116 results on '"Cytryn E"'
Search Results
2. Temporal and spatial assessment of microbial communities in commercial silages from bunker silos
- Author
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Kraut-Cohen, J., Tripathi, V., Chen, Y., Gatica, J., Volchinski, V., Sela, S., Weinberg, Z., and Cytryn, E.
- Published
- 2016
- Full Text
- View/download PDF
3. MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
- Author
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Dueholm, M. K. D., Nierychlo, M., Andersen, K. S., Rudkjøbing, V., Knutsson, S., Arriaga, S., Bakke, R., Boon, N., Bux, F., Christensson, M., Chua, A. S. M., Curtis, T. P., Cytryn, E., Erijman, L., Etchebehere, C., Fatta-Kassinos, D., Frigon, D., Garcia-Chaves, M. C., Gu, A. Z., Horn, H., Jenkins, D., Kreuzinger, N., Kumari, S., Lanham, A., Law, Y., Leiknes, T. O., Morgenroth, E., Muszyński, A., Petrovski, S., Pijuan, M., Pillai, S. B., Reis, M. A. M., Rong, Q., Rossetti, S., Seviour, R., Tooker, N., Vainio, P., Loosdrecht, M. Van, Vikraman, R., Wanner, J., Weissbrodt, D., Wen, X., Zhang, T., Nielsen, P. H., Albertsen, M., and Consortium, MiDAS Global
- Subjects
Chemical engineering ,ddc:660 - Abstract
Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.
- Published
- 2022
4. MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
- Author
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Dueholm, MKD, Nierychlo, M, Andersen, KS, Rudkjøbing, V, Knutsson, S, Arriaga, S, Bakke, R, Boon, N, Bux, F, Christensson, M, Chua, ASM, Curtis, TP, Cytryn, E, Erijman, L, Etchebehere, C, Fatta-Kassinos, D, Frigon, D, Garcia-Chaves, MC, Gu, AZ, Horn, H, Jenkins, D, Kreuzinger, N, Kumari, S, Lanham, A, Law, Y, Leiknes, TO, Morgenroth, E, Muszyński, A, Petrovski, Steve, Pijuan, M, Pillai, SB, Reis, MAM, Rong, Q, Rossetti, S, Seviour, Robert, Tooker, N, Vainio, P, van Loosdrecht, M, Vikraman, R, Wanner, J, Weissbrodt, D, Wen, X, Zhang, T, Nielsen, PH, and Albertsen, M
- Subjects
FOS: Biological sciences ,90409 Wastewater Treatment Processes ,Microbiology ,FOS: Chemical engineering - Abstract
Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.
- Published
- 2022
- Full Text
- View/download PDF
5. Antibiotic resistance genes in treated wastewater and in the receiving water bodies: A pan-European survey of urban settings
- Author
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Cacace, Damiano, Fatta-Kassinos, D., Manaia, Celia M., Cytryn, E., Kreuzinger, Norbert, Rizzo, L., Karaolia, Popi, Schwartz, Thomas, Alexander, Johannes, Merlin, Christophe, Garelick, H., Schmitt, H., Schwermer, Carsten U., Meric, Sureyya, Ozkal, Can Burak, Pons, Marie Noelle, Kneis, D., Berendonk, Thomas U., One Health Microbieel, dIRAS RA-I&I I&I, Veritati - Repositório Institucional da Universidade Católica Portuguesa, Institut für Hydrobiologie, Technische Universität Dresden = Dresden University of Technology (TU Dresden), University of Cyprus [Nicosia], Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Universidade Católica Portuguesa [Porto], Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - the Volcani Center, Vienna University of Technology (TU Wien), Università degli Studi di Salerno (UNISA), Karlsruhe Institute of Technology (KIT), Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Middlesex University [London], Institute for Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Utrecht University [Utrecht], Norwegian Institute for Water Research (NIVA), Namik Kemal University, Laboratoire Réactions et Génie des Procédés (LRGP), and Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)
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0208 environmental biotechnology ,Dissemination ,02 engineering and technology ,Wastewater ,010501 environmental sciences ,Integron ,01 natural sciences ,Integrons ,Persistence (computer science) ,Pan european ,Antibiotic resistance genes ,Surveys and Questionnaires ,Bacterial Community ,Treatment Plants ,Waste Management and Disposal ,ComputingMilieux_MISCELLANEOUS ,Water Science and Technology ,2. Zero hunger ,biology ,Ecological Modeling ,Drug Resistance, Microbial ,Pollution ,6. Clean water ,Anti-Bacterial Agents ,3. Good health ,Europe ,qPCR ,Impact ,Sewage treatment ,Life sciences ,Environmental Engineering ,Freshwater ,Quantification ,ddc:570 ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,Effluent ,0105 earth and related environmental sciences ,Civil and Structural Engineering ,business.industry ,Hospital Effluent ,Mcr-1 ,020801 environmental engineering ,Biotechnology ,Resistome ,Genes, Bacterial ,13. Climate action ,biology.protein ,business ,Escherichia-Coli ,Removal - Abstract
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 bla(OXA-58) as a possible resistance gene for future studies investigating the impact of WWTPs on their receiving water. (C) 2019 The Authors. Published by Elsevier Ltd. German Federal Ministry of Education and ResearchFederal Ministry of Education & Research (BMBF) [02WU1351A]; project STARE -Stopping Antibiotic Resistance Evolution [WaterJPI/0001/2013]; project HYREKA (BMBF)Federal Ministry of Education & Research (BMBF); Working Group 5: Wastewater Reuse and Contaminants of Emerging Concern from Norman activities; NIVA's Strategic Research Initiative on Emerging Environmental Contaminants (Research Council of Norway) [208430] The study has been funded by the German Federal Ministry of Education and Research [02WU1351A]. CMM, TB, TS, DFK acknowledge the national funding agencies through the project WaterJPI/0001/2013 STARE -Stopping Antibiotic Resistance Evolution and the project HYREKA (BMBF). This work was supported by Working Group 5: Wastewater Reuse and Contaminants of Emerging Concern from Norman activities (http://www.norman-network.net/?q=node/106).CS acknowledges the financial support from NIVA's Strategic Research Initiative on Emerging Environmental Contaminants (Research Council of Norway; contract no. 208430).
- Published
- 2019
6. Impact of ribotype 027 on Clostridium difficile infection in a geriatric department
- Author
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Mascart, G., Delmée, M., Van Broeck, J., Cytryn, E., Karmali, R., and Cherifi, S.
