microbiology · 2026Review
- Exploring the modulatory effects of spotted pumpkin (Translational animal science · 2026Article
- Article
- Antibiotic resistance inFrontiers in microbiology · 2026Review
- Genomic surveillance of multidrug-resistant Escherichia coli and Klebsiella in clinical and wastewater isolates from a paediatric hospital in Lima, Peru.Access microbiology · 2026Article
- Comparative Analysis of Phenotypic and Genotypic Antibiotic Susceptibility ofAntibiotics (Basel, Switzerland) · 2025Article
- Water-Mediated Dissemination and Detection of Antibiotic Resistance Across Livestock, Agri-Food, and Aquaculture Systems.Micromachines · 2025Review
- The Role of Genomic Islands in the Pathogenicity and Evolution of Plant-Pathogenic Gammaproteobacteria.Microorganisms · 2025Review
- Metagenomic Analysis of Ready-to-Eat Foods on Retail Sale in the UK Identifies Diverse Genes Related to Antimicrobial Resistance.Microorganisms · 2025Article
- Genomic insights into the diversity, antimicrobial resistance and zoonotic potential ofMicrobial genomics · 2025Article
- Companion Animals as Reservoirs of Multidrug Resistance-A Rare Case of an XDR, NDM-1-ProducingVeterinary sciences · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
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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.