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Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L. Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain. EFSA J 2021; 19:e06651. [PMID: 34178158 PMCID: PMC8210462 DOI: 10.2903/j.efsa.2021.6651] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
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Lee J, Ju F, Maile-Moskowitz A, Beck K, Maccagnan A, McArdell CS, Dal Molin M, Fenicia F, Vikesland PJ, Pruden A, Stamm C, Bürgmann H. Unraveling the riverine antibiotic resistome: The downstream fate of anthropogenic inputs. WATER RESEARCH 2021; 197:117050. [PMID: 33784606 DOI: 10.1016/j.watres.2021.117050] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/20/2021] [Accepted: 03/12/2021] [Indexed: 05/12/2023]
Abstract
River networks are one of the main routes by which the public could be exposed to environmental sources of antibiotic resistance, that may be introduced e.g. via treated wastewater. In this study, we applied a comprehensive integrated analysis encompassing mass-flow concepts, chemistry, bacterial plate counts, resistance gene quantification and shotgun metagenomics to track the fate of the resistome (collective antibiotic resistance genes (ARGs) in a microbial community) of treated wastewater in two Swiss rivers at the kilometer scale. The levels of certain ARGs and the class 1 integron integrase gene (intI1) commonly associated with anthropogenic sources of ARGs decreased quickly over short distances (2-2.5 km) downstream of wastewater discharge points. Mass-flow analysis based on conservative tracers suggested this decrease was attributable mainly to dilution but ARG loadings frequently also decreased (e.g., 55.0-98.5 % for ermB and tetW) over the longest studied distances (6.8 and 13.7 km downstream). Metagenomic analysis confirmed that ARG of wastewater-origin did not persist in rivers after 5 ~ 6.8 km downstream distance. sul1 and intI1 levels and loadings were more variable and even increased sharply at 5 ~ 6.8 km downstream distance on one occasion. While input from agriculture and in-situ positive selection pressure for organisms carrying ARGs cannot be excluded, in-system growth of biomass is a more probable explanation. The potential for direct human exposure to the resistome of wastewater-origin thus appeared to typically abate rapidly in the studied rivers. However, the riverine aquatic resistome was also dynamic, as evidenced by the increase of certain gene markers downstream, without obvious sources of anthropogenic contamination. This study provides new insight into drivers of riverine resistomes and pinpoints key monitoring targets indicative of where human sources and exposures are likely to be most acute.
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Affiliation(s)
- Jangwoo Lee
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland; Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Andreas Maccagnan
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Christa S McArdell
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Marco Dal Molin
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland; The Centre of Hydrogeology and Geothermics (CHYN), University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Fabrizio Fenicia
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Christian Stamm
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum or CH-8600 Dübendorf, Switzerland.
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Majeed HJ, Riquelme MV, Davis BC, Gupta S, Angeles L, Aga DS, Garner E, Pruden A, Vikesland PJ. Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant. Front Microbiol 2021; 12:657954. [PMID: 34054755 PMCID: PMC8155483 DOI: 10.3389/fmicb.2021.657954] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
Wastewater treatment plants (WWTPs) receive a confluence of sewage containing antimicrobials, antibiotic resistant bacteria, antibiotic resistance genes (ARGs), and pathogens and thus are a key point of interest for antibiotic resistance surveillance. WWTP monitoring has the potential to inform with respect to the antibiotic resistance status of the community served as well as the potential for ARGs to escape treatment. However, there is lack of agreement regarding suitable sampling frequencies and monitoring targets to facilitate comparison within and among individual WWTPs. The objective of this study was to comprehensively evaluate patterns in metagenomic-derived indicators of antibiotic resistance through various stages of treatment at a conventional WWTP for the purpose of informing local monitoring approaches that are also informative for global comparison. Relative abundance of total ARGs decreased by ∼50% from the influent to the effluent, with each sampling location defined by a unique resistome (i.e., total ARG) composition. However, 90% of the ARGs found in the effluent were also detected in the influent, while the effluent ARG-pathogen taxonomic linkage patterns identified in assembled metagenomes were more similar to patterns in regional clinical surveillance data than the patterns identified in the influent. Analysis of core and discriminatory resistomes and general ARG trends across the eight sampling events (i.e., tendency to be removed, increase, decrease, or be found in the effluent only), along with quantification of ARGs of clinical concern, aided in identifying candidate ARGs for surveillance. Relative resistome risk characterization further provided a comprehensive metric for predicting the relative mobility of ARGs and likelihood of being carried in pathogens and can help to prioritize where to focus future monitoring and mitigation. Most antibiotics that were subject to regional resistance testing were also found in the WWTP, with the total antibiotic load decreasing by ∼40–50%, but no strong correlations were found between antibiotics and corresponding ARGs. Overall, this study provides insight into how metagenomic data can be collected and analyzed for surveillance of antibiotic resistance at WWTPs, suggesting that effluent is a beneficial monitoring point with relevance both to the local clinical condition and for assessing efficacy of wastewater treatment in reducing risk of disseminating antibiotic resistance.
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Affiliation(s)
- Haniyyah J Majeed
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Maria V Riquelme
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Benjamin C Davis
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Suraj Gupta
- Interdisciplinary Ph.D Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Luisa Angeles
- Department of Chemistry, University at Buffalo, Buffalo, NY, United States
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, Buffalo, NY, United States
| | - Emily Garner
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Peter J Vikesland
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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54
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Li L, Nesme J, Quintela-Baluja M, Balboa S, Hashsham S, Williams MR, Yu Z, Sørensen SJ, Graham DW, Romalde JL, Dechesne A, Smets BF. Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5939-5949. [PMID: 33886308 DOI: 10.1021/acs.est.0c08548] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated and quantitative observations of the occurrence of ARGs in the UWS to characterize the sources and identify processes that contribute to their fate. We sampled the UWSs from three medium-size cities in Denmark, Spain, and the United Kingdom and quantified 70 clinically important extended-spectrum β-lactamase and carbapenemase genes along with the mobile genetic elements and microbial communities. Results from all three countries showed that sewage-especially from hospitals-carried substantial loads of ARGs (106-107 copies per person equivalent), but these loads progressively declined along sewers and through sewage treatment plants, resulting in minimal emissions (101-104 copies per person equivalent). Removal was primarily during sewage conveyance (65 ± 36%) rather than within sewage treatment (34 ± 23%). The extended-spectrum β-lactamase and carbapenemase genes were clustered in groups based on their persistence in the UWS compartments. The less-persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while the more persistent groups appeared horizontally transferred and correlated significantly with total cell numbers and mobile genetic elements. This documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based antibiotic resistance surveillance.
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Affiliation(s)
- Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | | | - Sabela Balboa
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Syed Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing 48824, Michigan, USA
| | - Maggie R Williams
- School of Engineering and Technology, Central Michigan University, Mt. Pleasant 48859, Michigan, USA
| | - Zhuofeng Yu
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
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55
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Hayward JL, Huang Y, Hansen LT, Yost CK, Lake C, Jamieson RC. Fate and distribution of determinants of antimicrobial resistance in lateral flow sand filters used for treatment of domestic wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:145481. [PMID: 33636762 DOI: 10.1016/j.scitotenv.2021.145481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Residuals of antimicrobial products from anthropogenic uses can create a selective environment in domestic wastewater treatment systems and receiving environments and contribute to the spread of antimicrobial resistance (AMR). On-site wastewater treatment systems are widely used for domestic wastewater management in rural and remote regions, but the fate of determinants of AMR in these types of environments has received little attention. In this study, the mechanisms responsible for the attenuation of determinants of AMR in lateral flow sand filters were explored using a combination of lab, field and modeling investigations. The degradation kinetics and adsorption potential in the sand filter medium of three antibiotic resistance genes (ARGs; sul1, tetO, and ermB) and culturable bacteria resistant to sulfamethoxazole, tetracycline, and erythromycin were measured using lab experiments. The spatial distribution of ARGs and antibiotic resistant bacteria were also assessed in field scale sand filters, and mechanistic modeling was conducted to characterize filtration processes. The results indicated that the primary mechanisms responsible for AMR attenuation within the sand filters were degradation and filtration. The spatial distribution of AMR determinants illustrated that attenuation was occurring along the entire length of each filter. This study provides new insights on primary mechanisms of AMR attenuation in on-site wastewater treatment systems and supports the use of conservative design guidelines and separation distances for reducing AMR transmission.