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- 2013
- Full Text
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7. COST Action ES1403
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Fatta-kassinos, Despo, Manaia, C., Berendonk, Thomas U., Cytryn, E., Bayona, J., Chefetz, B., Slobodnik, J., Kreuzinger, N., Rizzo, L., Malato, S., Lundy, L., Ledin, A., Veritati - Repositório Institucional da Universidade Católica Portuguesa, and Fatta-Kassinos, Despo [0000-0003-1173-0941]
- Subjects
wastewater disinfection ,Engineering ,antibiotic resistance ,Health, Toxicology and Mutagenesis ,Public Policy ,Reuse ,Wastewater ,World Health Organization ,Waste Disposal, Fluid ,Water Purification ,Food chain ,antibiotic resistance, wastewater disinfection, wastewater reuse, wastewater treatment ,Environmental protection ,Drug Resistance, Bacterial ,Environmental Chemistry ,Humans ,Recycling ,Effluent ,Food security ,Waste management ,Bacteria ,business.industry ,General Medicine ,wastewater reuse ,Food safety ,Pollution ,Anti-Bacterial Agents ,wastewater treatment ,Sustainability ,Sewage treatment ,business ,Water Pollutants, Chemical ,Environmental Studies–Pollution - Abstract
Treated urban wastewater is currently widely reused to compensate for dwindling water supplies, as it is considered to be a reliable alternative water source. In addition, the increasing demand for food due to the expanding world population, both in respect to food security and food safety, and therefore for irrigation water, renders wastewater reuse a practice of utmost importance. As a consequence, sustainable and safe urban water cycles are presently of high priority on the policy agendas of many countries around the world. Although reuse has a number of benefits and major advances have been made with respect to producing treated effluents for reuse (e.g., successful removal of metals, reduction of chemical oxygen demand and of other pollution parameters), several important questions are still unanswered and barriers exist regarding the safety/sustainability of reuse practice. Knowledge gaps associated with wastewater reuse include the following: (a) possible elemental interactions that may influence the accumulation of metals/elements in the soil and their subsequent uptake by plants and crops, (b) the fateof organic microcontaminants in receiving environments, and (c) the epidemiological potential of antibiotic resistant bacteria and/or resistance genes (ARB&ARG) released in the environment via treated effluent. Possible implications on food-chain contamination (biomagnification) require much attention, since treated wastewater is not exempt of such contaminants. The effluents’ residual organic matter after conventional treatment consists of a number of recalcitrant organic compounds including potential endocrine disrupting compounds, many types of pharmaceuticals including antibiotics, disinfection by-products, personal care products, metabolites and transformation products, other organic substances (i.e. pesticides, surfactants, biocides, etc.), and not to be forgotten ARB&ARG. In fact, preliminary results suggest that the relative abundance of certain ARG or ARB may even be enriched during the wastewater treatment (Rizzo et al. 2013). This leads to their subsequent release in the terrestrial and aquatic environments through disposal and reuse applications, and the level of risk to environmental and human health is yet to be evaluated. Contamination of the environment, food chain, drinking water, etc with ARB&ARG is presently considered to be a serious public health problem. For this reason, the World Health Organization (WHO) (WHO 2013) characterized the development of AR as one of the major global threats to society and recommends intensive monitoring for the identification/surveillance of critical hot spots (e.g., wastewater treatment plants), aiming at reducing its propagation. In September 2014, a national strategy (The White House 2014) was announced in the USA by the White House that lays out a series of steps to address the decreasing effectiveness of antibiotics, many being similar to those identified by WHO. According to the European Centre for Disease Prevention and Control, it is estimated that infections caused by a subset of ARB are responsible for about 25,000 deaths in Europe annually. In addition, the extra healthcare costs and productivity losses due to ARB are estimated to reach EUR 1.5 billion (European Centre for Disease Prevention and Control 2013). In the USA, equally dramatic numbers are reported by the Centers for Disease Control and Prevention, with AR infections killing at least 23,000 people and sickening 2 million each year (The White House 2014). All these issues have not received significant attention in the framework of the wastewater reuse practice. The EU- COST Action ES1403 (NEREUS) aims at consolidating the existing scattered data related to wastewater reuse and will address the open challenges associated with it. It will provide the platform for a systematic consolidation of data and standardization of methods for assessing emerging hazards associated with wastewater reuse. The Action is chaired by D. Fatta-Kassinos from Nireas-International Water Research Center and Department of Civil and Environmental Engineering of the University of Cyprus and vice-chaired by C. Manaiafrom Escola Superior de Biotecnologia, Universidade Católica Portugeusa.
- Published
- 2015
8. The potential implications of reclaimed wastewater reuse for irrigation on the agricultural environment: The knowns and unknowns of the fate of antibiotics and antibiotic resistant bacteria and resistance genes - A review
- Author
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Christou, A., Agüera, A., Bayona, J. M., Cytryn, E., Fotopoulos, V., Lambropoulou, D., Manaia, C. M., Michael, C., Revitt, M., Schröder, P., Fatta-Kassinos, Despo, Fatta-Kassinos, Despo [0000-0003-1173-0941], and Veritati - Repositório Institucional da Universidade Católica Portuguesa
- Subjects
0301 basic medicine ,Engineering ,Irrigation ,Agricultural Irrigation ,Environmental Engineering ,Biosolids ,Agricultural Biotechnology ,Antibiotics ,Accumulation ,Human health risks ,Antibiotic-resistance genes ,Uptake ,Reclaimed wastewater irrigation ,Wastewater ,010501 environmental sciences ,Waste Disposal, Fluid ,01 natural sciences ,Water scarcity ,03 medical and health sciences ,Antibiotic resistance ,Humans ,Recycling ,Antibiotic-resistance Genes ,Human Health Risks ,Reclaimed Wastewater Irrigation ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,Bacteria ,Resistance (ecology) ,Agricultural Sciences ,business.industry ,Ecological Modeling ,fungi ,food and beverages ,Pollution ,Manure ,Anti-Bacterial Agents ,Biotechnology ,030104 developmental biology ,Agriculture ,business - Abstract
The use of reclaimed wastewater (RWW) for the irrigation of crops may result in the continuous exposure of the agricultural environment to antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). In recent years, certain evidence indicate that antibiotics and resistance genes may become disseminated in agricultural soils as a result of the amendment with manure and biosolids and irrigation with RWW. Antibiotic residues and other contaminants may undergo sorption/desorption and transformation processes (both biotic and abiotic), and have the potential to affect the soil micro- biota. Antibiotics found in the soil pore water (bioavailable fraction) as a result of RWW irrigation may be taken up by crop plants, bioaccumulate within plant tissues and subsequently enter the food webs; potentially resulting in detrimental public health implications. It can be also hypothesized that ARGs can spread among soil and plant-associated bacteria, a fact that may have serious human health implications. The majority of studies dealing with these environmental and social challenges related with the use of RWW for irrigation were conducted under laboratory or using, somehow, controlled conditions. This critical review discusses the state of the art on the fate of antibiotics, ARB and ARGs in agricultural environment where RWW is applied for irrigation. The implications associated with the uptake of antibiotics by plants (uptake mechanisms) and the potential risks to public health are highlighted. Additionally, knowledge gaps as well as challenges and opportunities are addressed, with the aim of boostingfuture research towards an enhanced understanding of the fate and implications of these contaminants of emerging concern in the agricultural environment. These are key issues in a world where the increasing water scarcity and the continuous appeal of circular economy demand answers for a long- term safe use of RWW for irrigation.
