ArticleMicroorganisms2021
EpicPCR 2.0: Technical and Methodological Improvement of a Cutting-Edge Single-Cell Genomic Approach.
Article in Microorganisms, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
- ERMA: a harmonizing epicPCR data analysis tool.BMC genomics · 2026Article
- Assessing resistome host range across water reclamation in three geographically distinct communities using Hi-C sequencing.Applied and environmental microbiology · 2026Article
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.Frontiers in cellular and infection microbiology · 2026Article
- A Practical Framework for Environmental Antibiotic Resistance Monitoring in Freshwater Ecosystems.Antibiotics (Basel, Switzerland) · 2025Review
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Review
- Portable microfluidic devices for monitoring antibiotic resistance genes in wastewater.Mikrochimica acta · 2024Review
- Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria.FEMS microbiology reviews · 2024Review
- Bacterial hosts of clinically significant beta-lactamase genes in Croatian wastewaters.FEMS microbiology ecology · 2024Article
- Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era.Nature reviews. Microbiology · 2024Review
- What are the missing pieces needed to stop antibiotic resistance?Microbial biotechnology · 2023Review
- Uncovering the diverse hosts of tigecycline resistance geneWater research X · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.
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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.