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Affiliation(s)
- Jennifer L Hayward
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
| | - Yannan Huang
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
| | | | - Christopher K Yost
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada.
| | - Craig Lake
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
| | - Rob C Jamieson
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
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Sobierajski T, Mazińska B, Wanke-Rytt M, Hryniewicz W. Knowledge-Based Attitudes of Medical Students in Antibiotic Therapy and Antibiotic Resistance. A Cross-Sectional Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3930. [PMID: 33918039 PMCID: PMC8068920 DOI: 10.3390/ijerph18083930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022]
Abstract
We aimed to evaluate the knowledge-based attitudes of antibiotics and antibiotic resistance among medical students of Medical University of Warsaw using the questionnaire prepared by the study's authors. In May-June 2018, we carried out a cross-sectional study among the students of all years, embracing 291 respondents. The students were divided into two groups: A (students in their first to third years) and B (students in their fourth to sixth years). Our study has shown that students are aware of the dangers of antibiotic resistance, seeing the leading cause as antibiotic misuse. We have shown that they are also aware of their insufficient knowledge and believe that more antibiotic therapy classes should be included in the curriculum of Medical University of Warsaw. Our questionnaire also focused on attitudes towards antibiotics based on knowledge. One in four respondents (23.7%), based on their knowledge, negated antibiotic therapy ordered by a doctor in the event of their illness, and four in ten (40.9%) in the occurrence of disease of a family member or friend. The vast majority of students (92.4%) would like to broaden their knowledge on antibiotic therapy. However, only one-fifth of students have heard about the European Antibiotic Awareness Day campaign. We recommend increasing the number of hours on antibiotic therapy and resistance education combined with topics on hand hygiene.
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Affiliation(s)
- Tomasz Sobierajski
- Faculty of Applied Social Sciences and Resocialization, University of Warsaw, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
| | - Beata Mazińska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (B.M.); (W.H.)
| | - Monika Wanke-Rytt
- Department of Pediatrics with Clinical Assessment Unit, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland;
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (B.M.); (W.H.)
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57
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Franklin AM, Brinkman NE, Jahne MA, Keely SP. Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments. J Microbiol Methods 2021; 184:106174. [PMID: 33774111 DOI: 10.1016/j.mimet.2021.106174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/03/2021] [Accepted: 02/17/2021] [Indexed: 12/26/2022]
Abstract
Antimicrobial resistance (AMR) in the environment is a growing global health concern, especially the dissemination of AMR into surface waters due to human and agricultural inputs. Within recent years, research has focused on trying to understand the impact of AMR in surface waters on human, agricultural and ecological health (One Health). While surface water quality assessments and surveillance of AMR have historically utilized culture-based methods, culturing bacteria has limitations due to difficulty in isolating environmental bacteria and the need for a priori information about the bacteria for selective isolation. The use of molecular techniques to analyze AMR at the genetic level has helped to overcome the difficulties with culture-based techniques since they do not require advance knowledge of the bacterial population and can analyze uncultivable environmental bacteria. The aim of this review is to provide an overview of common contemporary molecular methods available for analyzing AMR in surface waters, which include high throughput real-time polymerase chain reaction (HT-qPCR), metagenomics, and whole genome sequencing. This review will also feature how these methods may provide information on human and animal health risks. HT-qPCR works at the nanoliter scale, requires only a small amount of DNA, and can analyze numerous gene targets simultaneously, but may lack in analytical sensitivity and the ability to optimize individual assays compared to conventional qPCR. Metagenomics offers more detailed genomic information and taxonomic resolution than PCR by sequencing all the microbial genomes within a sample. Its open format allows for the discovery of new antibiotic resistance genes; however, the quantity of DNA necessary for this technique can be a limiting factor for surface water samples that typically have low numbers of bacteria per sample volume. Whole genome sequencing provides the complete genomic profile of a single environmental isolate and can identify all genetic elements that may confer AMR. However, a main disadvantage of this technique is that it only provides information about one bacterial isolate and is challenging to utilize for community analysis. While these contemporary techniques can quickly provide a vast array of information about AMR in surface waters, one technique does not fully characterize AMR nor its potential risks to human, animal, or ecological health. Rather, a combination of techniques (including both molecular- and culture-based) are necessary to fully understand AMR in surface waters from a One Health perspective.
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Affiliation(s)
- A M Franklin
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA.
| | - N E Brinkman
- Office of Research and Development, Center for Environmental Solutions and Emergency Response, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
| | - M A Jahne
- Office of Research and Development, Center for Environmental Solutions and Emergency Response, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
| | - S P Keely
- Office of Research and Development, Center for Environmental Measurement and Modeling, US Environmental Protection Agency, 26 Martin Luther King West, Cincinnati, OH 45268, USA
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Asiimwe BB, Kiiru J, Mshana SE, Neema S, Keenan K, Kesby M, Mwanga JR, Sloan DJ, Mmbaga BT, Smith VA, Gillespie SH, Lynch AG, Sandeman A, Stelling J, Elliott A, Aanensen DM, Kibiki GE, Sabiiti W, Holden MTG. Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR): Holistic Approach to Unravel Antibacterial Resistance in East Africa (HATUA). BMJ Open 2021; 11:e041418. [PMID: 34006022 PMCID: PMC7942251 DOI: 10.1136/bmjopen-2020-041418] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Antimicrobial resistance (AMR) is a global health threat that requires urgent research using a multidisciplinary approach. The biological drivers of AMR are well understood, but factors related to treatment seeking and the social contexts of antibiotic (AB) use behaviours are less understood. Here we describe the Holistic Approach to Unravel Antibacterial Resistance in East Africa, a multicentre consortium that investigates the diverse drivers of drug resistance in urinary tract infections (UTIs) in East Africa. METHODS AND ANALYSIS This study will take place in Uganda, Kenya and Tanzania. We will conduct geospatial mapping of AB sellers, and conduct mystery client studies and in-depth interviews (IDIs) with drug sellers to investigate AB provision practices. In parallel, we will conduct IDIs with doctors, alongside community focus groups. Clinically diagnosed patients with UTI will be recruited from healthcare centres, provide urine samples and complete a questionnaire capturing retrospective treatment pathways, sociodemographic characteristics, attitudes and knowledge. Bacterial isolates from urine and stool samples will be subject to culture and antibiotic sensitivity testing. Genomic DNA from bacterial isolates will be extracted with a subset being sequenced. A follow-up household interview will be conducted with 1800 UTI-positive patients, where further environmental samples will be collected. A subsample of patients will be interviewed using qualitative tools. Questionnaire data, microbiological analysis and qualitative data will be linked at the individual level. Quantitative data will be analysed using statistical modelling, including Bayesian network analysis, and all forms of qualitative data analysed through iterative thematic content analysis. ETHICS AND DISSEMINATION Approvals have been obtained from all national and local ethical review bodies in East Africa and the UK. Results will be disseminated in communities, with local and global policy stakeholders, and in academic circles. They will have great potential to inform policy, improve clinical practice and build regional pathogen surveillance capacity.