- Published
- 2017
9. Soil-borne disease suppression and plant growth promotion by biochar soil amendments and possible mode of action
- Author
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Jaiswal, A.K., primary, Elad, Y., additional, Graber, E.R., additional, Cytryn, E., additional, and Frenkel, O., additional
- Published
- 2018
- Full Text
- View/download PDF
10. Viral and Microbial Pathogens, Indicator Microorganisms, Microbial Source Tracking Indicators, and Antibiotic Resistance Genes in a Confined Managed Effluent Recharge System
- Author
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Elkayam, R., primary, Aharoni, A., additional, Vaizel-Ohayon, D., additional, Sued, O., additional, Katz, Y., additional, Negev, I., additional, Marano, R. B. M., additional, Cytryn, E., additional, Shtrasler, L., additional, and Lev, O., additional
- Published
- 2018
- Full Text
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11. COST Action ES1403: New and Emerging challenges and opportunities in wastewater REUSe (NEREUS)
- Author
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Fatta-Kassinos, Despo, primary, Manaia, C., additional, Berendonk, T. U., additional, Cytryn, E., additional, Bayona, J., additional, Chefetz, B., additional, Slobodnik, J., additional, Kreuzinger, N., additional, Rizzo, L., additional, Malato, S., additional, Lundy, L., additional, and Ledin, A., additional
- Published
- 2015
- Full Text
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12. Prospective comparison of START-STOPP and MAI for the detection of inappropriate prescriptions in an acute geriatric ward
- Author
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Lanoy, C, Karmali, R, Cytryn, E, Cappelle, S, Van Puyvelde, Katrien, Beyer, Ingo, and Frailty in Ageing
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screening tool ,adverse drug events ,inappropriate prescribing - Abstract
Introduction.- Inappropriate prescription (IP) and adverse drug events (ADEs) are crucial in older persons that account for 40% of all medication use. About 40% of geriatric patients suffer from ADEs, responsible for 10 to 30% of admissions in geriatric wards. Thirty to 60% of ADEs are preventable. To prevent ADEs inappropriate prescription must be detected: either by implicit evaluation based on physicians' knowledge as in the Medication Appropriateness Index (MAI), or by explicit lists of IP as the ''Screening Tool of older Persons' Prescriptions''-''Screening Tool to Alert doctors to the Right Treatment'' (STOPP-START). Our study aimed to compare STOPP-START to MAI for detection of IP and of drugs related to ADEs. Method.- Prospective evaluation of consecutive admissions to a 24-bed acute geriatric ward in a general teaching hospital during 3 months. Blinded evaluation of admission and discharge treatments with STOPP-START versus 2 senior geriatricians based on MAI. Results.- Eighty-seven patients were included. Mean age was 82.8 years and 63% were female. MAI and STOPP detected overpre- scription in 68 and 74% (n.s.) of patients at admission and in 47 and 76% (P
- Published
- 2010
13. Prescription inappropriée dans un service de gériatrie aiguë
- Author
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Cappelle, S, Lanoy, C, Decorte, Laurence, Cytryn, E, Beyer, Ingo, and Fragiliteit binnen Gerontologie en Geriatrie
- Subjects
Medication Appropriateness Index (MAI) ,screening tool ,inappropriate prescribing ,START STOPP criteria - Abstract
Introduction : Les affections iatrogènes sont estimées à l'origine de près de 30% des hospitalisations chez la personne âgée et une évaluation systématique des prescriptions est requise. Une évaluation dite implicite et basée sur le jugement du médecin pourrait toutefois être insuffisante. Afin de rendre l'évaluation implicite plus pertinente elle a été structurée dans le « Medication Appropriateness Index » (MAI). Par ailleurs, la collaboration avec un pharmacien clinicien constitue une approche très prometteuse, mais actuellement trop peu accessible. L'échelle de Beers constitue une démarche dite explicite et basée sur des critères pré-définis. Près de 60% des personnes âgées recevraient un médicament inapproprié selon les études faites avec cette échelle. L'échelle de Beers ne tient toutefois pas compte de certains médicaments prescrits fréquemment aux personnes âgées, ni des interactions médicamenteuses ou de la possibilité d'une sous-prescription. Dans ce contexte le « Screening Tool of Older Persons' Prescriptions » (STOPP) et le « Screening Tool to Action the Right indicated Treatments » (START) ont été élaborées et publiées en 2008 comme alternative. Objectif : Evaluation rétrospective de la prévalence de la prescription inappropriée (PI) dans un service de gériatrie aiguë. Comparaison d'une démarche implicite basée sur le MAI (plus recherche implicite de sous-prescription) à une démarche explicite utilisant les échelles START et STOPP. Recherche des facteurs associés à la PI. Evaluation de la faisabilité d'une étude prospective d'utilisation des échelles START et STOPP. Méthodologie : Analyse rétrospective des rapports d'hospitalisation de patients admis dans une unité gériatrique aiguë de 24 lits de juillet à septembre 2008. Exclusion des patients décédés en raison de leurs rapports d'hospitalisation incomplets. Evaluation implicite des traitements de façon indépendante par 3 gériatres basée sur le MAI et application des échelles START et STOPP par une étudiante en médecine. Chaque intervenant étant« aveugle » par rapport à la démarche de l'autre. Regroupement ultérieur des résultats de l'évaluation implicite après consensus entre les 3 médecins. Résultats : 114 patients ont été hospitalisés, dont 16 décès. 6 dossiers incomplets ont du être exclus de l'analyse. 92 dossiers ont été analysés. Une corrélation positive (p
- Published
- 2009
14. Transient development of filamentous Thiothrix species in a marine sulfide oxidizing, denitrifying fluidized bed reactor
- Author
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Cytryn, E., Minz, D., Gieseke, A., and van Rijn, J.
- Abstract
In this study, microscopic and molecular microbial analyses were integrated to characterize rapidly developing white filamentous tufts in a fluidized bed reactor used for nitrate removal from a marine recirculating fish culture system. Formation and rapid elongation of the tufts (often exceeding 50 mm day −1) was strongly correlated to transient elevated sulfide concentrations (>50 μM) in the reactor. The dominant bacterial constituents of these tufts were filamentous gram-negative bacteria with densely packed intracellular sulfur granules. Using 16S rRNA gene analysis and fluorescence in situ hybridization it was found that these filamentous bacteria represented a novel Thiothrix phylotype closely related (97% sequence identity) to a previously identified Thiothrix strain endogenous to the marine crustacean Urothoe poseidonis. In addition to filamentous morphotypes, rosette-shaped morphotypes of Thiothrix were also detectable within the tufts.
- Published
- 2006
15. Group B streptococcus arthritis
- Author
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Colebunders, R., Cytryn, E., and Thys, J. -P.
- Published
- 1983
- Full Text
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16. Anemia and transfusions in geriatric patients: a time for evaluation
- Author
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Beyer, I., primary, Compté, N., additional, Busuioc, A., additional, Cappelle, S., additional, Lanoy, C., additional, and Cytryn, E., additional
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- 2010
- Full Text
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17. ANAEMIA IN THE ELDERLY
- Author
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Van Puyvelde, K., primary, Cytryn, E., additional, Mets, T., additional, and Beyer, I., additional
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- 2009
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18. Double-Blind Crossover Study of Nabumetone versus Naproxen in the Treatment of Osteoarthritis
- Author
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Verbruggen, L A, Cytryn, E, and Pintens, H
- Abstract
Twenty-one patients entered a double-blind crossover study to compare nabumetone with naproxen. After a I-week run-in period using a coated acetylsalicylic acid preparation, ten patients received nabumetone (1 g at night) over a period of 2 weeks, followed by 2 weeks on naproxen (250 mg b.i.d), while eleven patients received the same treatments in the reverse order.Morning stiffness, overall pain and night pain showed no significant difference after either treatment. A wide range of objective measurements were made relating to the hips, knees, and cervical and lumbar spine. No statistically significant differences were observed in the relatively small number of patients involved. Both treatments, however, appeared to produce a similar improvement in the patients. The physician's assessment showed that improvement occurred in a majority of the patients over the total trial period.Both drugs were considered to be equally effective and were both well tolerated. There was no special patient preference for either the first or second treatment. A total of eight patients reported side-effects, three during naproxen alone, three during both treatments, and two during the run-in period. In terms of tolerance, fifteen patients had no drug preference, six preferred nabumetone, none preferred naproxen. No evidence was found of changes in renal, hepatic or haematopoietic function with the two drugs tested.
