ArticleFEMS microbes2023
Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.
Article in FEMS microbes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 75 citations in OpenAlex.
- Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.Gut microbes · 2026Trial
- Effect of the Food Matrix on the Survival to the Gastrointestinal Transit of Lacticaseibacillus rhamnosus CRL1505: A Randomized, Controlled, Crossover Study.Molecular nutrition & food research · 2025Trial
- Article
- Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.Animal microbiome · 2026Article
- Antimicrobial resistance profiling in poultry industry: a culture-independent resistome analysis and risk factor assessment.BMC veterinary research · 2026Article
- Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.Antibiotics (Basel, Switzerland) · 2026Article
- Plastics as vectors for pathogens and antibiotic resistance genes in aquatic systems.Water science and technology : a journal of the International Association on Water Pollution Research · 2026Review
- BCS2.0: a capture sequencing platform for rapid differential diagnosis of bacterial infections and antimicrobial resistance.Frontiers in microbiology · 2026Article
- A Hydroxynaphthol Blue-Based Loop-Mediated Isothermal Amplification Assay for Closed-Tube Detection of the Streptomycin Resistance GeneVeterinary sciences · 2025Article
- A Practical Framework for Environmental Antibiotic Resistance Monitoring in Freshwater Ecosystems.Antibiotics (Basel, Switzerland) · 2025Review
- Determinants of Campylobacter species diversity in infants and association with family members, livestock, and household environments in rural Eastern Ethiopia.Gut pathogens · 2025Article
- Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.Antibiotics (Basel, Switzerland) · 2025Review
- Resistance genes are not like chemical pollutants and surveillance of them should reflect that.Future microbiology · 2025Article
- Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (mSphere · 2025Article
- Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study.BMC research notes · 2025Article
- Mechanisms of Antimicrobial Resistance inInfection and drug resistance · 2025Review
- Harnessing beneficial bacteria to remediate antibiotic-polluted agricultural soils: integrating source diversity, bioavailability modulators, and ecological impacts.Frontiers in microbiology · 2025Review
- Antimicrobial resistance genes in weaned pigs: quantitative abundance and group dynamics assessed by qPCR.Frontiers in veterinary science · 2025Article
- A Surveillance Study of Culturable and Antimicrobial-Resistant Bacteria in Two Urban WWTPs in Northern Spain.Antibiotics (Basel, Switzerland) · 2024Article
- Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons.Journal of water and health · 2024Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.
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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.