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Affiliation(s)
- Benon B Asiimwe
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - John Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Stella Neema
- College of Humanities and Social Science, Makerere University, Kampala, Uganda
| | - Katherine Keenan
- Geography and Sustainable Development, University of St Andrews, St Andrews, Fife, UK
| | - Mike Kesby
- Geography and Sustainable Development, University of St Andrews, St Andrews, Fife, UK
| | - Joseph R Mwanga
- School of Public Health, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Derek J Sloan
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre and Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - V Anne Smith
- School of Biology, University of St Andrews, St Andrews, UK
| | | | - Andy G Lynch
- School of Medicine, University of St Andrews, St Andrews, UK
- School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Alison Sandeman
- School of Medicine, University of St Andrews, St Andrews, UK
| | - John Stelling
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison Elliott
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Institute, Kampala, Uganda
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Wilber Sabiiti
- School of Medicine, University of St Andrews, St Andrews, UK
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Pulami D, Schauss T, Eisenberg T, Wilharm G, Blom J, Goesmann A, Kämpfer P, Glaeser SP. Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. FEMS Microbiol Ecol 2021; 96:5896450. [PMID: 32832994 DOI: 10.1093/femsec/fiaa176] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
Studies considering environmental multidrug-resistant Acinetobacter spp. are scarce. The application of manure on agricultural fields is one source of multidrug-resistant bacteria from livestock into the environment. Here, Acinetobacter spp. were quantified by quantitative polymerase chain reaction in manure applied to biogas plants and in the output of the anaerobic digestion, and Acinetobacter spp. isolated from those samples were comprehensively characterized. The concentration of Acinetobacter 16S ribosomal ribonucleic acid (rRNA) gene copies per g fresh weight was in range of 106-108 in manure and decreased (partially significantly) to a still high concentration (105-106) in digestates. 16S rRNA, gyrB-rpoB and blaOXA51-like gene sequencing identified 17 different Acinetobacter spp., including six A. baumannii strains. Multilocus sequence typing showed no close relation of the six strains with globally relevant clonal complexes; however, they represented five novel sequence types. Comparative genomics and physiological tests gave an explanation how Acinetobacter could survive the anaerobic biogas process and indicated copper resistance and the presence of intrinsic beta-lactamases, efflux-pump and virulence genes. However, the A. baumannii strains lacked acquired resistance against carbapenems, colistin and quinolones. This study provided a detailed characterization of Acinetobacter spp. including A. baumannii released via manure through mesophilic or thermophilic biogas plants into the environment.
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Affiliation(s)
- Dipen Pulami
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Thorsten Schauss
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), D-35392 Giessen, Germany; Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, D-35392, Giessen, Germany
| | - Gottfried Wilharm
- Project Group P2, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, D-35392 Giessen, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, D-35392 Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
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60
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Hassan AY, Lin JT, Ricker N, Anany H. The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications? Pharmaceuticals (Basel) 2021; 14:199. [PMID: 33670836 PMCID: PMC7997343 DOI: 10.3390/ph14030199] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023] Open
Abstract
Extended overuse and misuse of antibiotics and other antibacterial agents has resulted in an antimicrobial resistance crisis. Bacteriophages, viruses that infect bacteria, have emerged as a legitimate alternative antibacterial agent with a wide scope of applications which continue to be discovered and refined. However, the potential of some bacteriophages to aid in the acquisition, maintenance, and dissemination of negatively associated bacterial genes, including resistance and virulence genes, through transduction is of concern and requires deeper understanding in order to be properly addressed. In particular, their ability to interact with mobile genetic elements such as plasmids, genomic islands, and integrative conjugative elements (ICEs) enables bacteriophages to contribute greatly to bacterial evolution. Nonetheless, bacteriophages have the potential to be used as therapeutic and biocontrol agents within medical, agricultural, and food processing settings, against bacteria in both planktonic and biofilm environments. Additionally, bacteriophages have been deployed in developing rapid, sensitive, and specific biosensors for various bacterial targets. Intriguingly, their bioengineering capabilities show great promise in improving their adaptability and effectiveness as biocontrol and detection tools. This review aims to provide a balanced perspective on bacteriophages by outlining advantages, challenges, and future steps needed in order to boost their therapeutic and biocontrol potential, while also providing insight on their potential role in contributing to bacterial evolution and survival.
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Affiliation(s)
- Ahmad Y. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Janet T. Lin
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON N1G 2W1, Canada
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61
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Kutilova I, Medvecky M, Leekitcharoenphon P, Munk P, Masarikova M, Davidova-Gerzova L, Jamborova I, Bortolaia V, Pamp SJ, Dolejska M. Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic: Culture-based and metagenomic approaches. ENVIRONMENTAL RESEARCH 2021; 193:110487. [PMID: 33232750 DOI: 10.1016/j.envres.2020.110487] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/31/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
Wastewaters serve as important hot spots for antimicrobial resistance and monitoring can be used to analyse the abundance and diversity of antimicrobial resistance genes at the level of large bacterial and human populations. In this study, whole genome sequencing of beta-lactamase-producing Escherichia coli and metagenomic analysis of whole-community DNA were used to characterize the occurrence of antimicrobial resistance in hospital, municipal and river waters in the city of Brno (Czech Republic). Cefotaxime-resistant E. coli were mainly extended-spectrum beta-lactamase (ESBL) producers (95.6%, n = 158), of which the majority carried blaCTX-M (98.7%; n = 151) and were detected in all water samples except the outflow from hospital wastewater treatment plant. A wide phylogenetic diversity was observed among the sequenced E. coli (n = 78) based on the detection of 40 sequence types and single nucleotide polymorphisms (average number 34,666 ± 15,710) between strains. The metagenomic analysis revealed a high occurrence of bacterial genera with potentially pathogenic members, including Pseudomonas, Escherichia, Klebsiella, Aeromonas, Enterobacter and Arcobacter (relative abundance >50%) in untreated hospital and municipal wastewaters and predominance of environmental bacteria in treated and river waters. Genes encoding resistance to aminoglycosides, beta-lactams, quinolones and macrolides were frequently detected, however blaCTX-M was not found in this dataset which may be affected by insufficient sequencing depth of the samples. The study pointed out municipal treated wastewater as a possible source of multi-drug resistant E. coli and antimicrobial resistance genes for surface waters. Moreover, the combination of two different approaches provided a more holistic view on antimicrobial resistance in water environments. The culture-based approach facilitated insight into the dynamics of ESBL-producing E. coli and the metagenomics shows abundance and diversity of bacteria and antimicrobial resistance genes vary across water sites.
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Affiliation(s)
- Iva Kutilova
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42, Brno, Czech Republic
| | - Matej Medvecky
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; Biomedical Center, Faculty of Medicine, Charles University, alej Svobody 1655/76, 323 00, Plzen, Czech Republic
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Martina Masarikova
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42, Brno, Czech Republic
| | - Lenka Davidova-Gerzova
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42, Brno, Czech Republic
| | - Ivana Jamborova
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic
| | - Valeria Bortolaia
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Sünje J Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Monika Dolejska
- CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho tr. 1946/1, 612 42, Brno, Czech Republic; Biomedical Center, Faculty of Medicine, Charles University, alej Svobody 1655/76, 323 00, Plzen, Czech Republic.
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62
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Calderón-Franco D, van Loosdrecht MCM, Abeel T, Weissbrodt DG. Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater. WATER RESEARCH 2021; 189:116592. [PMID: 33171295 DOI: 10.1016/j.watres.2020.116592] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 11/01/2020] [Indexed: 05/11/2023]
Abstract
The free-floating extracellular DNA (exDNA) fraction of microbial ecosystems harbors antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Natural transformation of these xenogenetic elements can generate microbial cells resistant to one or more antibiotics. Isolating and obtaining a high yield of exDNA is challenging due to its low concentration in wastewater environments. Profiling exDNA is crucial to unravel the ecology of free-floating ARGs and MGEs and their contribution to horizontal genetransfer. We developed a method using chromatography to isolate and enrich exDNA without causing cell lysis from complex wastewater matrices like influent (9 µg exDNA out of 1 L), activated sludge (5.6 µg out of 1 L), and treated effluent (4.3 µg out of 1 L). ARGs and MGEs were metagenomically profiled for both the exDNA and intracellular DNA (iDNA) of activated sludge, and quantified by qPCR in effluent water. qPCR revealed that ARGs and MGEs are more abundant in the iDNA fraction while still significant on exDNA (100-1000 gene copies mL-1) in effluent water. The metagenome highlighted that exDNA is mainly composed of MGEs (65%). According to their relatively low abundance in the resistome of exDNA, ARGs uptake by natural transformation is likely not the main transfer mechanism. Although ARGs are not highly abundant in exDNA, the prevalence of MGEs in the exDNA fraction can indirectly promote antibiotic resistance development. The combination of this method with functional metagenomics can help to elucidate the transfer and development of resistances in microbial communities. A systematic profiling of the different DNA fractions will foster microbial risk assessments across water systems, supporting water authorities to delineate measures to safeguard environmental and public health.
