ArticleBMC research notes2025
Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study.
Article in BMC research notes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Antimicrobial resistance in wastewater-impacted coastal waters: implications for environmental surveillance and public health.Microbiology (Reading, England) · 2026Article
- Source-Resolved Wastewater Metagenomics Reveals Distinct Resistome and Virulome Landscapes Across an Urban Wastewater Continuum.Antibiotics (Basel, Switzerland) · 2026Article
- AMR in wild animals and plants: global trends and future priorities in wildlife-associated antimicrobial resistance research.npj antimicrobials and resistance · 2026Article
- Environmental Risks of Antibiotics and Antibiotic Resistance Elements: Occurrence, Fate, and Assessment.International journal of molecular sciences · 2026Review
- Artificial intelligence for early detection and risk prediction of antimicrobial resistance in aquatic ecosystems.npj antimicrobials and resistance · 2026Review
- Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.Antibiotics (Basel, Switzerland) · 2026Article
- Fosfomycin Resistance: An Update on the Anthropogenic Impact Through Agriculture.Pathogens (Basel, Switzerland) · 2025Review
- Comparative Analysis of Concentration and Quantification Methods for Antibiotic Resistance Genes and Their Phage-Mediated Dissemination in Treated Wastewater and Biosolids.Pathogens (Basel, Switzerland) · 2025Article
- A Practical Framework for Environmental Antibiotic Resistance Monitoring in Freshwater Ecosystems.Antibiotics (Basel, Switzerland) · 2025Review
- Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725-920 CE.PloS one · 2025Article
- Antimicrobial resistance genes in weaned pigs: quantitative abundance and group dynamics assessed by qPCR.Frontiers in veterinary science · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveThe World Health Organization (WHO) has declared antimicrobial resistance (AMR) as one of the top threats to global public health. While AMR surveillance of human clinical isolates is well-established in many countries, the increasing threat of AMR has intensified efforts to detect antibiotic resistance genes (ARGs) accurately and sensitively in environmental samples, wastewater, animals, and food. Using five ARGs and the 16S rRNA gene, we compared quantitative PCR (qPCR) and metagenomic sequencing (MGS), two commonly used methods to uncover the wastewater resistome. We compared both methods by evaluating ARG detection through a municipal wastewater treatment chain.
resultsOur results demonstrate that qPCR was more sensitive than MGS, particularly in diluted samples with low ARG concentrations such as oxidation pond water. However, MGS was potentially more specific and has less risk of off-target binding in concentrated samples such as raw sewage. MGS analysis revealed multiple subtypes of each gene which could not be distinguished by qPCR; these subtypes varied across different sample types. Our findings affect the conclusions that can be drawn when comparing different sample types, particularly in terms of inferring removal rates or origins of genes. We conclude that both methods appear suitable to profile the resistome of wastewater and other environmental samples, depending on the research question and type of sample.
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Registered trials
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