ArticlePloS one2024
Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater.
Article in PloS one, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Antibiotic Resistance Genes in Dust from Kindergarten Environments: A Systematic Review of Occurrence, Diversity, Determinants, and Exposure Implications.International journal of environmental research and public health · 2026Pooled it
- Integrated qPCR and Shotgun Metagenomics for Surveillance of Antimicrobial Resistance in Municipal Wastewater from Central Italy.Antibiotics (Basel, Switzerland) · 2026Article
- The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.FEMS microbiology ecology · 2026Review
- Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.Antibiotics (Basel, Switzerland) · 2026Article
- Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.Biology methods & protocols · 2026Review
- Comprehensive resistome and antibiotic profiling in wastewater and biosolids: a case study.Frontiers in microbiology · 2026Article
- Fosfomycin Resistance: An Update on the Anthropogenic Impact Through Agriculture.Pathogens (Basel, Switzerland) · 2025Review
- Culture-Based Wastewater Surveillance for the Detection and Monitoring of Antimicrobial Resistance in Staphylococcal Species.Veterinary sciences · 2025Article
- Hospital Wastewater Surveillance and Antimicrobial Resistance: A Narrative Review.Microorganisms · 2025Review
- 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
- Monitoring of Pathogens Carried by Imported Flies and Cockroaches at Shenzhen Ports.Tropical medicine and infectious disease · 2025Article
- Can Wastewater Surveillance Enhance Genomic Tracking of Climate-Driven Pathogens?Microorganisms · 2025Review
- Proximity-Ligation Metagenomic Sequence Analysis Reveals That the Antibiotic Resistome Makes Significant Transitions During Municipal Wastewater Treatment.Environmental microbiology · 2025Article
- Resistome in the indoor dust samples from workplaces and households: a pilot study.Frontiers in cellular and infection microbiology · 2024Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.
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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.