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Affiliation(s)
| | | | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
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63
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Tompkins K, Juliano JJ, van Duin D. Antimicrobial Resistance in Enterobacterales and Its Contribution to Sepsis in Sub-saharan Africa. Front Med (Lausanne) 2021; 8:615649. [PMID: 33575265 PMCID: PMC7870712 DOI: 10.3389/fmed.2021.615649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Antibiotic resistant Enterobacterales (formerly Enterobactereaceae) are a growing threat to Sub-Saharan Africa. Genes causing antibiotic resistance are easily spread between the environment and humans and infections due to drug resistant organisms contribute to sepsis mortality via delayed time to appropriate antimicrobial therapy. Additionally, second or third-line antibiotics are often not available or are prohibitively expensive in resource-constrained settings leading to limited treatment options. Lack of access to water and sanitation facilities, unregulated use of antibiotics, and malnutrition are contributors to high rates of antibiotic resistance in the region. Improvements in the monitoring of drug resistant infections and antibiotic stewardship are needed to preserve the efficacy of antibiotics for the future.
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Affiliation(s)
- Kathleen Tompkins
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Jonathan J Juliano
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States.,Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - David van Duin
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
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64
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Davis BC, Riquelme MV, Ramirez-Toro G, Bandaragoda C, Garner E, Rhoads WJ, Vikesland P, Pruden A. Demonstrating an Integrated Antibiotic Resistance Gene Surveillance Approach in Puerto Rican Watersheds Post-Hurricane Maria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15108-15119. [PMID: 33205660 DOI: 10.1021/acs.est.0c05567] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Comprehensive surveillance approaches are needed to assess sources, clinical relevance, and mobility of antibiotic resistance genes (ARGs) in watersheds. Here, we examined metrics derived from shotgun metagenomic sequencing and relationship to human fecal markers (HFMs; crAssphage, enterococci) and anthropogenic antibiotic resistance markers (AARMs; intI1, sul1) in three distinct Puerto Rican watersheds as a function of adjacent land use and wastewater treatment plant (WWTP) input 6 months after Hurricane Maria, a category V storm. Relative abundance and diversity of total ARGs increased markedly downstream of WWTP inputs, with ARGs unique to WWTP and WWTP-impacted river samples predominantly belonging to the aminoglycoside and β-lactam resistance classes. WWTP and other anthropogenic inputs were similarly associated with elevated resistome risk scores and mobility incidence (M%). Contig analysis indicated a wide variety of mobile β-lactam ARGs associated with pathogens downstream of WWTP discharge that were consistent with regional clinical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposase. HFMs and AARMs correlated strongly with the absolute abundance of total ARGs, but AARMs better predicted the majority of ARGs in general (85.4 versus <2%) and β-lactam ARGs in particular. This study reveals sensitive, quantitative, mobile, clinically relevant, and comprehensive targets for antibiotic resistance surveillance in watersheds.
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Affiliation(s)
- Benjamin C Davis
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Maria Virginia Riquelme
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Graciela Ramirez-Toro
- Center for Environmental Education, Conservation and Research, Inter American University, San Germán, Puerto Rico 00683, United States
| | - Christina Bandaragoda
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Emily Garner
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - William J Rhoads
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Peter Vikesland
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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65
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Redhead S, Nieuwland J, Esteves S, Lee DH, Kim DW, Mathias J, Cha CJ, Toleman M, Dinsdale R, Guwy A, Hayhurst E. Fate of antibiotic resistant E. coli and antibiotic resistance genes during full scale conventional and advanced anaerobic digestion of sewage sludge. PLoS One 2020; 15:e0237283. [PMID: 33259486 PMCID: PMC7707479 DOI: 10.1371/journal.pone.0237283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistant bacteria (ARB) and their genes (ARGs) have become recognised as significant emerging environmental pollutants. ARB and ARGs in sewage sludge can be transmitted back to humans via the food chain when sludge is recycled to agricultural land, making sludge treatment key to control the release of ARB and ARGs to the environment. This study investigated the fate of antibiotic resistant Escherichia coli and a large set of antibiotic resistance genes (ARGs) during full scale anaerobic digestion (AD) of sewage sludge at two U.K. wastewater treatment plants and evaluated the impact of thermal hydrolysis (TH) pre-treatment on their abundance and diversity. Absolute abundance of 13 ARGs and the Class I integron gene intI1 was calculated using single gene quantitative (q) PCR. High through-put qPCR analysis was also used to determine the relative abundance of 370 ARGs and mobile genetic elements (MGEs). Results revealed that TH reduced the absolute abundance of all ARGs tested and intI1 by 10-12,000 fold. After subsequent AD, a rebound effect was seen in many ARGs. The fate of ARGs during AD without pre-treatment was variable. Relative abundance of most ARGs and MGEs decreased or fluctuated, with the exception of macrolide resistance genes, which were enriched at both plants, and tetracyline and glycopeptide resistance genes which were enriched in the plant employing TH. Diversity of ARGs and MGEs decreased in both plants during sludge treatment. Principal coordinates analysis revealed that ARGs are clearly distinguished according to treatment step, whereas MGEs in digested sludge cluster according to site. This study provides a comprehensive within-digestor analysis of the fate of ARGs, MGEs and antibiotic resistant E. coli and highlights the effectiveness of AD, particularly when TH is used as a pre-treatment, at reducing the abundance of most ARGs and MGEs in sludgeand preventing their release into the environment.
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Affiliation(s)
- Sky Redhead
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Jeroen Nieuwland
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Sandra Esteves
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Centre for Antibiotic Resistome, College of Biotechnology & Natural Resources, Chung-Ang University, Anseong, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Centre for Antibiotic Resistome, College of Biotechnology & Natural Resources, Chung-Ang University, Anseong, Republic of Korea
| | - Jordan Mathias
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Centre for Antibiotic Resistome, College of Biotechnology & Natural Resources, Chung-Ang University, Anseong, Republic of Korea
| | - Mark Toleman
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Richard Dinsdale
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Alan Guwy
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Emma Hayhurst
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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66
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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, Cytryn E. A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2020; 144:106035. [PMID: 32835921 DOI: 10.1016/j.envint.2020.106035] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 05/29/2023]
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 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status.