- Published
- 1982
- Full Text
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19. Oesophageal stenosis caused by benign mucous membrane pemphigoid in a patient with an inactive rheumatoid arthritis
- Author
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Cytryn, E., primary, Laduron, J., additional, Colebunders, R., additional, and Dony, A., additional
- Published
- 1985
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20. LACTATE ACCUMULATION IN METHANOL POISONING
- Author
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Cytryn, E., primary and Futeral, B., additional
- Published
- 1983
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21. In Flight Checkout of the LEM Environmental Control System
- Author
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Cytryn, E. P., primary
- Published
- 1964
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22. A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants
- Author
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Yunho Lee, Manika Choudhury, Om Prakash, Donald Morrison, Hélène Guilloteau, Heidrun Mayrhofer, María Inmaculada Polo-López, Belen Esteban, Katarzyna Slipko, Leonardo Pantoja Munoz, Samira Nahim–Granados, José Manuel Guillén-Navarro, Marco Guida, Stela Krizanovic, Hemda Garelick, Pilar Caballero, Traore Ousmane, Marcos Quintela-Baluja, Sara Rodríguez-Mozaz, Helmut Bürgmann, Nikolina Udiković-Kolić, Carsten Ulrich Schwermer, Agnieszka Kalinowska, Milena Milaković, Ester Heath, Marta Piotrowska, Andrea Di Cesare, Célia M. Manaia, Ying Yang, Amy Pruden, Anne F.C. Leonard, Erica Donner, Tanel Telson, Christophe Merlin, Karin Beck, Ana Agüera, Anhony A Adegoke, Marie-Noëlle Pons, Bastian Herzog, Joana Abreu-Silva, Leonie Henn, Norbert Kreuzinger, Younggun Yoon, Stefanie Heß, Olga C. Nunes, Alice L. Petre, Despo Fatta-Kassinos, Gianluca Brunetti, Roberto B. M. Marano, Stella Michael, Thor A. Stenström, Ayella Maile-Moskowitz, Popi Karaolia, Joshua T. Bunce, Giovanni Libralato, Jérôme Ory, Yogesh Nimonkar, Alfieri Pollice, Aneta Luczkiewicz, Carlo Salerno, Andrew Scott, Shichun Zou, Antoni Oliver, Barbara Drigo, Isabel Martínez-Alcalá, Virginia Riquelme, Veljo Kisand, Anna Baraniak, William H. Gaze, Edward Topp, Edouard Jurkevitch, Isabel Henriques, Telma Fernandes, Eddie Cytryn, José Luis Balcázar, Marta Tacão, Thomas Schwartz, Thomas Jäger, Gianluca Corno, Mailis Laht, Thomas U. Berendonk, Roberto Rosal, Magdalena Popowska, Pawel Krzeminski, Connor L. Brown, Veritati - Repositório Institucional da Universidade Católica Portuguesa, Marano, R. B. M., Fernandes, T., Manaia, C. M., Nunes, O., Morrison, D., Berendonk, T. U., Kreuzinger, N., Telson, T., Corno, G., Fatta-Kassinos, D., Merlin, C., Topp, E., Jurkevitch, E., Henn, L., Scott, A., Hess, S., Slipko, K., Laht, M., Kisand, V., Di Cesare, A., Karaolia, P., Michael, S. G., Petre, A. L., Rosal, R., Pruden, A., Riquelme, V., Aguera, A., Esteban, B., Luczkiewicz, A., Kalinowska, A., Leonard, A., Gaze, W. H., Adegoke, A. A., Stenstrom, T. A., Pollice, A., Salerno, C., Schwermer, C. U., Krzeminski, P., Guilloteau, H., Donner, E., Drigo, B., Libralato, G., Guida, M., Burgmann, H., Beck, K., Garelick, H., Tacao, M., Henriques, I., Martinez-Alcala, I., Guillen-Navarro, J. M., Popowska, M., Piotrowska, M., Quintela-Baluja, M., Bunce, J. T., Polo-Lopez, M. I., Nahim-Granados, S., Pons, M. -N., Milakovic, M., Udikovic-Kolic, N., Ory, J., Ousmane, T., Caballero, P., Oliver, A., Rodriguez-Mozaz, S., Balcazar, J. L., Jager, T., Schwartz, T., Yang, Y., Zou, S., Lee, Y., Yoon, Y., Herzog, B., Mayrhofer, H., Prakash, O., Nimonkar, Y., Heath, E., Baraniak, A., Abreu-Silva, J., Choudhury, M., Munoz, L. P., Krizanovic, S., Brunetti, G., Maile-Moskowitz, A., Brown, C., Cytryn, E., The Robert H. Smith Faculty of Agriculture, Food and Environment, Department of Animal Sciences, The Hebrew University of Jerusalem (HUJ), Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - the Volcani Center, Centro de Química Fina e Biotecnologia (CQFB), Requimte, Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Universidade do Porto, Edinburgh Napier University, Institute for Hydrobiology, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Vienna University of Technology, Institute of Technology [Tartu, Estonia], University of Tartu, CNR Water Research Institute (IRSA), Consiglio Nazionale delle Ricerche (CNR), University of Cyprus (UCY), Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Agriculture and Agri-Food [Ottawa] (AAFC), Department of Biology, University of Western Ontario, University of Western Ontario (UWO), Estonian Environmental Research Centre (EKUK), Universidad de Alcalá - University of Alcalá (UAH), Virginia Tech [Blacksburg], Area de Quimica Inorganica - Centro de Investigacion en Energia Solar (CIESOL) (CIESOL), Universidad de Almería (UAL), Gdańsk University of Technology (GUT), University of Exeter Medical School, University of Exeter, Durban University of Technology, Universidad Nacional de Cuyo [Mendoza] (UNCUYO), Norwegian Institute for Water Research (NIVA), University of South Australia [Adelaide], Università degli studi di Napoli Federico II, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Middlesex University [London], Universidade de Aveiro, Universidade de Coimbra [Coimbra], Universidad Católica San Antonio de Murcia (UCAM), Department of Applied Microbiology [Warsaw], Institute of Microbiology [Warsaw], Faculty of Biology [Warsaw], University of Warsaw (UW)-University of Warsaw (UW)-Faculty of Biology [Warsaw], University of Warsaw (UW)-University of Warsaw (UW), School of Engineering [Newcastle], Newcastle University [Newcastle], Plataforma Solar de Almeria – CIEMAT, Tabernas, Almeria, Laboratoire Réactions et Génie des Procédés (LRGP), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Rudjer Boskovic Institute [Zagreb], Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), CHU Clermont-Ferrand, Laboratorio EMATSA, Instituto Catalán de Investigación del Agua - ICRA (SPAIN) (ICRA), Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Sun Yat-Sen University [Guangzhou] (SYSU), Gwangju Institute of Science and Technology (GIST), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), NCMR, Jozef Stefan Institute [Ljubljana] (IJS), National Medicines Institute - Narodowy Instytut Leków [Warsaw] (NIL), Agricultural Research Organisation (ARO), Volcani Center, Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade do Porto = University of Porto, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Cyprus [Nicosia] (UCY), Agriculture and Agri-Food (AAFC), University of Naples Federico II = Università degli studi di Napoli Federico II, Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Marano, Robert BM, Fernandes, Telma, Manaia, Celia M, Nunes, Olga, Donner, Erica, Drigo, Barbara, Brunetti, Gianluca, and Cytryn, Eddie
