Browsing by Author "Berendonk, Thomas U."
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- Antibiotic resistance genes in treated wastewater and in the receiving water bodies: a pan-European survey of urban settingsPublication . Cacace, Damiano; Fatta-Kassinos, Despo; Manaia, Célia M.; Cytryn, Eddie; Kreuzinger, Norbert; Rizzo, Luigi; Karaolia, Popi; Schwartz, Thomas; Alexander, Johannes; Merlin, Christophe; Garelick, Hemda; Schmitt, Heike; Vries, Daisy de; Schwermer, Carsten U.; Meric, Sureyya; Ozkal, Can Burak; Pons, Marie-Noelle; Kneis, David; Berendonk, Thomas U.There is increasing public concern regarding the fate of antibiotic resistance genes (ARGs) during wastewater treatment, their persistence during the treatment process and their potential impacts on the receiving water bodies. In this study, we used quantitative PCR (qPCR) to determine the abundance of nine ARGs and a class 1 integron associated integrase gene in 16 wastewater treatment plant (WWTP) effluents from ten different European countries. In order to assess the impact on the receiving water bodies, gene abundances in the latter were also analysed. Six out of the nine ARGs analysed were detected in all effluent and river water samples. Among the quantified genes, intI1 and sul1 were the most abundant. Our results demonstrate that European WWTP contribute to the enrichment of the resistome in the receiving water bodies with the particular impact being dependent on the effluent load and local hydrological conditions. The ARGs concentrations in WWTP effluents were found to be inversely correlated to the number of implemented biological treatment steps, indicating a possible option for WWTP management. Furthermore, this study has identified blaOXA-58 as a possible resistance gene for future studies investigating the impact of WWTPs on their receiving water.
- Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalencePublication . Pärnänen, Katariina M. M.; Narciso-da-Rocha, Carlos; Kneis, David; Berendonk, Thomas U.; Cacace, Damiano; Do, Thi Thuy; Elpers, Christian; Fatta-Kassinos, Despo; Henriques, Isabel; Jaeger, Thomas; Karkman, Antti; Martinez, Jose Luis; Michael, Stella G.; Michael-Kordatou, Irene; O’Sullivan, Kristin; Rodriguez-Mozaz, Sara; Schwartz, Thomas; Sheng, Hongjie; Sørum, Henning; Stedtfeld, Robert D.; Tiedje, James M.; Giustina, Saulo Varela Della; Walsh, Fiona; Vaz-Moreira, Ivone; Virta, Marko; Manaia, Célia M.Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clinical AR prevalence in Europe, this study compared the influent and final effluent of 12 UWTPs located in seven countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway). Using highly parallel quantitative polymerase chain reaction, we analyzed 229 resistance genes and 25 mobile genetic elements. This first trans-Europe surveillance showed that UWTP AR profiles mirror the AR gradient observed in clinics. Antibiotic use, environmental temperature, and UWTP size were important factors related with resistance persistence and spread in the environment. These results highlight the need to implement regular surveillance and control measures, which may need to be appropriate for the geographic regions.
- Every fifth published metagenome is not available to sciencePublication . Eckert, Ester M.; Cesare, Andrea Di; Fontaneto, Diego; Berendonk, Thomas U.; Bürgmann, Helmut; Cytryn, Eddie; Fatta-Kassinos, Despo; Franzetti, Andrea; Larsson, D. G. Joakim; Manaia, Célia M.; Pruden, Amy; Singer, Andrew C.; Udikovic-Kolic, Nikolina; Corno, GianlucaHave you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.
