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- 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.
- Toward a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistancePublication . Vikesland, Peter J.; Pruden, Amy; Alvarez, Pedro J. J.; Aga, Diana; Bürgmann, Helmut; Li, Xiang-dong; Manaia, Célia M.; Nambi, Indumath; Wigginton, Krista; Zhang, Tong; Zhu, Yong-GuanAntibiotic resistance is a pervasive global health threat. To combat the spread of resistance, it is necessary to consider all possible sources and understand the pathways and mechanisms by which resistance disseminates. Best management practices are urgently needed to provide barriers to the spread of resistance and maximize the lifespan of antibiotics as a precious resource. Herein we advise upon the need for coordinated national and international strategies, highlighting three essential components: (1) Monitoring, (2) Risk Assessment, and (3) Mitigation of antibiotic resistance. Central to all three components is What exactly to monitor, assess, and mitigate? We address this question within an environmental framework, drawing from fundamental microbial ecological processes driving the spread of resistance.
- Water and sanitation: an essential battlefront in the war on antimicrobial resistancePublication . Burgmann, Helmut; Frigon, Dominic; Gaze, William H.; Manaia, Célia M.; Pruden, Amy; Singer, Andrew C.; Smets, Barth F.; Zhang, TongWater and sanitation represent a key battlefront in combatting the spread of antimicrobial resistance (AMR). Basic water sanitation infrastructure is an essential first step towards protecting public health, thereby limiting the spread of pathogens and the need for antibiotics. AMR presents unique human health risks, meriting new risk assessment frameworks specifically adapted to water and sanitation-borne AMR. There are numerous exposure routes to AMR originating from human waste, each of which must be quantified for its relative risk to human health. Wastewater treatment plants play a vital role in centralized collection and treatment of human sewage, but there are numerous unresolved issues in terms of the microbial ecological processes occurring within them and the extent to which they attenuate or amplify AMR. Research is needed to advance understanding of the fate of resistant bacteria and antibiotic resistance genes in various waste management systems, depending on the local constraints and intended reuse applications. World Health Organization and national AMR action plans would benefit from a more holistic ’One Water’ nderstanding. In this article we provide a framework for research, policy, practice and public engagement aimed at limiting the spread of AMR from water and sanitation in low-, medium- and high-income countries.
- 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.