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Cefotaxime ,010504 meteorology & atmospheric sciences ,Coliforms ,Antibiotic resistance ,Sewage ,Microorganismes -- Resistència als medicaments ,Wastewater treatment ,Wastewater ,010501 environmental sciences ,01 natural sciences ,Surveys and Questionnaires ,Microorganisms -- Drug resistance ,ComputingMilieux_MISCELLANEOUS ,lcsh:Environmental sciences ,General Environmental Science ,lcsh:GE1-350 ,6. Clean water ,Anti-Bacterial Agents ,3. Good health ,Europe ,Interdisciplinary Natural Sciences ,Health ,Sewage treatment ,Biotechnology ,medicine.drug ,Life sciences ,biology ,Aigua -- Reutilització ,Asia ,Quantification methods ,Aigües residuals -- Plantes de tractament ,Culture and Communities ,Water Purification ,Applied microbiology ,Water reuse ,Environmental health ,ddc:570 ,medicine ,Microbiology Research Group ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,antibiotic resistance ,coliforms ,ESBLs ,wastewater treatment ,wastewater reuse ,Sewage disposal plants ,Effluent ,0105 earth and related environmental sciences ,[SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health ,Coliform ,business.industry ,Australia ,Fecal coliform ,Antibiotic resistance, Coliforms, ESBLs, Wastewater treatment, Water reuse ,ESBL ,North America ,Environmental science ,business - Abstract
The 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 (
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- 2020
23. Every fifth published metagenome is not available to science
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Nikolina Udiković-Kolić, Célia M. Manaia, Despo Fatta-Kassinos, Andrew C. Singer, Diego Fontaneto, D. G. Joakim Larsson, Ester M. Eckert, Helmut Bürgmann, Andrea Di Cesare, Amy Pruden, Thomas U. Berendonk, Andrea Franzetti, Gianluca Corno, Eddie Cytryn, Veritati - Repositório Institucional da Universidade Católica Portuguesa, Eckert, E, Di Cesare, A, Fontaneto, D, Berendonk, T, Burgmann, H, Cytryn, E, Fatta-Kassinos, D, Franzetti, A, Joakim Larsson, D, Manaia, C, Pruden, A, Singer, A, Udikovic-Kolic, N, and Corno, G
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0301 basic medicine ,Metagenomic dna ,Binomials ,Polynomials ,Open Science ,0302 clinical medicine ,Open Data ,Biology (General) ,Data Management ,General Neuroscience ,Publications ,Genomics ,Research Assessment ,Open data ,Interdisciplinary Natural Sciences ,Open Access Publishing ,Physical Sciences ,Journal Impact Factor ,General Agricultural and Biological Sciences ,Computer and Information Sciences ,Essay ,Science Policy ,QH301-705.5 ,MEDLINE ,Biology ,Bibliometrics ,Research and Analysis Methods ,scientometrics ,General Biochemistry, Genetics and Molecular Biology ,Access to Information ,03 medical and health sciences ,metagenomics ,scientific publishing ,open data ,data management ,metadata ,Genetics ,Scientific Publishing ,Metadata ,General Immunology and Microbiology ,Biology and Life Sciences ,Scientific publishing ,Metagenomics ,Virus testing ,Open access publishing ,Data science ,Data sharing ,Algebra ,030104 developmental biology ,Biology and Microbiology ,Metagenome ,Publication Practices ,Mathematics ,030217 neurology & neurosurgery - Abstract
Have 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., Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? This Essay reveals that every fifth published metagenome is not available to science, and asks whether data accessibility should be considered a mandatory component of manuscript submission.
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- 2020
24. Regulation of Antibiotic Resistance Genes on Agricultural Land Is Dependent on Both Choice of Organic Amendment and Prevalence of Predatory Bacteria.
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Rosberg AK, Silva MJ, Skøtt Feidenhans'l C, Cytryn E, Jurkevitch E, and Lood R
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Antibiotic resistance genes (ARGs) are widespread in the environment, and soils, specifically, are hotspots for microorganisms with inherent antibiotic resistance. Manure and sludge used as fertilizers in agricultural production have been shown to contain vast amounts of ARGs, and due to continued applications, ARGs accumulate in agricultural soils. Some soils, however, harbor a resilience capacity that could depend on specific soil properties, as well as the presence of predatory bacteria that are able to hydrolyse living bacteria, including bacteria of clinical importance. The objectives of this study were to (i) investigate if the antibiotic resistance profile of the soil microbiota could be differently affected by the addition of cow manure, chicken manure, and sludge, and (ii) investigate if the amendments had an effect on the presence of predatory bacteria. The three organic amendments were mixed separately with a field soil, divided into pots, and incubated in a greenhouse for 28 days. Droplet digital PCR (ddPCR) was used to quantify three ARGs, two predatory bacteria, and total number of bacteria. In this study, we demonstrated that the choice of organic amendment significantly affected the antibiotic resistance profile of soil, and promoted the growth of predatory bacteria, while the total number of bacteria was unaffected.
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- 2024
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25. Making waves: The NORMAN antibiotic resistant bacteria and resistance genes database (NORMAN ARB&ARG)-An invitation for collaboration to tackle antibiotic resistance.
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Alygizakis N, Ng K, Čirka Ľ, Berendonk T, Cerqueira F, Cytryn E, Deviller G, Fortunato G, Iakovides IC, Kampouris I, Michael-Kordatou I, Lai FY, Lundy L, Manaia CM, Marano RBM, Paulus GK, Piña B, Radu E, Rizzo L, Ślipko K, Kreuzinger N, Thomaidis NS, Ugolini V, Vaz-Moreira I, Slobodnik J, and Fatta-Kassinos D
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- Drug Resistance, Bacterial genetics, Anti-Bacterial Agents pharmacology, Bacteria genetics, Bacteria drug effects, China, Genes, Bacterial, Drug Resistance, Microbial genetics
- Abstract
With the global concerns on antibiotic resistance (AR) as a public health issue, it is pivotal to have data exchange platforms for studies on antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. For this purpose, the NORMAN Association is hosting the NORMAN ARB&ARG database, which was developed within the European project ANSWER. The present article provides an overview on the database functionalities, the extraction and the contribution of data to the database. In this study, AR data from three studies from China and Nepal were extracted and imported into the NORMAN ARB&ARG in addition to the existing AR data from 11 studies (mainly European studies) on the database. This feasibility study demonstrates how the scientific community can share their data on AR to generate an international evidence base to inform AR mitigation strategies. The open and FAIR data are of high potential relevance for regulatory applications, including the development of emission limit values / environmental quality standards in relation to AR. The growth in sharing of data and analytical methods will foster collaboration on risk management of AR worldwide, and facilitate the harmonization in the effort for identification and surveillance of critical hotspots of AR. The NORMAN ARB&ARG database is publicly available at: https://www.norman-network.com/nds/bacteria/., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
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- 2024
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26. A pipeline for rapidly evaluating activity and inferring mechanisms of action of prospective antifungal compounds.
