{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T06:58:30Z","timestamp":1792133910454,"version":"4.4.0"},"reference-count":63,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T00:00:00Z","timestamp":1712275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020873","name":"Center for Membranes and Advanced Water Technology, Khalifa University","doi-asserted-by":"publisher","award":["RC2-2018-009"],"award-info":[{"award-number":["RC2-2018-009"]}],"id":[{"id":"10.13039\/501100020873","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004070","name":"Khalifa University of Science, Technology and Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004070","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>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 21<jats:sup>st<\/jats:sup> 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.<\/jats:p>","DOI":"10.1371\/journal.pone.0298325","type":"journal-article","created":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T16:23:01Z","timestamp":1712334181000},"page":"e0298325","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":44,"title":["Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater"],"prefix":"10.1371","volume":"19","author":[{"given":"Gihan","family":"Daw Elbait","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8651-965X","authenticated-orcid":true,"given":"Mariane","family":"Daou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miral","family":"Abuoudah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1645-6462","authenticated-orcid":true,"given":"Ahmed","family":"Elmekawy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shadi W.","family":"Hasan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dean B.","family":"Everett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Habiba","family":"Alsafar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1386-5372","authenticated-orcid":true,"given":"Andreas","family":"Henschel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5734-489X","authenticated-orcid":true,"given":"Ahmed F.","family":"Yousef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,4,5]]},"reference":[{"key":"pone.0298325.ref001","doi-asserted-by":"crossref","first-page":"140804","DOI":"10.1016\/j.scitotenv.2020.140804","article-title":"Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review","volume":"743","author":"N Hassoun-Kheir","year":"2020","journal-title":"Sci Total Environ"},{"key":"pone.0298325.ref002","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.jes.2020.10.010","article-title":"Temporal variation and sharing of antibiotic resistance genes between water and wild fish gut in a peri-urban river","volume":"103","author":"Z-C Zhou","year":"2021","journal-title":"J Envi Sci"},{"key":"pone.0298325.ref003","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.1007\/s10653-020-00759-0","article-title":"Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment","volume":"43","author":"Z Lin","year":"2021","journal-title":"Environ Geochem Health"},{"key":"pone.0298325.ref004","doi-asserted-by":"crossref","first-page":"144814","DOI":"10.1016\/j.scitotenv.2020.144814","article-title":"Behavior of antibiotic resistance genes in a wastewater treatment plant with different upgrading processes","volume":"771","author":"Z-J Lin","year":"2021","journal-title":"Sci Total Environ"},{"key":"pone.0298325.ref005","doi-asserted-by":"crossref","first-page":"688","DOI":"10.3389\/fmicb.2019.00688","article-title":"Prevalence and diversity of antibiotic resistance genes in Swedish aquatic environments impacted by household and hospital wastewater.","volume":"10","author":"FA Khan","year":"2019","journal-title":"Front Microbiol."},{"key":"pone.0298325.ref006","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1016\/j.envint.2018.10.032","article-title":"Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments.","volume":"121","author":"Z-C Zhou","year":"2018","journal-title":"Environ Int."},{"issue":"7","key":"pone.0298325.ref007","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1093\/trstmh\/trw048","article-title":"Antibiotic resistance is the quintessential One Health issue","volume":"110","author":"TP Robinson","year":"2016","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"pone.0298325.ref008","unstructured":"Jonas OB, Irwin A, Berthe FCJ, Le Gall FG, Marquez PV. 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