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Affiliation(s)
- Roberto B M Marano
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel; Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
| | - Telma Fernandes
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Olga Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Donald Morrison
- School Applied Sciences, Edinburgh Napier University, EH11 4BN, UK
| | | | - Norbert Kreuzinger
- Vienna University of Technology, Institute for Water Quality and Resources Management, Vienna, Austria
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Estonia
| | - Gianluca Corno
- CNR-IRSA Molecular Ecology Group, Largo Tonolli 50, 28922 Verbania, Italy
| | - Despo Fatta-Kassinos
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | | | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre (ON), Canada; Department of Biology, University of Western Ontario, London, ON, Canada
| | - Edouard Jurkevitch
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Leonie Henn
- School Applied Sciences, Edinburgh Napier University, EH11 4BN, UK
| | - Andrew Scott
- Agriculture and Agri-Food Canada, London Research and Development Centre (ON), Canada
| | - Stefanie Heß
- Institute of Hydrobiology, TU Dresden, Dresden, Germany; Institute of Microbiology, TU Dresden, Dresden, Germany
| | - Katarzyna Slipko
- Vienna University of Technology, Institute for Water Quality and Resources Management, Vienna, Austria
| | - Mailis Laht
- Institute of Technology, University of Tartu, Estonia; Estonian Environmental Research Centre, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Estonia
| | - Andrea Di Cesare
- CNR-IRSA Molecular Ecology Group, Largo Tonolli 50, 28922 Verbania, Italy
| | - Popi Karaolia
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Stella G Michael
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Alice L Petre
- Department of Chemical Engineering, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Roberto Rosal
- Department of Chemical Engineering, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Virginia Riquelme
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain
| | - Belen Esteban
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain
| | - Aneta Luczkiewicz
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, G. Narutowicza 11/12 street, 80-233 Gdańsk, Poland
| | - Agnieszka Kalinowska
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, G. Narutowicza 11/12 street, 80-233 Gdańsk, Poland
| | - Anne Leonard
- University of Exeter Medical School, European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter, Penryn campus, TR10 9FE, UK
| | - William H Gaze
- University of Exeter Medical School, European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter, Penryn campus, TR10 9FE, UK
| | - Anthony A Adegoke
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban South Africa; Department of Microbiology, University of Uyo, Uyo, Nigeria
| | - Thor A Stenstrom
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban South Africa
| | | | | | - Carsten U Schwermer
- Norwegian Institute for Water Research, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Pawel Krzeminski
- Norwegian Institute for Water Research, Gaustadalléen 21, N-0349 Oslo, Norway
| | | | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Giovanni Libralato
- Department of Biology, University of Naples Federico II, via Cinthia 21, 80126 Naples, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, via Cinthia 21, 80126 Naples, Italy
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Hemda Garelick
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Marta Tacão
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Portugal
| | - Isabel Henriques
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Portugal; University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Isabel Martínez-Alcalá
- Department of Civil Engineering, Av. de los Jerónimos, 135, 30107 Guadalupe, Murcia, Spain
| | - Jose M Guillén-Navarro
- Department of Civil Engineering, Av. de los Jerónimos, 135, 30107 Guadalupe, Murcia, Spain
| | - Magdalena Popowska
- Institute of Microbiology, Department of Applied Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Marta Piotrowska
- Institute of Microbiology, Department of Applied Microbiology, Faculty of Biology, University of Warsaw, Poland
| | | | - Joshua T Bunce
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK
| | - Maria I Polo-López
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain; Plataforma Solar de Almería - CIEMAT, P.O. Box 22, 04200 Tabernas, Almería, Spain
| | - Samira Nahim-Granados
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain; Plataforma Solar de Almería - CIEMAT, P.O. Box 22, 04200 Tabernas, Almería, Spain
| | | | | | | | - Jérôme Ory
- Laboratoire "Microorganisme: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, F-63170 Campus Universitaire des Cézeaux, Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Traore Ousmane
- Laboratoire "Microorganisme: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, F-63170 Campus Universitaire des Cézeaux, Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Antoni Oliver
- Laboratori EMATSA, Ctra Valls Km 3, 43130 Tarragona, Spain
| | | | - Jose L Balcazar
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain
| | - Thomas Jäger
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas Schwartz
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Ying Yang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shichun Zou
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Younggun Yoon
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Bastian Herzog
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Germany
| | - Heidrun Mayrhofer
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Germany
| | - Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Pune 411007, India
| | - Yogesh Nimonkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Pune 411007, India
| | - Ester Heath
- Jozef Stefan Institute, Jamova 39 1000 Ljubljana, Slovenia
| | - Anna Baraniak
- National Medicines Institute, Department of Molecular Microbiology, Chelmska 30/34, 00-725 Warsaw, Poland
| | - Joana Abreu-Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Manika Choudhury
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Leonardo P Munoz
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | | | - Gianluca Brunetti
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | | | - Connor Brown
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel.
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Korajkic A, McMinn BR, Staley ZR, Ahmed W, Harwood VJ. Antibiotic-Resistant Enterococcus Species in Marine Habitats: A Review. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2020; 19:92-100. [PMID: 33134649 PMCID: PMC7592714 DOI: 10.1016/j.coesh.2020.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibiotic-resistant Enterococcus (ARE) are among leading causes of nosocomial infections worldwide. Enterococcus spp. are ubiquitous in sewage, which can contaminate surface waters via many pathways, providing a route of exposure for humans. This review focuses on ARE in marine and estuarine habitats, including marine animals. Phylogenetic confirmation of the genus Enterococcus and intermediate or full resistance to clinically relevant antibiotics were inclusion criteria. The proportion of resistant isolates varied greatly among antibiotics, for example, 24.2% for ampicillin and 2.4% for vancomycin. The water column contained the highest proportion of ARE observations (18.8%), followed by animal feces and tissues (14.8%), sediment (9.4%), and sand (2.0%). The proportion of multidrug-resistant isolates was the greatest in animal tissue and fecal samples, followed by water and sediments. This review indicates that clinically relevant ARE are present in marine/estuarine habitats and that animals may be important reservoirs.
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Affiliation(s)
- Asja Korajkic
- United Stated Environmental Protection Agency, Cincinnati, OH, USA
| | - Brian R. McMinn
- United Stated Environmental Protection Agency, Cincinnati, OH, USA
| | | | - Warish Ahmed
- Commonwealth Scientific and Industrial Research Organisation, Australia
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68
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Nadimpalli ML, Marks SJ, Montealegre MC, Gilman RH, Pajuelo MJ, Saito M, Tsukayama P, Njenga SM, Kiiru J, Swarthout J, Islam MA, Julian TR, Pickering AJ. Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission. Nat Microbiol 2020; 5:787-795. [PMID: 32467623 DOI: 10.1038/s41564-020-0722-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/07/2020] [Indexed: 12/24/2022]
Abstract
Antimicrobial resistance (AMR) is a growing public health challenge that is expected to disproportionately burden lower- and middle-income countries (LMICs) in the coming decades. Although the contributions of human and veterinary antibiotic misuse to this crisis are well-recognized, environmental transmission (via water, soil or food contaminated with human and animal faeces) has been given less attention as a global driver of AMR, especially in urban informal settlements in LMICs-commonly known as 'shanty towns' or 'slums'. These settlements may be unique hotspots for environmental AMR transmission given: (1) the high density of humans, livestock and vermin living in close proximity; (2) frequent antibiotic misuse; and (3) insufficient drinking water, drainage and sanitation infrastructure. Here, we highlight the need for strategies to disrupt environmental AMR transmission in urban informal settlements. We propose that water and waste infrastructure improvements tailored to these settings should be evaluated for their effectiveness in limiting environmental AMR dissemination, lowering the community-level burden of antimicrobial-resistant infections and preventing antibiotic misuse. We also suggest that additional research is directed towards developing economic and legal incentives for evaluating and implementing water and waste infrastructure in these settings. Given that almost 90% of urban population growth will occur in regions predicted to be most burdened by the AMR crisis, there is an urgent need to build effective, evidence-based policies that could influence massive investments in the built urban environment in LMICs over the next few decades.
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Affiliation(s)
- Maya L Nadimpalli
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA.,Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
| | - Sara J Marks
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MA, USA.,Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Monica J Pajuelo
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MA, USA.,Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Pablo Tsukayama
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Medicina Tropical 'Alexander von Humboldt', Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - John Kiiru
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Jenna Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Mohammad Aminul Islam
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Amy J Pickering
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA. .,Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA.
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69
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Buelow E, Rico A, Gaschet M, Lourenço J, Kennedy SP, Wiest L, Ploy MC, Dagot C. Hospital discharges in urban sanitation systems: Long-term monitoring of wastewater resistome and microbiota in relationship to their eco-exposome. WATER RESEARCH X 2020; 7:100045. [PMID: 32072151 PMCID: PMC7013138 DOI: 10.1016/j.wroa.2020.100045] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/03/2020] [Accepted: 01/26/2020] [Indexed: 05/05/2023]
Abstract
Wastewaters (WW) are important sources for the dissemination of antimicrobial resistance (AMR) into the environment. Hospital WW (HWW) contain higher loads of micro-pollutants and AMR markers than urban WW (UWW). Little is known about the long-term dynamics of H and U WW and the impact of their joined treatment on the general burden of AMR. Here, we characterized the resistome, microbiota and eco-exposome signature of 126 H and U WW samples treated separately for three years, and then mixed, over one year. Multi-variate analysis and machine learning revealed a robust signature for each WW with no significant variation over time before mixing, and once mixed, both WW closely resembled Urban signatures. We demonstrated a significant impact of pharmaceuticals and surfactants on the resistome and microbiota of H and U WW. Our results present considerable targets for AMR related risk assessment of WW.
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Affiliation(s)
- Elena Buelow
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
- Corresponding author. UMR Inserm 1092, Agents Anti-Microbiens, CBRS, 1 rue du Pr Bernard Descottes, 87000, Limoges, France.
| | - Andreu Rico
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Madrid, Spain
| | - Margaux Gaschet
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - Sean P. Kennedy
- Biomics Pole, CITECH, Institut Pasteur, Paris, 75015, France
| | - Laure Wiest
- Univ Lyon, CNRS, Université Claude Bernard Lyon, Institut des Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100, Villeurbanne, France
| | - Marie-Cecile Ploy
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
| | - Christophe Dagot
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000, Limoges, France
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70
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Pérez-Etayo L, González D, Vitas AI. The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli. Microorganisms 2020; 8:microorganisms8040568. [PMID: 32326434 PMCID: PMC7232254 DOI: 10.3390/microorganisms8040568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 12/31/2022] Open
Abstract
One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10−1 ± 5 × 10−1, being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10−4 ± 2.85 × 10−4 and 9.61 × 10−4 ± 1.96 × 10−3, respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs.