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Kraut-Cohen J, Frenkel O, Covo S, Marcos-Hadad E, Carmeli S, Belausov E, Minz D, and Cytryn E
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- Fungicides, Industrial pharmacology, Fusarium drug effects
- Abstract
Background: Fungal phytopathogens are a significant threat to crops and food security, and there is a constant need to develop safe and effective compounds that antagonize them. In-planta assays are complex and tedious and are thus not suitable for initial high-throughput screening of new candidate antifungal compounds. We propose an in vitro screening pipeline that integrates five rapid quantitative and qualitative methods to estimate the efficacy and mode of action of prospective antifungal compounds., Results: The pipeline was evaluated using five documented antifungal compounds (benomyl, catechol, cycloheximide, 2,4-diacetylphloroglucinol, and phenylacetic acid) that have different modes of action and efficacy, against the model soilborne fungal pathogen Fusarium oxysporum f. sp. radicis cucumerinum. We initially evaluated the five compounds' ability to inhibit fungal growth and metabolic activity using green fluorescent protein (GFP)-labeled F. oxysporum and PrestoBlue staining, respectively, in multiwell plate assays. We tested the compounds' inhibition of both conidial germination and hyphal elongation. We then employed FUN-1 and SYTO9/propidium iodide staining, coupled to confocal microscopy, to differentiate between fungal growth inhibition and death at the cellular level. Finally, using a reactive oxygen species (ROS)-detection assay, we were able to quantify ROS production in response to compound application., Conclusions: Collectively, the proposed pipeline provides a wide array of quantitative and qualitative data on the tested compounds that can help pinpoint promising novel compounds; these can then be evaluated more vigorously using in planta screening assays. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry., (© 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.)
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- 2024
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27. A Burkholderia cenocepacia -like environmental isolate strongly inhibits the plant fungal pathogen Zymoseptoria tritici .
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Song T, Gupta S, Sorokin Y, Frenkel O, Cytryn E, and Friedman J
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- Triticum microbiology, Antibiosis, Multigene Family, Ascomycota genetics, Burkholderia cenocepacia genetics, Burkholderia cenocepacia drug effects, Plant Diseases microbiology
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Fungal phytopathogens cause significant reductions in agricultural yields annually, and overusing chemical fungicides for their control leads to environmental pollution and the emergence of resistant pathogens. Exploring natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We isolated and characterized a novel bacterial strain associated with the species Burkholderia cenocepacia , termed APO9, which strongly inhibits Zymoseptoria tritici , a commercially important pathogenic fungus causing Septoria tritici blotch in wheat. Additionally, this strain exhibits inhibitory activity against four other phytopathogens. We found that physical contact plays a crucial role for APO9's antagonistic capacity. Genome sequencing of APO9 and biosynthetic gene cluster (BGC) analysis identified nine classes of BGCs and three types of secretion systems (types II, III, and IV), which may be involved in the inhibition of Z. tritic i and other pathogens. To identify genes driving APO9's inhibitory activity, we screened a library containing 1,602 transposon mutants and identified five genes whose inactivation reduced inhibition efficiency. One such gene encodes for a diaminopimelate decarboxylase located in a terpenoid biosynthesis gene cluster. Phylogenetic analysis revealed that while some of these genes are also found across the Burkholderia genus, as well as in other Betaproteobacteria , the combination of these genes is unique to the Burkholderia cepacia complex. These findings suggest that the inhibitory capacity of APO9 is complex and not limited to a single mechanism, and may play a role in the interaction between various Burkholderia species and various phytopathogens within diverse plant ecosystems., Importance: The detrimental effects of fungal pathogens on crop yields are substantial. The overuse of chemical fungicides contributes not only to environmental pollution but also to the emergence of resistant pathogens. Investigating natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We discovered and examined a unique bacterial strain that demonstrates significant inhibitory activity against several phytopathogens. Our research demonstrates that this strain has a wide spectrum of inhibitory actions against plant pathogens, functioning through a complex mechanism. This plays a vital role in the interactions between plant microbiota and phytopathogens., Competing Interests: The authors declare no conflict of interest.
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- 2024
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28. The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.
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Manaia CM, Aga DS, Cytryn E, Gaze WH, Graham DW, Guo J, Leonard AFC, Li L, Murray AK, Nunes OC, Rodriguez-Mozaz S, Topp E, and Zhang T
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- Humans, Bacteria, Angiotensin Receptor Antagonists pharmacology, Angiotensin-Converting Enzyme Inhibitors pharmacology, Drug Resistance, Microbial genetics, Pharmaceutical Preparations, Anti-Bacterial Agents pharmacology, Genes, Bacterial, Cosmetics
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Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2024;43:637-652. © 2022 SETAC., (© 2022 SETAC.)
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- 2024
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29. Candidate biomarkers of antibiotic resistance for the monitoring of wastewater and the downstream environment.
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Teixeira AM, Vaz-Moreira I, Calderón-Franco D, Weissbrodt D, Purkrtova S, Gajdos S, Dottorini G, Nielsen PH, Khalifa L, Cytryn E, Bartacek J, and Manaia CM
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- Humans, RNA, Ribosomal, 16S genetics, Angiotensin Receptor Antagonists analysis, Angiotensin-Converting Enzyme Inhibitors analysis, Drug Resistance, Microbial genetics, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents analysis, Water analysis, Wastewater, Genes, Bacterial
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Urban wastewater treatment plants (UWTPs) are essential for reducing the pollutants load and protecting water bodies. However, wastewater catchment areas and UWTPs emit continuously antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with recognized impacts on the downstream environments. Recently, the European Commission recommended to monitor antibiotic resistance in UWTPs serving more than 100 000 population equivalents. Antibiotic resistance monitoring in environmental samples can be challenging. The expected complexity of these systems can jeopardize the interpretation capacity regarding, for instance, wastewater treatment efficiency, impacts of environmental contamination, or risks due to human exposure. Simplified monitoring frameworks will be essential for the successful implementation of analytical procedures, data analysis, and data sharing. This study aimed to test a set of biomarkers representative of ARG contamination, selected based on their frequent human association and, simultaneously, rare presence in pristine environments. In addition to the 16S rRNA gene, ten potential biomarkers (intI1, sul1, ermB, ermF, aph(3'')-Ib, qacEΔ1, uidA, mefC, tetX, and crAssphage) were monitored in DNA extracts (n = 116) from raw wastewater, activated sludge, treated wastewater, and surface water (upstream and downstream of UWTPs) samples collected in the Czech Republic, Denmark, Israel, the Netherlands, and Portugal. Each biomarker was sensitive enough to measure decreases (on average by up to 2.5 log-units gene copy/mL) from raw wastewater to surface water, with variations in the same order of magnitude as for the 16S rRNA gene. The use of the 10 biomarkers allowed the typing of water samples whose origin or quality could be predicted in a blind test. The results show that, based on appropriate biomarkers, qPCR can be used for a cost-effective and technically accessible approach to monitoring wastewater and the downstream environment., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)
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- 2023
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30. Corrigendum: Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity.
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Moshe M, Gupta CL, Jain RM, Sela N, Minz D, Banin E, Frenkel O, and Cytryn E
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[This corrects the article DOI: 10.3389/fmicb.2023.996287.]., (Copyright © 2023 Moshe, Gupta, Jain, Sela, Minz, Banin, Frenkel and Cytryn.)
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- 2023
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31. Complete genome sequence of multi-drug-resistant Salmonella enterica subsp. enterica serovar Typhimurium strain Bnaya isolated from a dairy calf in Israel.
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Davidovich C, Awwad A, Fleker M, Weisblit L, Cytryn E, and Blum SE
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This manuscript reports the complete genome sequence of a Salmonella enterica subsp. enterica serovar Typhimurium strain (designated "Bnaya"), isolated from a dead dairy calf with severe diarrhea in Israel. The isolate exhibited multi-drug resistance, which is highly unusual in bovine Salmonella spp. in Israel, prompting further investigation., Competing Interests: The authors declare no conflict of interest.
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- 2023
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32. Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation.
