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Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including <jats:italic>aadA<\/jats:italic> and <jats:italic>aadB<\/jats:italic> (conferring resistance to aminoglycosides); <jats:italic>ampC<\/jats:italic>, <jats:italic>bla<\/jats:italic><jats:sub>TEM<\/jats:sub>, <jats:italic>bla<\/jats:italic><jats:sub>SHV<\/jats:sub>, and <jats:italic>mecA<\/jats:italic> (resistance to beta-lactams); <jats:italic>dfrA<\/jats:italic>1 (resistance to trimethoprim); <jats:italic>ermB<\/jats:italic> (resistance to macrolides); <jats:italic>fosA<\/jats:italic> (resistance to fosfomycin); <jats:italic>qnrS<\/jats:italic> (resistance to quinolones); and <jats:italic>tetA<\/jats:italic>(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade\u2009&gt;\u200970%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs\u2019 biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (&gt;\u200990%), good linearity of the standard curve (<jats:italic>R<\/jats:italic><jats:sup>2<\/jats:sup>\u2009&gt;\u20090.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.<\/jats:p>","DOI":"10.1007\/s00248-024-02385-0","type":"journal-article","created":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T08:02:05Z","timestamp":1715760125000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR"],"prefix":"10.1007","volume":"87","author":[{"given":"Lizandra","family":"Perez-Bou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Gonzalez-Martinez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan J.","family":"Cabrera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Belen","family":"Juarez-Jimenez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Belen","family":"Rodelas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesus","family":"Gonzalez-Lopez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Correa-Galeote","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,15]]},"reference":[{"issue":"4","key":"2385_CR1","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/s10661-022-09846-4","volume":"194","author":"LO Omuferen","year":"2022","unstructured":"Omuferen LO, Maseko B, Olowoyo JO (2022) Occurrence of antibiotics in wastewater from hospital and convectional wastewater treatment plants and their impact on the effluent receiving rivers: current knowledge between 2010 and 2019. 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