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- 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.
- Impact of disinfection processes on bacterial community in urban wastewater: Should we rethink microbial assessment methods?Publication . Cesare, Andrea Di; Corno, Gianluca; Manaia, Célia M.; Rizzo, LuigiThe development of new methods and technologies for microbial characterization as well as their increasing availability at more affordable costs, has made evident the limitations of the conventional and routinely applied (typically cultivation based) methods to exhaustively and fully characterize the actual effect of disinfection process in urban wastewater treatment plants (UWWTPs). Such problem is even more relevant and of concern if microbial challenges, such as the occurrence of pathogens as well as the spread of antibiotic resistance, are taken into account. Such threats move scientists to investigate new and more effective disinfection processes from one side and new methods, techniques and approaches to characterize disinfection process efficiency from the other side. In this opinion paper, the limitations of routine detection methods are discussed according to the relevant and updated scientific literature to explain how research oriented methods and technologies (namely, quantitative real-time PCR, flow cytometry, metagenetics and metagenomics) can allow a better evaluation of disinfection processes. After a short introduction to the main disinfection processes, the application of different microbial characterization methods is discussed according to distinct challenges, such as pathogens inactivation or antibiotic resistance dissemination, when wastewater safety is of concern (for example in reuse scenarios). The routine and research oriented techniques can be successfully used in complementary way to evaluate disinfection process efficiency. Recommendations for UWWTPs managers for internal control of disinfection process are proposed.
- 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.