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Yalin D, Craddock HA, Assouline S, Ben Mordechay E, Ben-Gal A, Bernstein N, Chaudhry RM, Chefetz B, Fatta-Kassinos D, Gawlik BM, Hamilton KA, Khalifa L, Kisekka I, Klapp I, Korach-Rechtman H, Kurtzman D, Levy GJ, Maffettone R, Malato S, Manaia CM, Manoli K, Moshe OF, Rimelman A, Rizzo L, Sedlak DL, Shnit-Orland M, Shtull-Trauring E, Tarchitzky J, Welch-White V, Williams C, McLain J, and Cytryn E
- Abstract
Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Hila Korach-Rechtman reports a relationship with Kando Environmental Services LTD that includes: employment., (© 2023 The Author(s).)
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- 2023
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33. Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere.
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Lin C, Li LJ, Ren K, Zhou SY, Isabwe A, Yang LY, Neilson R, Yang XR, Cytryn E, and Zhu YG
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Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health., (© 2023. ISME Publications B.V.)
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- 2023
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34. Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.
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Yin X, Chen X, Jiang XT, Yang Y, Li B, Shum MH, Lam TTY, Leung GM, Rose J, Sanchez-Cid C, Vogel TM, Walsh F, Berendonk TU, Midega J, Uchea C, Frigon D, Wright GD, Bezuidenhout C, Picão RC, Ahammad SZ, Nielsen PH, Hugenholtz P, Ashbolt NJ, Corno G, Fatta-Kassinos D, Bürgmann H, Schmitt H, Cha CJ, Pruden A, Smalla K, Cytryn E, Zhang Y, Yang M, Zhu YG, Dechesne A, Smets BF, Graham DW, Gillings MR, Gaze WH, Manaia CM, van Loosdrecht MCM, Alvarez PJJ, Blaser MJ, Tiedje JM, Topp E, and Zhang T
- Subjects
- Animals, Humans, RNA, Ribosomal, 16S genetics, Drug Resistance, Microbial genetics, Metagenomics methods, Anti-Bacterial Agents pharmacology, Genes, Bacterial
- Abstract
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.
- Published
- 2023
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35. Microbiome and Resistome Profiles along a Sewage-Effluent-Reservoir Trajectory Underline the Role of Natural Attenuation in Wastewater Stabilization Reservoirs.
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Leão I, Khalifa L, Gallois N, Vaz-Moreira I, Klümper U, Youdkes D, Palmony S, Dagai L, Berendonk TU, Merlin C, Manaia CM, and Cytryn E
- Subjects
- Sewage microbiology, Angiotensin Receptor Antagonists, Genes, Bacterial, RNA, Ribosomal, 16S genetics, Escherichia coli genetics, Polypropylenes, Anti-Bacterial Agents pharmacology, Angiotensin-Converting Enzyme Inhibitors, Bacteria genetics, Wastewater, Microbiota
- Abstract
Antibiotic-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., Competing Interests: The authors declare no conflict of interest.- Published
- 2023
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36. Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity.
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Moshe M, Gupta CL, Sela N, Minz D, Banin E, Frenkel O, and Cytryn E
- Abstract
Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S-10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Moshe, Gupta, Sela, Minz, Banin, Frenkel and Cytryn.)
- Published
- 2023
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37. Freshwater microbial metagenomes sampled across different water body characteristics, space and time in Israel.
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Al-Ashhab A, Marmen S, Schweitzer-Natan O, Bolotin E, Patil H, Viner-Mozzini D, Aharonovich D, Hershberg R, Minz D, Carmeli S, Cytryn E, Sukenik A, and Sher D
- Subjects
- Ecosystem, Israel, Lakes, Cyanobacteria, Metagenome
- Abstract
Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages - a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013-2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches., (© 2022. The Author(s).)
- Published
- 2022
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38. Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles.
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Gupta CL, Avidov R, Kattusamy K, Saadi I, Varma VS, Blum SE, Zhu YG, Zhou XY, Su JQ, Laor Y, and Cytryn E
- Abstract
Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae , Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside ( aac (6')-Ib(aka aac A4), aad A5), tetracycline ( tet G), vancomycin ( van C), phenicol ( flo R) and MLSB ( mph B) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus , which was linked to vancomycin ( vanSA , vanC1 ), MLSB ( vatE, ermB ) and tetracycline ( tetK ) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)
- Published
- 2021
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39. Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes.
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Gupta CL, Blum SE, Kattusamy K, Daniel T, Druyan S, Shapira R, Krifucks O, Zhu YG, Zhou XY, Su JQ, and Cytryn E
- Subjects
- Animals, Cloaca microbiology, Escherichia coli, Longitudinal Studies, Staphylococcus aureus, Anti-Bacterial Agents therapeutic use, Chickens, Drug Resistance, Bacterial genetics, Microbiota
- Abstract
Background: Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae)., Results: Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified., Conclusions: Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract., (© 2021. The Author(s).)
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- 2021
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40. Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture.
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Marmen S, Fadeev E, Al Ashhab A, Benet-Perelberg A, Naor A, Patil HJ, Cytryn E, Viner-Mozzini Y, Sukenik A, Lalzar M, and Sher D
- Abstract
Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Marmen, Fadeev, Al Ashhab, Benet-Perelberg, Naor, Patil, Cytryn, Viner-Mozzini, Sukenik, Lalzar and Sher.)
- Published
- 2021
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41. Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils.
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Marano RBM, Gupta CL, Cozer T, Jurkevitch E, and Cytryn E
- Subjects
- Agricultural Irrigation, Angiotensin Receptor Antagonists, Angiotensin-Converting Enzyme Inhibitors, Anti-Bacterial Agents pharmacology, Drug Resistance, Microbial genetics, Genes, Bacterial, Humans, Soil Microbiology, Soil, Wastewater analysis
- Abstract
Treated-wastewater (TW) irrigation transfers antibiotic-resistant bacteria (ARB) to soil, but persistence of these bacteria is generally low due to resilience of the soil microbiome. Nonetheless, wastewater-derived bacteria and associated antibiotic resistance genes (ARGs) may persist below detection levels and potentially proliferate under copiotrophic conditions. To test this hypothesis, we exposed soils from microcosm, lysimeter, and field experiments to short-term enrichment in copiotroph-stimulating media. In microcosms, enrichment stimulated growth of multidrug-resistant Escherichia coli up to 2 weeks after falling below detection limits. Lysimeter and orchard soils irrigated in-tandem with either freshwater or TW were subjected to culture-based, qPCR and shotgun metagenomic analyses prior, and subsequent, to enrichment. Although native TW- and freshwater-irrigated soil microbiomes and resistomes were similar to each other, enrichment resulted in higher abundances of cephalosporin- and carbapenem-resistant Enterobacteriaceae and in substantial differences in the composition of microbial communities and ARGs. Enrichment stimulated ARG-harboring Bacillaceae in the freshwater-irrigated soils, whereas in TWW-irrigated soils, ARG-harboring γ-proteobacterial families Enterobacteriaceae and Moraxellaceae were more profuse. We demonstrate that TW-derived ARB and associated ARGs can persist at below detection levels in irrigated soils and believe that similar short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.
- Published
- 2021
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42. Pectin Induced Colony Expansion of Soil-Derived Flavobacterium Strains.