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Affiliation(s)
- Lara Pérez-Etayo
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain; (D.G.); (A.I.V.)
- Correspondence: ; Tel.: +34-948-425-600
| | - David González
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain; (D.G.); (A.I.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Ana Isabel Vitas
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain; (D.G.); (A.I.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
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71
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Rizzo L, Gernjak W, Krzeminski P, Malato S, McArdell CS, Perez JAS, Schaar H, Fatta-Kassinos D. Best available technologies and treatment trains to address current challenges in urban wastewater reuse for irrigation of crops in EU countries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136312. [PMID: 32050367 DOI: 10.1016/j.scitotenv.2019.136312] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/21/2019] [Accepted: 12/22/2019] [Indexed: 05/09/2023]
Abstract
Conventional urban wastewater treatment plants (UWTPs) are poorly effective in the removal of most contaminants of emerging concern (CECs), including antibiotics, antibiotic resistant bacteria and antibiotic resistance genes (ARB&ARGs). These contaminants result in some concern for the environment and human health, in particular if UWTPs effluents are reused for crop irrigation. Recently, stakeholders' interest further increased in Europe, because the European Commission is currently developing a regulation on water reuse. Likely, conventional UWTPs will require additional advanced treatment steps to meet water quality limits yet to be officially established for wastewater reuse. Even though it seems that CECs will not be included in the proposed regulation, the aim of this paper is to provide a technical contribution to this discussion as well as to support stakeholders by recommending possible advanced treatment options, in particular with regard to the removal of CECs and ARB&ARGs. Taking into account the current knowledge and the precautionary principle, any new or revised water-related Directive should address such contaminants. Hence, this review paper gathers the efforts of a group of international experts, members of the NEREUS COST Action ES1403, who for three years have been constructively discussing the efficiency of the best available technologies (BATs) for urban wastewater treatment to abate CECs and ARB&ARGs. In particular, ozonation, activated carbon adsorption, chemical disinfectants, UV radiation, advanced oxidation processes (AOPs) and membrane filtration are discussed with regard to their capability to effectively remove CECs and ARB&ARGs, as well as their advantages and drawbacks. Moreover, a comparison among the above-mentioned processes is performed for CECs relevant for crop uptake. Finally, possible treatment trains including the above-discussed BATs are discussed, issuing end-use specific recommendations which will be useful to UWTPs managers to select the most suitable options to be implemented at their own facilities to successfully address wastewater reuse challenges.
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Affiliation(s)
- Luigi Rizzo
- Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy.
| | - Wolfgang Gernjak
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Pawel Krzeminski
- Section of Systems Engineering and Technology, Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349 Oslo, Norway
| | - Sixto Malato
- Plataforma Solar de Almería (CIEMAT), Carretera de Senés, km. 4, Tabernas, Almería 04200, Spain; Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, Universitiy of Almeria, Ctra. Sacramento s/n, ES04120 Almería, Spain
| | - Christa S McArdell
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Jose Antonio Sanchez Perez
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, Universitiy of Almeria, Ctra. Sacramento s/n, ES04120 Almería, Spain; Department of Chemical Engineering, University of Almeria, Ctra. Sacramento s/n, ES04120 Almería, Spain
| | - Heidemarie Schaar
- Technische Universität Wien, Institute for Water Quality and Resource Management, Karlsplatz 13/2261, 1040 Vienna, Austria
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas, International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus.
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72
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Marti E, Osorio V, Llorca M, Paredes L, Gros M. Environmental risks of sewage sludge reuse in agriculture. WASTEWATER TREATMENT AND REUSE – LESSONS LEARNED IN TECHNOLOGICAL DEVELOPMENTS AND MANAGEMENT ISSUES 2020. [DOI: 10.1016/bs.apmp.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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73
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Mahon BM, Brehony C, Cahill N, McGrath E, O'Connor L, Varley A, Cormican M, Ryan S, Hickey P, Keane S, Mulligan M, Ruane B, Jolley KA, Maiden MC, Brisse S, Morris D. Detection of OXA-48-like-producing Enterobacterales in Irish recreational water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:1-6. [PMID: 31299565 DOI: 10.1016/j.scitotenv.2019.06.480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 06/10/2023]
Abstract
The rapid dissemination of carbapenemase-producing Enterobacterales (CPE) is a major public health concern. The role that the aquatic environment plays in this dissemination is underexplored. This study aimed to examine seawater as a reservoir for CPE. Seawater sampling took place at a bathing site throughout the 2017 bathing season. Each 30 L sample (n = 6) was filtered using the CapE filtration system. Wastewater samples (200 mL) (pre-treatment (n = 3) and post-treatment (n = 3)) were obtained from a nearby secondary wastewater treatment plant, during the same time period. All samples were examined for CPE. Whole genome sequencing of confirmed CPE was carried out using Illumina sequencing. Isolate genomes were hosted in corresponding BIGSdb databases and analyses were performed using multiple web-based tools. CPE was detected in 2/6 seawater samples. It was not detected in any wastewater samples. OXA-48-like-producing ST131 Escherichia coli (Ec_BM707) was isolated from a seawater sample collected in May 2017 and OXA-48-like-producing ST101 Klebsiella pneumoniae (Kp_BM758) was isolated from a seawater sample collected in August 2017. The genomes of the environmental isolates were compared to a collection of previously described Irish clinical OXA-48-like-producing Enterobacterales (n = 105). Ec_BM707 and Kp_BM758 harboured blaOXA-48 on similar mobile genetic elements to those identified in the clinical collection (pOXA-48 fragment in Ec_BM707 and IncL(pOXA-48) plasmid in Kp_BM758). Genetic similarities were observed between Ec_BM707 and several of the clinical ST131 E. coli, with allele matches at up to 98.2% of 2513 core genome multilocus sequence type (cgMLST) loci. In contrast, Kp_BM758 and the 34 clinical K. pneumoniae were genetically distant. The source of the CPE at this site was not identified. The detection of OXA-48-like-producing ST131 E. coli and OXA-48-like-producing ST101 K. pneumoniae in Irish recreational water is a concern. The potential for contamination of the aquatic environment to contribute to dissemination of CPE in Europe warrants further study.
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Affiliation(s)
- Bláthnaid M Mahon
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland.
| | - Carina Brehony
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland
| | - Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
| | - Elaine McGrath
- Carbapenemase-Producing Enterobacterales Reference Laboratory, Department of Medical Microbiology, University Hospital Galway, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
| | - Aine Varley
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland; Carbapenemase-Producing Enterobacterales Reference Laboratory, Department of Medical Microbiology, University Hospital Galway, Galway, Ireland
| | - Sinead Ryan
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland
| | - Paul Hickey
- Environmental Health Service, HSE West, Galway, Ireland
| | - Shane Keane
- Environmental Health Service, HSE West, Galway, Ireland
| | | | | | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Martin C Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland
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74
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Singer AC, Xu Q, Keller VDJ. Translating antibiotic prescribing into antibiotic resistance in the environment: A hazard characterisation case study. PLoS One 2019; 14:e0221568. [PMID: 31483803 PMCID: PMC6726141 DOI: 10.1371/journal.pone.0221568] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/11/2019] [Indexed: 01/06/2023] Open
Abstract
The environment receives antibiotics through a combination of direct application (e.g., aquaculture and fruit production), as well as indirect release through pharmaceutical manufacturing, sewage and animal manure. Antibiotic concentrations in many sewage-impacted rivers are thought to be sufficient to select for antibiotic resistance genes. Yet, because antibiotics are nearly always found associated with antibiotic-resistant faecal bacteria in wastewater, it is difficult to distinguish the selective role of effluent antibiotics within a 'sea' of gut-derived resistance genes. Here we examine the potential for macrolide and fluoroquinolone prescribing in England to select for resistance in the River Thames catchment, England. We show that 64% and 74% of the length of the modelled catchment is chronically exposed to putative resistance-selecting concentrations (PNEC) of macrolides and fluoroquinolones, respectively. Under current macrolide usage, 115 km of the modelled River Thames catchment (8% of total length) exceeds the PNEC by 5-fold. Similarly, under current fluoroquinolone usage, 223 km of the modelled River Thames catchment (16% of total length) exceeds the PNEC by 5-fold. Our results reveal that if reduced prescribing was the sole mitigating measure, that macrolide and fluoroquinolone prescribing would need to decline by 77% and 85%, respectively, to limit resistance selection in the catchment. Significant reductions in antibiotic prescribing are feasible, but innovation in sewage-treatment will be necessary for achieving substantially-reduced antibiotic loads and inactivation of DNA-pollution from resistant bacteria. Greater confidence is needed in current risk-based targets for antibiotics, particularly in mixtures, to better inform environmental risk assessments and mitigation.