- A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plantsPublication . Marano, Roberto B.M.; Fernandes, Telma; Manaia, Célia M.; Nunes, Olga; Morrison, Donald; Berendonk, Thomas U.; Kreuzinger, Norbert; Tenson, Tanel; Corno, Gianluca; Fatta-Kassinos, Despo; Merlin, Christophe; Topp, Edward; Henn, Leonie; Scott, Andrew; Heß, Stefanie; Slipko, Katarzyna; Laht, Mailis; Kisand, Veljo; Cesare, Andrea Di; Karaolia, Popi; Michael, Stella G.; Petre, Alice L.; Rosal, Roberto; Pruden, Amy; Riquelme, Virginia; Agüera, Ana; Esteban, Belen; Luczkiewicz, Aneta; Kalinowska, Agnieszka; Leonard, Anne; Gaze, William H.; Adegoke, Anthony A.; Stenstrom, Thor A.; Pollice, Alfieri; Salerno, Carlo; Schwermer, Carsten U.; Krzeminski, Pawel; Guilloteau, Hélène; Donner, Erica; Drigo, Barbara; Libralato, Giovanni; Guida, Marco; Bürgmann, Helmut; Beck, Karin; Garelick, Hemda; Tacão, Marta; Henriques, Isabel; Martínez-Alcalá, Isabel; Guillén-Navarro, Jose M.; Popowska, Magdalena; Piotrowska, Marta; Quintela-Baluja, Marcos; Bunce, Joshua T.; Polo-López, Maria I.; Nahim–Granados, Samira; Pons, Marie-Noëlle; Milakovic, Milena; Udikovic-Kolic, Nikolina; Ory, Jérôme; Ousmane, Traore; Caballero, Pilar; Oliver, Antoni; Rodriguez-Mozaz, Sara; Balcazar, Jose L.; Jäger, Thomas; Schwartz, Thomas; Yang, Ying; Zou, Shichun; Lee, Yunho; Yoon, Younggun; Herzog, Bastian; Mayrhofer, Heidrun; Prakash, Om; Nimonkar, Yogesh; Heath, Ester; Baraniak, Anna; Abreu-Silva, Joana; Choudhury, Manika; P. Munoz, Leonardo; Krizanovic, Stela; Brunetti, Gianluca; Maile-Moskowitz, Ayella; Brown, Connor; Cytryn, EddieThe World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status.
- Inter-laboratory calibration of quantitative analyses of antibiotic resistance genesPublication . Rocha, Jaqueline; Cacace, Damiano; Kampouris, Ioannis; Guilloteau, Hélène; Jäger, Thomas; Marano, Roberto B.M.; Karaolia, Popi; Manaia, Célia M.; Merlin, Christophe; Fatta-Kassinos, Despo; Cytryn, Eddie; Berendonk, Thomas U.; Schwartz, ThomasAntibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are widely distributed in the environment where they represent potential public health threats. Quantitative PCR (qPCR) is a suitable approach to detect and quantify ARGs in environmental samples. However, the comparison of gene quantification data between different laboratories is challenging since the data are predominantly obtained under non-harmonized conditions, using different qPCR protocols. This study aimed at carrying out an inter-laboratory calibration in order to assess the variability inherent to the qPCR procedures for quantification of ARGs. With this aim, samples of treated wastewater collected in three different countries were analysed based on common DNA extract pools and identical protocols as well as distinct equipment, reagents batches, and operators. The genes analysed were the 16S rRNA, vanA, blaTEM, qnrS, sul1, blaCTXM-32 and intI1 and the artificial pNORM1 plasmid containing fragments from the seven targeted genes was used as a reference. The 16S rRNA gene was the most abundant, in all the analysed samples, followed by intI1, sul1, qnrS, and blaTEM, while blaCTXM-32 and vanA were below the limit of quantification in most or all the samples. For the genes 16S rRNA, sul1, intI1, blaTEM and qnrS the inter-laboratory variation was below 28% (3–8%, 6–18%, 8–21%, 10–24%, 15–28%, respectively). While it may be difficult to fully harmonize qPCR protocols due to equipment, reagents and operator variations, the inter-laboratory calibration is an adequate and necessary step to increase the reliability of comparative data on ARGs abundance in different environmental compartments and/or geographic regions.