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Kraut-Cohen J, Shapiro OH, Dror B, and Cytryn E
- Abstract
The genus Flavobacterium is characterized by the capacity to metabolize complex organic compounds and a unique gliding motility mechanism. Flavobacteria are often abundant in root microbiomes of various plants, but the factors contributing to this high abundance are currently unknown. In this study, we evaluated the effect of various plant-associated poly- and mono-saccharides on colony expansion of two Flavobacterium strains. Both strains were able to spread on pectin and other polysaccharides such as microcrystalline cellulose. However, only pectin (but not pectin monomers), a component of plant cell walls, enhanced colony expansion on solid surfaces in a dose- and substrate-dependent manner. On pectin, flavobacteria exhibited bi-phasic motility, with an initial phase of rapid expansion, followed by growth within the colonized area. Proteomic and gene expression analyses revealed significant induction of carbohydrate metabolism related proteins when flavobacteria were grown on pectin, including selected SusC/D, TonB-dependent glycan transport operons. Our results show a positive correlation between colony expansion and the upregulation of proteins involved in sugar uptake, suggesting an unknown linkage between specific operons encoding for glycan uptake and metabolism and flavobacterial expansion. Furthermore, within the context of flavobacterial-plant interactions, they suggest that pectin may facilitate flavobacterial expansion on plant surfaces in addition to serving as an essential carbon source., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Kraut-Cohen, Shapiro, Dror and Cytryn.)
- Published
- 2021
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43. Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome.
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Dror B, Wang Z, Brady SF, Jurkevitch E, and Cytryn E
- Abstract
Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores, and others. Despite their involvement in bacterium-bacterium and bacterium-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics, and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low-similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria , while the remaining were not associated with known bacteria. One Streptomyces -derived BGC was predicted to encode a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic data sets revealed higher abundances of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs. IMPORTANCE We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary-metabolite-encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in interbacterial and bacterium-plant interactions., (Copyright © 2020 Dror et al.)
- Published
- 2020
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44. Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment.
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Patil HJ, Gatica J, Zolti A, Benet-Perelberg A, Naor A, Dror B, Al Ashhab A, Marman S, Hasan NA, Colwell RR, Sher D, Minz D, and Cytryn E
- Abstract
Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp ( Hypophthalmichthys molitrix ) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes ( sul1, sul2, dfrA1, tetA and blaTEM ) and class-1 integrons ( int1 ). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.
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- 2020
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45. A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants.
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Marano RBM, Fernandes T, Manaia CM, Nunes O, Morrison D, Berendonk TU, Kreuzinger N, Tenson T, Corno G, Fatta-Kassinos D, Merlin C, Topp E, Jurkevitch E, Henn L, Scott A, Heß S, Slipko K, Laht M, Kisand V, Di Cesare A, Karaolia P, Michael SG, Petre AL, Rosal R, Pruden A, Riquelme V, Agüera A, Esteban B, Luczkiewicz A, Kalinowska A, Leonard A, Gaze WH, Adegoke AA, Stenstrom TA, Pollice A, Salerno C, Schwermer CU, Krzeminski P, Guilloteau H, Donner E, Drigo B, Libralato G, Guida M, Bürgmann H, Beck K, Garelick H, Tacão M, Henriques I, Martínez-Alcalá I, Guillén-Navarro JM, Popowska M, Piotrowska M, Quintela-Baluja M, Bunce JT, Polo-López MI, Nahim-Granados S, Pons MN, Milakovic M, Udikovic-Kolic N, Ory J, Ousmane T, Caballero P, Oliver A, Rodriguez-Mozaz S, Balcazar JL, Jäger T, Schwartz T, Yang Y, Zou S, Lee Y, Yoon Y, Herzog B, Mayrhofer H, Prakash O, Nimonkar Y, Heath E, Baraniak A, Abreu-Silva J, Choudhury M, Munoz LP, Krizanovic S, Brunetti G, Maile-Moskowitz A, Brown C, and Cytryn E
- Subjects
- Anti-Bacterial Agents pharmacology, Asia, Australia, Europe, North America, Surveys and Questionnaires, Wastewater, Cefotaxime pharmacology, Water Purification
- Abstract
The 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 10
3 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., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)- Published
- 2020
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46. Changes in Antibiotic Resistance Gene Levels in Soil after Irrigation with Treated Wastewater: A Comparison between Heterogeneous Photocatalysis and Chlorination.
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Zammit I, Marano RBM, Vaiano V, Cytryn E, and Rizzo L
- Subjects
- Agricultural Irrigation, Drug Resistance, Microbial genetics, Halogenation, RNA, Ribosomal, 16S, Waste Disposal, Fluid, Soil, Wastewater analysis
- Abstract
Wastewater (WW) reuse is expected to be increasingly indispensable in future water management to mitigate water scarcity. However, this increases the risk of antibiotic resistance (AR) dissemination via irrigation. Herein, a conventional (chlorination) and an advanced oxidation process (heterogeneous photocatalysis (HPC)) were used to disinfect urban WW to the same target of Escherichia coli <10 CFU/100 mL and used to irrigate lettuce plants ( Lactuca sativa ) set up in four groups, each receiving one of four water types, secondary WW (positive control), fresh water (negative control), chlorinated WW, and HPC WW. Four genes were monitored in water and soil, 16S rRNA as an indicator of total bacterial load, intI1 as a gene commonly associated with anthropogenic activity and AR, and two AR genes bla
OXA-10 and qnrS . Irrigation with secondary WW resulted in higher dry soil levels of intI1 (from 1.4 × 104 copies/g before irrigation to 3.3 × 105 copies/g after). HPC-treated wastewater showed higher copy numbers of intI1 in the irrigated soil than chlorination, but the opposite was true for blaOXA-10 . The results indicate that the current treatment is insufficient to prevent dissemination of AR markers and that HPC does not offer a clear advantage over chlorination.- Published
- 2020
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47. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes.
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Lal Gupta C, Kumar Tiwari R, and Cytryn E
- Subjects
- Anti-Bacterial Agents pharmacology, Drug Resistance, Microbial genetics, Genes, Bacterial, Genome, Bacterial, Humans, Bacteria genetics, Metagenome
- Abstract
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)
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- 2020
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48. Every fifth published metagenome is not available to science.
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Eckert EM, Di Cesare A, Fontaneto D, Berendonk TU, Bürgmann H, Cytryn E, Fatta-Kassinos D, Franzetti A, Larsson DGJ, Manaia CM, Pruden A, Singer AC, Udikovic-Kolic N, and Corno G
- Subjects
- Bibliometrics, Journal Impact Factor, Open Access Publishing, Access to Information, Metagenome, Publications statistics & numerical data
- Abstract
Have 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., Competing Interests: The authors have declared that no competing interests exist.
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- 2020
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49. Challenges related to antimicrobial resistance in the framework of urban wastewater reuse.
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Fatta-Kassinos D, Cytryn E, Donner E, and Zhang T
- Subjects
- Anti-Bacterial Agents, Conservation of Natural Resources, Drug Resistance, Bacterial, Waste Disposal, Fluid, Water Supply, Wastewater, Water Purification
- Published
- 2020
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50. Myocardial metaiodobenzylguanidine tomoscintigraphy for the diagnosis of Lewy body disease in patients with high clinical suspicion and non-diagnostic ioflupane single-photon emission computed tomography.
- Author
-
Le Moine M, Cytryn E, Hambye AS, Bizimungu A, Colson C, Surquin M, and Segers K
- Subjects
- Humans, Tomography, Emission-Computed, Single-Photon, 3-Iodobenzylguanidine, Lewy Body Disease diagnostic imaging, Myocardial Perfusion Imaging, Radiopharmaceuticals
- Published
- 2019
- Full Text
- View/download PDF
Catalog
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