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Affiliation(s)
- Andrew C. Singer
- NERC Centre for Ecology & Hydrology, Benson Lane, Wallingford, United Kingdom
| | - Qiuying Xu
- NERC Centre for Ecology & Hydrology, Benson Lane, Wallingford, United Kingdom
- Environmental Diagnosis and Management, Royal Holloway University of London, Egham, United Kingdom
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75
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Charani E, Cunnington AJ, Yousif AHA, Seed Ahmed M, Ahmed AEM, Babiker S, Badri S, Buytaert W, Crawford MA, Elbashir MI, Elhag K, Elsiddig KE, Hakim N, Johnson MR, Miras AD, Swar MO, Templeton MR, Taylor-Robinson SD. In transition: current health challenges and priorities in Sudan. BMJ Glob Health 2019; 4:e001723. [PMID: 31543996 PMCID: PMC6730568 DOI: 10.1136/bmjgh-2019-001723] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/21/2019] [Accepted: 07/23/2019] [Indexed: 11/17/2022] Open
Abstract
A recent symposium and workshop in Khartoum, the capital of the Republic of Sudan, brought together broad expertise from three universities to address the current burden of communicable and non-communicable diseases facing the Sudanese healthcare system. These meetings identified common challenges that impact the burden of diseases in the country, most notably gaps in data and infrastructure which are essential to inform and deliver effective interventions. Non-communicable diseases, including obesity, type 2 diabetes, renal disease and cancer are increasing dramatically, contributing to multimorbidity. At the same time, progress against communicable diseases has been slow, and the burden of chronic and endemic infections remains considerable, with parasitic diseases (such as malaria, leishmaniasis and schistosomiasis) causing substantial morbidity and mortality. Antimicrobial resistance has become a major threat throughout the healthcare system, with an emerging impact on maternal, neonatal and paediatric populations. Meanwhile, malnutrition, micronutrient deficiency and poor perinatal outcomes remain common and contribute to a lifelong burden of disease. These challenges echo the United Nations (UN) sustainable development goals and concentrating on them in a unified strategy will be necessary to address the national burden of disease. At a time when the country is going through societal and political transition, we draw focus on the country and the need for resolution of its healthcare needs.
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Affiliation(s)
- Esmita Charani
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
| | | | | | | | - Ammar E M Ahmed
- Department of Medicine, University of Khartoum, Khartoum, Sudan
| | - Souad Babiker
- Department of Medicine, Ahfad University for Women, Omdurman, Sudan
| | - Shahinaz Badri
- Department of Pathology, School of Medicine, Ahfad University for Women, Omdurman, Sudan
| | | | | | | | - Kamal Elhag
- Department of Medicine, Ahfad University for Women, Omdurman, Sudan
| | | | - Nadey Hakim
- Department of Medicine, Imperial College London, London, UK
| | - Mark R Johnson
- Department of Medicine, Imperial College London, London, UK
| | | | - Mohamed O Swar
- Department of Medicine, Ahfad University for Women, Omdurman, Sudan
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76
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Kraemer SA, Ramachandran A, Perron GG. Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy. Microorganisms 2019; 7:E180. [PMID: 31234491 PMCID: PMC6616856 DOI: 10.3390/microorganisms7060180] [Citation(s) in RCA: 356] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 01/06/2023] Open
Abstract
The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.
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Affiliation(s)
- Susanne A Kraemer
- Department of Biology, Concordia University, 7141 Sherbrooke Street W, Montreal, QC H4B1R6, Canada.
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke Street W, Montreal, QC H4B1R6, Canada.
| | - Gabriel G Perron
- Department of Biology, Reem-Kayden Center for Sciences and Computation, Bard College, 31 Campus Road, Annandale-On-Hudson, NY 12504, USA.
- Center for the Study of Land, Water, and Air, Bard College, Annandale-On-Hudson, NY 12504, USA.
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77
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Prüss-Ustün A, Wolf J, Bartram J, Clasen T, Cumming O, Freeman MC, Gordon B, Hunter PR, Medlicott K, Johnston R. Burden of disease from inadequate water, sanitation and hygiene for selected adverse health outcomes: An updated analysis with a focus on low- and middle-income countries. Int J Hyg Environ Health 2019; 222:765-777. [PMID: 31088724 PMCID: PMC6593152 DOI: 10.1016/j.ijheh.2019.05.004] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND To develop updated estimates in response to new exposure and exposure-response data of the burden of diarrhoea, respiratory infections, malnutrition, schistosomiasis, malaria, soil-transmitted helminth infections and trachoma from exposure to inadequate drinking-water, sanitation and hygiene behaviours (WASH) with a focus on low- and middle-income countries. METHODS For each of the analysed diseases, exposure levels with both sufficient global exposure data for 2016 and a matching exposure-response relationship were combined into population-attributable fractions. Attributable deaths and disability-adjusted life years (DALYs) were estimated for each disease and, for most of the diseases, by country, age and sex group separately for inadequate water, sanitation and hygiene behaviours and for the cluster of risk factors. Uncertainty estimates were computed on the basis of uncertainty surrounding exposure estimates and relative risks. FINDINGS An estimated 829,000 WASH-attributable deaths and 49.8 million DALYs occurred from diarrhoeal diseases in 2016, equivalent to 60% of all diarrhoeal deaths. In children under 5 years, 297,000 WASH-attributable diarrhoea deaths occurred, representing 5.3% of all deaths in this age group. If the global disease burden from different diseases and several counterfactual exposure distributions was combined it would amount to 1.6 million deaths, representing 2.8% of all deaths, and 104.6 million DALYs in 2016. CONCLUSIONS Despite recent declines in attributable mortality, inadequate WASH remains an important determinant of global disease burden, especially among young children. These estimates contribute to global monitoring such as for the Sustainable Development Goal indicator on mortality from inadequate WASH.
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Affiliation(s)
- Annette Prüss-Ustün
- Department of Public Health, Environment and Social Determinants of Health, World Health Organization, Geneva, Switzerland.
| | - Jennyfer Wolf
- Department of Public Health, Environment and Social Determinants of Health, World Health Organization, Geneva, Switzerland.
| | - Jamie Bartram
- Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Thomas Clasen
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK.
| | - Matthew C Freeman
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Bruce Gordon
- Department of Public Health, Environment and Social Determinants of Health, World Health Organization, Geneva, Switzerland.
| | - Paul R Hunter
- The Norwich School of Medicine, University of East Anglia, Norwich, UK; Department of Environmental Health, Tshwane University of Technology, Pretoria, South Africa.
| | - Kate Medlicott
- Department of Public Health, Environment and Social Determinants of Health, World Health Organization, Geneva, Switzerland.
| | - Richard Johnston
- Department of Public Health, Environment and Social Determinants of Health, World Health Organization, Geneva, Switzerland.