- Microbiome and resistome profiles along a sewage-effluent-reservoir trajectory underline the role of natural attenuation in wastewater stabilization reservoirsPublication . Leão, Inês; Khalifa, Leron; Gallois, Nicolas; Vaz-Moreira, Ivone; Klümper, Uli; Youdkes, Daniel; Palmony, Shaked; Dagai, Lotan; Berendonk, Thomas U.; Merlin, Christophe; Manaia, Célia M.; Cytryn, EddieAntibiotic-resistant bacteria and antibiotic resistance gene (ARGs) loads dissipate through sewage treatment plants to receiving aquatic environments, but the mechanisms that mitigate the spread of these ARGs are not well understood due to the complexity of full-scale systems and the difficulty of source tracking in downstream environments. To overcome this problem, we targeted a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR), whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs and receiving aquatic ecosystems. We analyzed a large set of physicochemical measurements, concomitant with the cultivation of total and cefotaxime-resistant Escherichia coli, microbial community analyses, and quantitative PCR (qPCR)/digital droplet PCR (ddPCR) quantification of selected ARGs and mobile genetic elements (MGEs). The MABR removed most of the sewage-derived organic carbon and nitrogen, and simultaneously, E. coli, ARG, and MGE levels dropped by approximately 1.5- and 1.0-log unit mL(-1), respectively. Similar levels of E. coli, ARGs, and MGEs were removed in the reservoir, but interestingly, unlike in the MABR, the relative abundance (normalized to 16S rRNA gene-inferred total bacterial abundance) of these genes also decreased. Microbial community analyses revealed the substantial shifts in bacterial and eukaryotic community composition in the reservoir relative to the MABR. Collectively, our observations lead us to conclude that the removal of ARGs in the MABR is mainly a consequence of treatment-facilitated biomass removal, whereas in the stabilization reservoir, mitigation is linked to natural attenuation associated with ecosystem functioning, which includes abiotic parameters, and the development of native microbiomes that prevent the establishment of wastewater-derived bacteria and associated ARGs.IMPORTANCE Wastewater treatment plants are sources of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which can contaminate receiving aquatic environments and contribute to antibiotic resistance. We focused on a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR) that treated raw sewage, whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs. We evaluated ARB and ARG dynamics across the raw-sewage-MABR-effluent trajectory, concomitant with evaluation of microbial community composition and physicochemical parameters, in an attempt to identify mechanisms associated with ARB and ARG dissipation. We found that removal of ARB and ARGs in the MABR was primarily associated with bacterial death or sludge removal, whereas in the reservoir it was attributed to the inability of ARBs and associated ARGs to colonize the reservoir due to a dynamic and persistent microbial community. The study demonstrates the importance of ecosystem functioning in removing microbial contaminants from wastewater. Wastewater treatment plants are sources of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which can contaminate receiving aquatic environments and contribute to antibiotic resistance. We focused on a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR) that treated raw sewage, whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs.
- Tackling antibiotic resistance: the environmental frameworkPublication . Berendonk, Thomas U.; Manaia, Célia M.; Merlin, Christophe; Fatta‑Kassinos, Despo; Cytryn, Eddie; Walsh, Fiona; Bürgmann, Helmut; Sørum, Henning; Norström, Madelaine; Pons, Marie-Noëlle; Kreuzinger, Norbert; Huovinen, Pentti; Stefani, Stefania; Schwartz, Thomas; Kisand, Veljo; Baquero, Fernando; Martinez, José LuisAntibiotic resistance is a threat to human and animal health worldwide, and key measures are required to reduce the risks posed by antibiotic resistance genes that occur in the environment. These measures include the identification of critical points of control, the development of reliable surveillance and risk assessment procedures, and the implementation of technological solutions that can prevent environmental contamination with antibiotic resistant bacteria and genes. In this Opinion article, we discuss the main knowledge gaps, the future research needs and the policy and management options that should be prioritized to tackle antibiotic resistance in the environment.