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78
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Vikesland P, Garner E, Gupta S, Kang S, Maile-Moskowitz A, Zhu N. Differential Drivers of Antimicrobial Resistance across the World. Acc Chem Res 2019; 52:916-924. [PMID: 30848890 DOI: 10.1021/acs.accounts.8b00643] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) is one of the greatest threats faced by humankind. The development of resistance in clinical and hospital settings has been well documented ever since the initial discovery of penicillin and the subsequent introduction of sulfonamides as clinical antibiotics. In contrast, the environmental (i.e., community-acquired) dimensions of resistance dissemination have been only more recently delineated. The global spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) between air, water, soil, and food is now well documented, while the factors that affect ARB and ARG dissemination (e.g., water and air quality, antibiotic fluxes, urbanization, sanitation practices) in these and other environmental matrices are just now beginning to be more fully appreciated. In this Account, we discuss how the global perpetuation of resistance is dictated by highly interconnected socioeconomic risk factors and illustrate that development status should be more fully considered when developing global strategies to address AMR. We first differentiate low to middle income countries (LMICs) and high-income countries (HICs), then we summarize the modes of action of commercially available antibiotics, and then discuss the four primary mechanisms by which bacteria develop resistance to those antibiotics. Resistance is disseminated via both vertical gene transfer (VGT; parent to offspring) as well as by horizontal gene transfer (HGT; cell to cell transference of genetic material). A key challenge hindering attempts to control resistance dissemination is the presence of native, environmental bacteria that can harbor ARGs. Such environmental "resistomes" have potential to transfer resistance to pathogens via HGT. Of particular concern is the development of resistance to antibiotics of last-resort such as the cephalosporins, carbapenems, and polymyxins. We then illustrate how antibiotic use differs in LMICs relative to HICs in terms of the volumes of antibiotics used and their fate within local environments. Antibiotic use in HICs has remained flat over the past 15 years, while in LMICs use over the same period has increased substantially as a result of economic improvements and changes in diet. These use and fate differences impact local citizens and thus the local dissemination of AMR. Various physical, social, and economic circumstances within LMICs potentially favor AMR dissemination. We focus on three physical factors: changing population density, sanitation infrastructure, and solid-waste disposal. We show that high population densities in cities within LMICs that suffer from poor sanitation and solid-waste disposal can potentially impact the dissemination of resistance. In the final section, we discuss potential monitoring approaches to quantify the spread of resistance both within LMICs as well as in HICs. We posit that culture-based approaches, molecular approaches, and cutting-edge nanotechnology-based methods for monitoring ARB and ARGs should be considered both within HICs and, as appropriate, within LMICs.
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Affiliation(s)
- Peter Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia Tech Global Change Center and Virginia Tech Institute of Critical Technology and Applied Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Emily Garner
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Suraj Gupta
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Seju Kang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ni Zhu
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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79
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Tiedje JM. Editorial: Environmental aspects of antibiotic resistance. FEMS Microbiol Ecol 2019; 95:5421059. [PMID: 30923814 DOI: 10.1093/femsec/fiz019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
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80
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Collignon PJ, McEwen SA. One Health-Its Importance in Helping to Better Control Antimicrobial Resistance. Trop Med Infect Dis 2019; 4:E22. [PMID: 30700019 PMCID: PMC6473376 DOI: 10.3390/tropicalmed4010022] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 01/21/2023] Open
Abstract
Approaching any issue from a One Health perspective necessitates looking at the interactions of people, domestic animals, wildlife, plants, and our environment. For antimicrobial resistance this includes antimicrobial use (and abuse) in the human, animal and environmental sectors. More importantly, the spread of resistant bacteria and resistance determinants within and between these sectors and globally must be addressed. Better managing this problem includes taking steps to preserve the continued effectiveness of existing antimicrobials such as trying to eliminate their inappropriate use, particularly where they are used in high volumes. Examples are the mass medication of animals with critically important antimicrobials for humans, such as third generation cephalosporins and fluoroquinolones, and the long term, in-feed use of antimicrobials, such colistin, tetracyclines and macrolides, for growth promotion. In people it is essential to better prevent infections, reduce over-prescribing and over-use of antimicrobials and stop resistant bacteria from spreading by improving hygiene and infection control, drinking water and sanitation. Pollution from inadequate treatment of industrial, residential and farm waste is expanding the resistome in the environment. Numerous countries and several international agencies have now included a One Health Approach within their action plans to address antimicrobial resistance. Necessary actions include improvements in antimicrobial use, better regulation and policy, as well as improved surveillance, stewardship, infection control, sanitation, animal husbandry, and finding alternatives to antimicrobials.
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Affiliation(s)
- Peter J Collignon
- Infectious Diseases and Microbiology, Canberra Hospital, Garran, ACT 2605, Australia.
- Medical School, Australian National University, Acton ACT 2601, Australia.
| | - Scott A McEwen
- Department of Population Medicine, University of Guelph, Guelph N1G 2W1, Canada.
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81
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Fortunato G, Vaz-Moreira I, Becerra-Castro C, Nunes OC, Manaia CM. A rationale for the high limits of quantification of antibiotic resistance genes in soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:1696-1703. [PMID: 30300875 DOI: 10.1016/j.envpol.2018.09.128] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
The determination of values of abundance of antibiotic resistance genes (ARGs) per mass of soil is extremely useful to assess the potential impacts of relevant sources of antibiotic resistance, such as irrigation with treated wastewater or manure application. Culture-independent methods and, in particular, quantitative PCR (qPCR), have been regarded as suitable approaches for such a purpose. However, it is arguable if these methods are sensitive enough to measure ARGs abundance at levels that may represent a risk for environmental and human health. This study aimed at demonstrating the range of values of ARGs quantification that can be expected based on currently used procedures of DNA extraction and qPCR analyses. The demonstration was based on the use of soil samples spiked with known amounts of wastewater antibiotic resistant bacteria (ARB) (Enterococcus faecalis, Escherichia coli, Acinetobacter johnsonii, or Pseudomonas aeruginosa), harbouring known ARGs, and also on the calculation of expected values determined based on qPCR. The limits of quantification (LOQ) of the ARGs (vanA, qnrS, blaTEM, blaOXA, blaIMP, blaVIM) were observed to be approximately 4 log-units per gram of soil dry weight, irrespective of the type of soil tested. These values were close to the theoretical LOQ values calculated based on currently used DNA extraction methods and qPCR procedures. The observed LOQ values can be considered extremely high to perform an accurate assessment of the impacts of ARGs discharges in soils. A key message is that ARGs accumulation will be noticeable only at very high doses. The assessment of the impacts of ARGs discharges in soils, of associated risks of propagation and potential transmission to humans, must take into consideration this type of evidence, and avoid the simplistic assumption that no detection corresponds to risk absence.
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Affiliation(s)
- Gianuario Fortunato
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Cristina Becerra-Castro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal.
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82
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Prevalence of Multidrug-Resistant Escherichia coli Isolated from Drinking Water Sources. Int J Microbiol 2018; 2018:7204013. [PMID: 30210545 PMCID: PMC6120285 DOI: 10.1155/2018/7204013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 12/16/2022] Open
Abstract
The control of infectious diseases is badly endangered by the rise in the number of microorganisms that are resistant to antimicrobial agents. This is because infections caused by resistant microorganisms often fail to respond to conventional treatment, resulting in prolonged illness and greater risk of death. Antimicrobial-resistant bacteria are also present in various water sources. This study therefore sought to document the microbiological quality and antibiograms of bacterial isolates (E. coli strains) from six different water sources in order to determine their safety for human consumption and to provide updated antibiotic data for pragmatic treatment of patients. Bacteria isolation and identification was done using API and conventional methods. Antibiotic susceptibility testing was conducted using the Kirby-Bauer method. Results obtained indicated that all the water sources tested were of poor quality. Bacteria isolated included E. coli, Enterobacter spp., Klebsiella spp., Salmonella typhi, Streptococcus spp., Proteus vulgaris, Vibrio cholera, Shigella spp., Pseudomonas aeruginosa, and Enterococcus faecalis. The prevalence of multidrug-resistant E. coli was 49.48%. E. coli isolates showed high resistance patterns to the tested antibiotics. They were most resistant to penicillin (32.99%), cefuroxime (28.87%), erythromycin (23.71%), and tetracycline (21.45%). In contrast, they were susceptible to nitrofurantoin (93.8%), cefotaxime and amikacin (91.75%), gentamicin (90.7%), nalidixic acid (89.65%), ciprofloxacin (74.2%), chloramphenicol (69.07%), pipemidic acid (65.97%), and cefuroxime (52.58%). Sixty-three percent (63%) of the multidrug-resistant E. coli strains recorded a multiple antibiotic resistance (MAR) index value >0.2. The susceptible antibiotics, especially the nitrofurantoin, are hence recommended in the practical treatment of waterborne bacterial diseases.
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